From 2ad50c71ad3ae0b02c8bb47d288ce9b46107a1e8 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 16 Jan 2025 00:10:05 +0000
Subject: [PATCH 01/36] try to update to poetry 2

---
 .github/workflows/release.yml |  4 ++--
 .github/workflows/tests.yml   |  6 +++---
 .readthedocs.yml              |  2 +-
 dev-env.yml                   | 12 ++++++------
 noxfile.py                    | 18 ++----------------
 poetry.lock                   |  4 ++--
 6 files changed, 16 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 88afbf89..769c5573 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -26,7 +26,7 @@ jobs:
         if: ${{ steps.release.outputs.release_created }}
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'  # keep in sync with dev-env.yml
+          python-version: '3.9'  # keep in sync with dev-env.yml
 
       - name: Upgrade pip
         if: ${{ steps.release.outputs.release_created }}
@@ -37,7 +37,7 @@ jobs:
       - name: Install Poetry
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          pip install 'poetry==1.8.3' # keep version in sync with dev-env.yml
+          pip install 'poetry==2.0.1' # keep version in sync with dev-env.yml
           poetry --version
 
       - name: Build package
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8b9b6d63..0b71b842 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -21,10 +21,10 @@ jobs:
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
           # - { python: "3.11", os: "windows-latest", session: "tests" }
-          - { python: "3.8", os: "macos-13", session: "tests" }
+          - { python: "3.9", os: "macos-13", session: "tests" }
           - { python: "3.9", os: "macos-latest", session: "tests" }
-          - { python: "3.8", os: "ubuntu-latest", session: "size" }
-          - { python: "3.8", os: "ubuntu-latest", session: "coverage" }
+          - { python: "3.9", os: "ubuntu-latest", session: "size" }
+          - { python: "3.9", os: "ubuntu-latest", session: "coverage" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
diff --git a/.readthedocs.yml b/.readthedocs.yml
index c5516321..cce90b68 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.8"
+    python: "3.9"
   jobs:
     post_create_environment:
       # Install poetry
diff --git a/dev-env.yml b/dev-env.yml
index e3fede1e..4e338c21 100644
--- a/dev-env.yml
+++ b/dev-env.yml
@@ -3,13 +3,13 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - conda-forge::python=3.8 # the lowest version of python that we formally support
-  - conda-forge::pip==24.0
-  - bioconda::bcftools==1.20
+  - conda-forge::python=3.9 # the lowest version of python that we formally support; keep in sync with release.yml, tests.yml, .readthedocs.yaml, and noxfile.py
+  - conda-forge::pip==24.3.1
+  - bioconda::bcftools==1.21
   - bioconda::art==2016.06.05
-  - conda-forge::poetry==1.8.3 # keep in sync with release.yml
-  - conda-forge::nox==2024.4.15
+  - conda-forge::poetry==2.0.1 # keep in sync with release.yml
+  - conda-forge::nox==2024.10.9
   - conda-forge::poetry-plugin-export==1.8.0
   - pip:
     - nox-poetry==1.0.3
-    - poetry-conda==0.1.1
+    - poetry-conda==0.1.3
diff --git a/noxfile.py b/noxfile.py
index ebf9664f..1c35c8fa 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -21,20 +21,6 @@
 ]
 
 
-def install_handle_python(session):
-    """
-    handle incompatibilities between python and other packages
-    see https://github.com/cjolowicz/nox-poetry/issues/1116
-    """
-    # install the latest versions of all dependencies for py3.9+
-    # but install the locked versions for < py3.9 to ensure some stability in the CI and
-    # help us understand when we need to bump our version constraints
-    if session._session.python in ("3.9", "3.10", "3.11", "3.12"):
-        session._session.install(".")
-    else:
-        session.install(".")
-
-
 # detect whether conda/mamba is installed
 if os.getenv("CONDA_EXE"):
     conda_cmd = "conda"
@@ -56,7 +42,7 @@ def tests(session: Session) -> None:
             "pytest-cov",
             channel="conda-forge",
         )
-        install_handle_python(session)
+        session.install(".")
         session.run(
            "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )
@@ -68,7 +54,7 @@ def tests(session: Session) -> None:
     def tests(session: Session) -> None:
         """Run the test suite."""
         session.install("pytest", "pytest-cov")
-        install_handle_python_numpy(session)
+        session.install(".")
         session.run(
             "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )
diff --git a/poetry.lock b/poetry.lock
index 816910dd..9870d038 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1344,4 +1344,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.7.1,<4.0"
-content-hash = "87e8b482546b727dba3128340db5041a5d212eb3e48b179bd61618cad4b3b79d"
\ No newline at end of file
+content-hash = "87e8b482546b727dba3128340db5041a5d212eb3e48b179bd61618cad4b3b79d"

From 8b5a69b2eb57acaa65f6836895d413fa9ed351d1 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sat, 18 Jan 2025 10:21:26 -0800
Subject: [PATCH 02/36] update dev-env.yml

---
 dev-env.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev-env.yml b/dev-env.yml
index 4e338c21..c8778cf4 100644
--- a/dev-env.yml
+++ b/dev-env.yml
@@ -9,7 +9,7 @@ dependencies:
   - bioconda::art==2016.06.05
   - conda-forge::poetry==2.0.1 # keep in sync with release.yml
   - conda-forge::nox==2024.10.9
-  - conda-forge::poetry-plugin-export==1.8.0
+  - conda-forge::poetry-plugin-export==1.9.0
   - pip:
     - nox-poetry==1.0.3
-    - poetry-conda==0.1.3
+    - poetry-conda==0.1.4

From a49d536d79027c4848e1fe08f961b5a724b19cc0 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 21 Jan 2025 18:55:51 +0000
Subject: [PATCH 03/36] migrate pyproject for poetry 2

---
 poetry.lock    | 77 +++++++++++++++++++++++++++++++++++++++++++++++---
 pyproject.toml | 73 +++++++++++++++++++++++++++--------------------
 2 files changed, 116 insertions(+), 34 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9870d038..6c88cd2c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -6,6 +6,7 @@ version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
 optional = false
 python-versions = ">=3.6"
+groups = ["docs"]
 files = [
     {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
@@ -17,6 +18,7 @@ version = "2.14.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
     {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
@@ -34,6 +36,7 @@ version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
+groups = ["docs"]
 files = [
     {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
     {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
@@ -45,6 +48,7 @@ version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
+groups = ["docs"]
 files = [
     {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
     {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
@@ -144,6 +148,7 @@ version = "8.1.7"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
     {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
@@ -159,10 +164,12 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main", "docs", "tests"]
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
+markers = {main = "platform_system == \"Windows\"", docs = "sys_platform == \"win32\"", tests = "sys_platform == \"win32\""}
 
 [[package]]
 name = "coloredlogs"
@@ -170,6 +177,7 @@ version = "15.0.1"
 description = "Colored terminal output for Python's logging module"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
 files = [
     {file = "coloredlogs-15.0.1-py2.py3-none-any.whl", hash = "sha256:612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934"},
     {file = "coloredlogs-15.0.1.tar.gz", hash = "sha256:7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0"},
@@ -187,6 +195,7 @@ version = "7.2.7"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
 files = [
     {file = "coverage-7.2.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d39b5b4f2a66ccae8b7263ac3c8170994b65266797fb96cbbfd3fb5b23921db8"},
     {file = "coverage-7.2.7-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d040ef7c9859bb11dfeb056ff5b3872436e3b5e401817d87a31e1750b9ae2fb"},
@@ -262,6 +271,7 @@ version = "0.11.0"
 description = "Composable style cycles"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "cycler-0.11.0-py3-none-any.whl", hash = "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3"},
     {file = "cycler-0.11.0.tar.gz", hash = "sha256:9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f"},
@@ -273,6 +283,7 @@ version = "0.30.27"
 description = "fast vcf parsing with cython + htslib"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "cyvcf2-0.30.27-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ab4cc28e7adbad5459dfa0c90fb7693cf7f04680a5e21455f9aa52ef64f30a79"},
     {file = "cyvcf2-0.30.27-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40a95e00cdb7e4766aa33d81bc35b95e44deb3315e642cccc55d102a3000b2d1"},
@@ -315,6 +326,7 @@ version = "0.17.1"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["docs"]
 files = [
     {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"},
     {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
@@ -326,6 +338,8 @@ version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
     {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
@@ -340,6 +354,7 @@ version = "10.0"
 description = "Human friendly output for text interfaces using Python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
 files = [
     {file = "humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477"},
     {file = "humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc"},
@@ -355,6 +370,7 @@ version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
     {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
@@ -366,6 +382,7 @@ version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["docs"]
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -377,6 +394,8 @@ version = "6.7.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "tests"]
+markers = "python_version < \"3.8\""
 files = [
     {file = "importlib_metadata-6.7.0-py3-none-any.whl", hash = "sha256:cb52082e659e97afc5dac71e79de97d8681de3aa07ff18578330904a9d18e5b5"},
     {file = "importlib_metadata-6.7.0.tar.gz", hash = "sha256:1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4"},
@@ -397,6 +416,7 @@ version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
 files = [
     {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
@@ -408,6 +428,7 @@ version = "3.1.2"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
     {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
@@ -425,6 +446,7 @@ version = "1.3.2"
 description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"},
     {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"},
@@ -436,6 +458,7 @@ version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:05703cf211d585109fcd72207a31bb170a0f22144d68298dc5e61b3c946518af"},
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:146d14bebb7f1dc4d5fbf74f8a6cb15ac42baadee8912eb84ac0b3b2a3dc6ac3"},
@@ -552,6 +575,7 @@ version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:cd0f502fe016460680cd20aaa5a76d241d6f35a1c3350c474bac1273803893fa"},
     {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e09031c87a1e51556fdcb46e5bd4f59dfb743061cf93c4d6831bf894f125eb57"},
@@ -621,6 +645,7 @@ version = "3.1.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "matplotlib-3.1.2-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:98c2ffeab8b79a4e3a0af5dd9939f92980eb6e3fec10f7f313df5f35a84dacab"},
     {file = "matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2d6ab54015a7c0d727c33e36f85f5c5e4172059efdd067f7527f6e5d16ad01aa"},
@@ -650,6 +675,7 @@ version = "1.17.3"
 description = "NumPy is the fundamental package for array computing with Python."
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "numpy-1.17.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:4dd830a11e8724c9c9379feed1d1be43113f8bcce55f47ea7186d3946769ce26"},
     {file = "numpy-1.17.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:30c84e3a62cfcb9e3066f25226e131451312a044f1fe2040e69ce792cb7de418"},
@@ -680,6 +706,7 @@ version = "23.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
+groups = ["docs", "tests"]
 files = [
     {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
     {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
@@ -691,6 +718,7 @@ version = "1.2.0"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.7.1"
+groups = ["main"]
 files = [
     {file = "pandas-1.2.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:cba93d4fd3b0a42858b2b599495aff793fb5d94587979f45a14177d1217ba446"},
     {file = "pandas-1.2.0-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:9e18631d996fe131de6cb31a8bdae18965cc8f39eb23fdfbbf42808ecc63dabf"},
@@ -725,6 +753,7 @@ version = "0.5.4"
 description = "A Python package for describing statistical models and for building design matrices."
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "patsy-0.5.4-py2.py3-none-any.whl", hash = "sha256:0486413077a527db51ddea8fa94a5234d0feb17a4f4dc01b59b6086c58a70f80"},
     {file = "patsy-0.5.4.tar.gz", hash = "sha256:7dabc527597308de0e8f188faa20af7e06a89bdaa306756dfc7783693ea16af4"},
@@ -743,6 +772,7 @@ version = "0.90.1"
 description = "Python wrapper for pgenlib's basic reader and writer."
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "Pgenlib-0.90.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0c5823a8f3bb558c2d60243eb19ca6220cc2d5c759fc50139e5c09b179353b68"},
     {file = "Pgenlib-0.90.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:758b3927228029bb10758a28a8ded86a71844da973d6196b44913c4765cdf23d"},
@@ -762,6 +792,7 @@ version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
 files = [
     {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
     {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
@@ -780,6 +811,7 @@ version = "0.5.6"
 description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "pyfaidx-0.5.6.tar.gz", hash = "sha256:2b6ab4212158ccf8f8490ae33f21a162a5c5f7ab2717f227c30013ed7a6c40e8"},
 ]
@@ -794,6 +826,7 @@ version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
     {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
@@ -809,6 +842,7 @@ version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
+groups = ["main"]
 files = [
     {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
     {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
@@ -823,6 +857,8 @@ version = "2.1"
 description = "A python implmementation of GNU readline."
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform == \"win32\" and python_version < \"3.8\""
 files = [
     {file = "pyreadline-2.1.zip", hash = "sha256:4530592fc2e85b25b1a9f79664433da09237c1a270e4d78ea5aa3a2c7229e2d1"},
 ]
@@ -833,6 +869,8 @@ version = "3.4.1"
 description = "A python implementation of GNU readline."
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform == \"win32\" and python_version >= \"3.8\""
 files = [
     {file = "pyreadline3-3.4.1-py3-none-any.whl", hash = "sha256:b0efb6516fd4fb07b45949053826a62fa4cb353db5be2bbb4a7aa1fdd1e345fb"},
     {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"},
@@ -844,6 +882,7 @@ version = "0.15.4"
 description = "pysam"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "pysam-0.15.4-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:0b0f407ad96b3bd492017ee82a317ac0fc68dc858ecba9119e4ae69b1cda9910"},
     {file = "pysam-0.15.4-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:5b6a2258e326204ee94bf4d482d9a137ce8cbb3f3cefada42c7f26802d15b95d"},
@@ -871,6 +910,7 @@ version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
 files = [
     {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
     {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
@@ -894,6 +934,7 @@ version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
 files = [
     {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
     {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
@@ -912,6 +953,7 @@ version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+groups = ["main"]
 files = [
     {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
     {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
@@ -926,10 +968,12 @@ version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
+groups = ["main", "docs"]
 files = [
     {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
     {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
 ]
+markers = {docs = "python_version < \"3.9\""}
 
 [[package]]
 name = "requests"
@@ -937,6 +981,7 @@ version = "2.31.0"
 description = "Python HTTP for Humans."
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
     {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
@@ -958,6 +1003,7 @@ version = "0.23.1"
 description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "scikit-learn-0.23.1.tar.gz", hash = "sha256:e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8"},
     {file = "scikit_learn-0.23.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:058d213092de4384710137af1300ed0ff030b8c40459a6c6f73c31ccd274cc39"},
@@ -992,6 +1038,7 @@ version = "1.3.3"
 description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "scipy-1.3.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:a70308bb065562afb936c963780deab359966d71ab4f230368b154dde3136ea4"},
     {file = "scipy-1.3.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:7be424ee09bed7ced36c9457f99c826ce199fd0c0f5b272cf3d098ff7b29e3ae"},
@@ -1025,6 +1072,7 @@ version = "68.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "docs"]
 files = [
     {file = "setuptools-68.0.0-py3-none-any.whl", hash = "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f"},
     {file = "setuptools-68.0.0.tar.gz", hash = "sha256:baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235"},
@@ -1041,6 +1089,7 @@ version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["main"]
 files = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -1052,6 +1101,7 @@ version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 optional = false
 python-versions = "*"
+groups = ["docs"]
 files = [
     {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
     {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
@@ -1063,6 +1113,7 @@ version = "4.3.2"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.6"
+groups = ["docs"]
 files = [
     {file = "Sphinx-4.3.2-py3-none-any.whl", hash = "sha256:6a11ea5dd0bdb197f9c2abc2e0ce73e01340464feaece525e64036546d24c851"},
     {file = "Sphinx-4.3.2.tar.gz", hash = "sha256:0a8836751a68306b3fe97ecbe44db786f8479c3bf4b80e3a7f5c838657b4698c"},
@@ -1098,6 +1149,7 @@ version = "1.17.1"
 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "sphinx_autodoc_typehints-1.17.1-py3-none-any.whl", hash = "sha256:f16491cad05a13f4825ecdf9ee4ff02925d9a3b1cf103d4d02f2f81802cce653"},
     {file = "sphinx_autodoc_typehints-1.17.1.tar.gz", hash = "sha256:844d7237d3f6280b0416f5375d9556cfd84df1945356fcc34b82e8aaacab40f3"},
@@ -1116,6 +1168,7 @@ version = "1.3.0"
 description = "Read the Docs theme for Sphinx"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+groups = ["docs"]
 files = [
     {file = "sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl", hash = "sha256:46ddef89cc2416a81ecfbeaceab1881948c014b1b6e4450b815311a89fb977b0"},
     {file = "sphinx_rtd_theme-1.3.0.tar.gz", hash = "sha256:590b030c7abb9cf038ec053b95e5380b5c70d61591eb0b552063fbe7c41f0931"},
@@ -1135,6 +1188,7 @@ version = "1.0.2"
 description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
     {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
@@ -1150,6 +1204,7 @@ version = "1.0.2"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
     {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
@@ -1165,6 +1220,7 @@ version = "2.0.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
 python-versions = ">=3.6"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-htmlhelp-2.0.0.tar.gz", hash = "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"},
     {file = "sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl", hash = "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07"},
@@ -1180,6 +1236,7 @@ version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
 optional = false
 python-versions = ">=2.7"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"},
     {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"},
@@ -1194,6 +1251,7 @@ version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -1208,6 +1266,7 @@ version = "1.0.3"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
     {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
@@ -1223,6 +1282,7 @@ version = "1.1.5"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
     {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
@@ -1238,6 +1298,7 @@ version = "0.10.2"
 description = "Statistical computations and models for Python"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "statsmodels-0.10.2-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:e67e244ae4ca988b40783db7e1bac0de5b7f9f91062cdc0c93e219b189700388"},
     {file = "statsmodels-0.10.2-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:65f08024ef9a0bd40b63c455d02da34394658c53c16e3494dd6171e86e639f9b"},
@@ -1282,6 +1343,7 @@ version = "3.1.0"
 description = "threadpoolctl"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"},
     {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"},
@@ -1293,6 +1355,8 @@ version = "2.0.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.7"
+groups = ["tests"]
+markers = "python_full_version <= \"3.11.0a6\""
 files = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -1304,6 +1368,8 @@ version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "tests"]
+markers = "python_version < \"3.8\""
 files = [
     {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
@@ -1315,6 +1381,7 @@ version = "2.0.7"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.7"
+groups = ["docs"]
 files = [
     {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
     {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
@@ -1332,6 +1399,8 @@ version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "tests"]
+markers = "python_version < \"3.8\""
 files = [
     {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
     {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
@@ -1342,6 +1411,6 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker
 testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
-lock-version = "2.0"
-python-versions = ">=3.7.1,<4.0"
-content-hash = "87e8b482546b727dba3128340db5041a5d212eb3e48b179bd61618cad4b3b79d"
+lock-version = "2.1"
+python-versions = ">=3.7.1"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index d7d903ce..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,25 +1,56 @@
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=2.0.1"]
 build-backend = "poetry.core.masonry.api"
 
-[tool.poetry]
+[project]
 name = "trtools"
 version = "6.1.0"
 authors = [
-    "Melissa Gymrek <mgymrek@ucsd.edu>",
-    "Gymrek Lab",
+    {name = "Melissa Gymrek", email = "mgymrek@ucsd.edu"},
+    {name = "Gymrek Lab"},
 ]
 description = "Toolkit for genome-wide analysis of STRs"
 readme = "README.rst"
 license = "MIT"
-repository = "https://github.com/gymrek-lab/trtools"
-homepage = "https://trtools.readthedocs.org"
-documentation = "https://trtools.readthedocs.org"
 classifiers = [
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
+requires-python = ">=3.7.1"
+dependencies = [
+    "importlib-metadata>=3.0.0 ; python_version < '3.8'",
+    "cyvcf2>=0.30.27",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
+    "pandas>=1.2.0",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
+    "pyfaidx>=0.5.6",
+    "pgenlib>=0.90.1",
+]
+
+[project.urls]
+repository = "https://github.com/gymrek-lab/trtools"
+homepage = "https://trtools.readthedocs.org"
+documentation = "https://trtools.readthedocs.org"
+changelog = "https://github.com/gymrek-lab/TRTools/blob/master/CHANGELOG.md"
+
+[project.scripts]
+dumpSTR = "trtools.dumpSTR:run"
+mergeSTR = "trtools.mergeSTR:run"
+statSTR = "trtools.statSTR:run"
+compareSTR = "trtools.compareSTR:run"
+qcSTR = "trtools.qcSTR:run"
+associaTR = "trtools.associaTR:run"
+prancSTR = "trtools.prancSTR:run"
+simTR = "trtools.simTR:run"
+annotaTR = "trtools.annotaTR:run"
+
+[tool.poetry]
+requires-poetry = ">=2.0"
 exclude = [
     "trtools/testsupport/*",
     "doc",
@@ -30,20 +61,6 @@ exclude = [
     "trtools/qcSTR/images",
 ]
 
-[tool.poetry.dependencies]
-python = ">=3.7.1,<4.0"
-importlib-metadata = {version = ">=3.0.0", python = "<3.8"}
-cyvcf2 = ">=0.30.27"
-matplotlib = ">=3.1.2"
-numpy = ">=1.17.3"
-pandas = ">=1.2.0"
-pysam = ">=0.15.4"
-scikit-learn = ">=0.23.1"
-scipy = ">=1.3.3"
-statsmodels = ">=0.10.2"
-pyfaidx = ">=0.5.6"
-pgenlib = ">=0.90.1"
-
 [tool.poetry.group.tests.dependencies]
 pytest = ">=6.2.0"
 pytest-cov = ">=3.0.0"
@@ -56,15 +73,11 @@ sphinx-autodoc-typehints = ">=1.12.0"
 [tool.poetry.scripts]
 "test_trtools.sh" = {reference = "trtools/testsupport/test_trtools.sh", type = "file"}
 "trtools_prep_beagle_vcf.sh" = {reference = "scripts/trtools_prep_beagle_vcf.sh", type = "file"}
-dumpSTR = "trtools.dumpSTR:run"
-mergeSTR = "trtools.mergeSTR:run"
-statSTR = "trtools.statSTR:run"
-compareSTR = "trtools.compareSTR:run"
-qcSTR = "trtools.qcSTR:run"
-associaTR = "trtools.associaTR:run"
-prancSTR = "trtools.prancSTR:run"
-simTR = "trtools.simTR:run"
-annotaTR = "trtools.annotaTR:run"
+
+[tool.poetry.requires-plugins]
+poetry-conda = ">=0.1.4"
+poetry-plugin-export = ">=1.9"
+poetry-plugin-shell = ">=1.0.1"
 
 [tool.pytest.ini_options]
 addopts = """

From e04c98aaaf5bbeaf947732a820ac5b2640a2bbe7 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 21 Jan 2025 19:01:54 +0000
Subject: [PATCH 04/36] add poetry-plugin-shell to conda env

---
 dev-env.yml   | 1 +
 doc/index.rst | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/dev-env.yml b/dev-env.yml
index c8778cf4..e3814fbb 100644
--- a/dev-env.yml
+++ b/dev-env.yml
@@ -13,3 +13,4 @@ dependencies:
   - pip:
     - nox-poetry==1.0.3
     - poetry-conda==0.1.4
+    - poetry-plugin-shell==1.0.1
diff --git a/doc/index.rst b/doc/index.rst
index c926ac4b..f1d9dfcb 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -173,7 +173,7 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 #. If you need to add a dependency or update the version of a dependency, you can use the :code:`poetry add` command.
 
     * You should specify a `version constraint <https://python-poetry.org/docs/master/dependency-specification#version-constraints>`_ when adding a dependency. Use the oldest version compatible with your code. For example, to specify a version of :code:`numpy>=1.23.0`, you can run :code:`poetry add 'numpy>=1.23.0'`. Note: For most cases, a version constraint operator of :code:`>=` `is better than <https://iscinumpy.dev/post/bound-version-constraints>`_ poetry's default of :code:`^`.
-    * Afterward, double-check that the :code:`poetry.lock` file contains 1.23.0 in it. **All of our dependencies should be locked to their minimum versions at all times.** To downgrade to a specific version of :code:`numpy` in our lock file, you can explicitly add the version via :code:`poetry add 'numpy==1.23.0'`, manually edit the pyproject.toml file to use a :code:`>=` sign in front of the version number, and then run :code:`poetry lock --no-update`. The :code:`--no-update` is important because otherwise, poetry will try to update other dependencies in the lock file.
+    * Afterward, double-check that the :code:`poetry.lock` file contains 1.23.0 in it. **All of our dependencies should be locked to their minimum versions at all times.** To downgrade to a specific version of :code:`numpy` in our lock file, you can explicitly add the version via :code:`poetry add 'numpy==1.23.0'`, manually edit the pyproject.toml file to use a :code:`>=` sign in front of the version number, and then run :code:`poetry lock`.
     * Only PyPI packages can be added to our pyproject.toml file. So if a dependency is only available on conda, then you can add it to our :code:`dev-env.yml` file instead. Please note that anyone who installs TRTools from PyPI will not be guaranteed to have your dependency installed, so you should design your code accordingly. 
     * Any changes to our dependencies must also added to our bioconda recipe at the time of publication. See `PUBLISHING.rst <https://github.com/gymrek-lab/TRTools/blob/master/PUBLISHING.rst>`_ for more details.
 

From f1ee33244dce812409430b57f0fa0214f8616949 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 21 Jan 2025 23:11:35 +0000
Subject: [PATCH 05/36] try to lock for py3.9

---
 poetry.lock    | 515 ++++++++++++++++++++++++++++++++++++++-----------
 pyproject.toml |  18 +-
 2 files changed, 418 insertions(+), 115 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6c88cd2c..ea73eb1e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -641,63 +641,143 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.1.2"
+version = "3.3.3"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
 files = [
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-    {file = "matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2d6ab54015a7c0d727c33e36f85f5c5e4172059efdd067f7527f6e5d16ad01aa"},
-    {file = "matplotlib-3.1.2-cp36-cp36m-win32.whl", hash = "sha256:819d4860315468b482f38f1afe45a5437f60f03eaede495d5ff89f2eeac89500"},
-    {file = "matplotlib-3.1.2-cp36-cp36m-win_amd64.whl", hash = "sha256:08ccc8922eb4792b91c652d3e6d46b1c99073f1284d1b6705155643e8046463a"},
-    {file = "matplotlib-3.1.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:1f9e885bfa1b148d16f82a6672d043ecf11197f6c71ae222d0546db706e52eb2"},
-    {file = "matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:8cc0e44905c2c8fda5637cad6f311eb9517017515a034247ab93d0cf99f8bb7a"},
-    {file = "matplotlib-3.1.2-cp37-cp37m-win32.whl", hash = "sha256:161dcd807c0c3232f4dcd4a12a382d52004a498174cbfafd40646106c5bcdcc8"},
-    {file = "matplotlib-3.1.2-cp37-cp37m-win_amd64.whl", hash = "sha256:ee59b7bb9eb75932fe3787e54e61c99b628155b0cedc907864f24723ba55b309"},
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-    {file = "matplotlib-3.1.2.tar.gz", hash = "sha256:8e8e2c2fe3d873108735c6ee9884e6f36f467df4a143136209cff303b183bada"},
+    {file = "matplotlib-3.3.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b2a5e1f637a92bb6f3526cc54cc8af0401112e81ce5cba6368a1b7908f9e18bc"},
+    {file = "matplotlib-3.3.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:c586ac1d64432f92857c3cf4478cfb0ece1ae18b740593f8a39f2f0b27c7fda5"},
+    {file = "matplotlib-3.3.3-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:9b03722c89a43a61d4d148acfc89ec5bb54cd0fd1539df25b10eb9c5fa6c393a"},
+    {file = "matplotlib-3.3.3-cp36-cp36m-win32.whl", hash = "sha256:2c2c5041608cb75c39cbd0ed05256f8a563e144234a524c59d091abbfa7a868f"},
+    {file = "matplotlib-3.3.3-cp36-cp36m-win_amd64.whl", hash = "sha256:c092fc4673260b1446b8578015321081d5db73b94533fe4bf9b69f44e948d174"},
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+    {file = "matplotlib-3.3.3.tar.gz", hash = "sha256:b1b60c6476c4cfe9e5cf8ab0d3127476fd3d5f05de0f343a452badaad0e4bdec"},
 ]
 
 [package.dependencies]
 cycler = ">=0.10"
 kiwisolver = ">=1.0.1"
-numpy = ">=1.11"
-pyparsing = ">=2.0.1,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
+numpy = ">=1.15"
+pillow = ">=6.2.0"
+pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
 python-dateutil = ">=2.1"
 
 [[package]]
 name = "numpy"
-version = "1.17.3"
+version = "1.21.6"
 description = "NumPy is the fundamental package for array computing with Python."
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7,<3.11"
+groups = ["main"]
+markers = "python_version <= \"3.8\""
+files = [
+    {file = "numpy-1.21.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8737609c3bbdd48e380d463134a35ffad3b22dc56295eff6f79fd85bd0eeeb25"},
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 ]
 
 [package.dependencies]
@@ -1030,7 +1288,10 @@ scipy = ">=0.19.1"
 threadpoolctl = ">=2.0.0"
 
 [package.extras]
-alldeps = ["numpy (>=1.13.3)", "scipy (>=0.19.1)"]
+benchmark = ["matplotlib (>=2.1.1)", "memory-profiler (>=0.57.0)", "pandas (>=0.25.0)"]
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+examples = ["matplotlib (>=2.1.1)", "pandas (>=0.25.0)", "scikit-image (>=0.13)", "seaborn (>=0.9.0)"]
+tests = ["flake8 (>=3.8.2)", "matplotlib (>=2.1.1)", "mypy (>=0.770)", "pandas (>=0.25.0)", "pyamg (>=4.0.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "scikit-image (>=0.13)"]
 
 [[package]]
 name = "scipy"
@@ -1039,6 +1300,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
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@@ -1066,6 +1328,50 @@ files = [
 [package.dependencies]
 numpy = ">=1.13.3"
 
+[[package]]
+name = "scipy"
+version = "1.13.1"
+description = "Fundamental algorithms for scientific computing in Python"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
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+    {file = "scipy-1.13.1.tar.gz", hash = "sha256:095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c"},
+]
+
+[package.dependencies]
+numpy = ">=1.22.4,<2.3"
+
+[package.extras]
+dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
+doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.12.0)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0)", "sphinx-design (>=0.4.0)"]
+test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "setuptools"
 version = "68.0.0"
@@ -1294,47 +1600,38 @@ test = ["pytest"]
 
 [[package]]
 name = "statsmodels"
-version = "0.10.2"
+version = "0.13.0"
 description = "Statistical computations and models for Python"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 groups = ["main"]
 files = [
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+    {file = "statsmodels-0.13.0.tar.gz", hash = "sha256:f2efc02011b7240a9e851acd76ab81150a07d35c97021cb0517887539a328f8a"},
 ]
 
 [package.dependencies]
-numpy = ">=1.11"
-pandas = ">=0.19"
-patsy = ">=0.4.0"
-scipy = ">=0.18"
+numpy = ">=1.17"
+pandas = ">=0.25"
+patsy = ">=0.5.2"
+scipy = ">=1.3"
 
 [package.extras]
-build = ["cython (>=0.24)"]
-develop = ["cython (>=0.24)"]
+build = ["cython (>=0.29.22)"]
+develop = ["cython (>=0.29.22)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
@@ -1413,4 +1710,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "21156ad75d6c733503fc5a7767eda2adf80e0b0266737ae83d7cab1aceed9a5f"
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..d5212d3b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,13 +21,19 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2",
-    "numpy>=1.17.3",
+    "matplotlib>=3.1.2 ; python_version <= '3.8'",
+    "matplotlib>=3.3.3 ; python_version > '3.8'",
+    "numpy>=1.17.3 ; python_version <= '3.8'",
+    "numpy>=1.21.6 ; python_version > '3.8'",
     "pandas>=1.2.0",
-    "pysam>=0.15.4",
-    "scikit-learn>=0.23.1",
-    "scipy>=1.3.3",
-    "statsmodels>=0.10.2",
+    "pysam>=0.15.4 ; python_version <= '3.8'",
+    "pysam>=0.18.0 ; python_version > '3.8'",
+    "scikit-learn>=0.23.1 ; python_version <= '3.8'",
+    "scikit-learn>=0.24.0 ; python_version > '3.8'",
+    "scipy>=1.3.3 ; python_version <= '3.8'",
+    "scipy>=1.13.1 ; python_version > '3.8'",
+    "statsmodels>=0.10.2 ; python_version <= '3.8'",
+    "statsmodels>=0.13.0 ; python_version > '3.8'",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From d2c66e9a9fd7ad70b73d3456067f7843fd69a88b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 21 Jan 2025 23:34:34 +0000
Subject: [PATCH 06/36] Revert "try to lock for py3.9"

This reverts commit f1ee33244dce812409430b57f0fa0214f8616949.
---
 poetry.lock    | 515 +++++++++++--------------------------------------
 pyproject.toml |  18 +-
 2 files changed, 115 insertions(+), 418 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index ea73eb1e..6c88cd2c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -641,143 +641,63 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.3.3"
+version = "3.1.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
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 kiwisolver = ">=1.0.1"
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-pillow = ">=6.2.0"
-pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
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 python-dateutil = ">=2.1"
 
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 [package.dependencies]
@@ -1288,10 +1030,7 @@ scipy = ">=0.19.1"
 threadpoolctl = ">=2.0.0"
 
 [package.extras]
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 [[package]]
 name = "scipy"
@@ -1300,7 +1039,6 @@ description = "SciPy: Scientific Library for Python"
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 python-versions = ">=3.5"
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@@ -1328,50 +1066,6 @@ files = [
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-    {file = "scipy-1.13.1.tar.gz", hash = "sha256:095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c"},
-]
-
-[package.dependencies]
-numpy = ">=1.22.4,<2.3"
-
-[package.extras]
-dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
-doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.12.0)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0)", "sphinx-design (>=0.4.0)"]
-test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
-
 [[package]]
 name = "setuptools"
 version = "68.0.0"
@@ -1600,38 +1294,47 @@ test = ["pytest"]
 
 [[package]]
 name = "statsmodels"
-version = "0.13.0"
+version = "0.10.2"
 description = "Statistical computations and models for Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 groups = ["main"]
 files = [
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+    {file = "statsmodels-0.10.2-cp37-none-win_amd64.whl", hash = "sha256:1d61edd4b73f1f4ef983007cd0d797e6cafd9e7de0125584761d93f79675cdd2"},
+    {file = "statsmodels-0.10.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:3b22ed234b80cd9d38988fba487da89cae484a4c2b9088b3e7783c0a937a4568"},
+    {file = "statsmodels-0.10.2-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:e3d36ff3653b50554d9ad2c95556224d1882a5db328eea8a9aa32a0eb08e4e80"},
+    {file = "statsmodels-0.10.2-cp38-none-win32.whl", hash = "sha256:f9271b4ff7430f63e6c20c28afacb75e97a384fafb336fe336985da80bcd8a49"},
+    {file = "statsmodels-0.10.2-cp38-none-win_amd64.whl", hash = "sha256:adb5e524be26842c867f7dfdd74d7cfb2078fe2a6159b948e2f7ccf0e3d92002"},
+    {file = "statsmodels-0.10.2.tar.gz", hash = "sha256:9cd2194c6642a8754e85f9a6e6912cdf996bebf6ff715d3cc67f65dadfd37cc9"},
 ]
 
 [package.dependencies]
-numpy = ">=1.17"
-pandas = ">=0.25"
-patsy = ">=0.5.2"
-scipy = ">=1.3"
+numpy = ">=1.11"
+pandas = ">=0.19"
+patsy = ">=0.4.0"
+scipy = ">=0.18"
 
 [package.extras]
-build = ["cython (>=0.29.22)"]
-develop = ["cython (>=0.29.22)"]
+build = ["cython (>=0.24)"]
+develop = ["cython (>=0.24)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
@@ -1710,4 +1413,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "21156ad75d6c733503fc5a7767eda2adf80e0b0266737ae83d7cab1aceed9a5f"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index d5212d3b..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,19 +21,13 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2 ; python_version <= '3.8'",
-    "matplotlib>=3.3.3 ; python_version > '3.8'",
-    "numpy>=1.17.3 ; python_version <= '3.8'",
-    "numpy>=1.21.6 ; python_version > '3.8'",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
     "pandas>=1.2.0",
-    "pysam>=0.15.4 ; python_version <= '3.8'",
-    "pysam>=0.18.0 ; python_version > '3.8'",
-    "scikit-learn>=0.23.1 ; python_version <= '3.8'",
-    "scikit-learn>=0.24.0 ; python_version > '3.8'",
-    "scipy>=1.3.3 ; python_version <= '3.8'",
-    "scipy>=1.13.1 ; python_version > '3.8'",
-    "statsmodels>=0.10.2 ; python_version <= '3.8'",
-    "statsmodels>=0.13.0 ; python_version > '3.8'",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From 6de4fe82c93f8f5d5da38e29e3e8e04342699f35 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 23 Jan 2025 17:16:04 +0000
Subject: [PATCH 07/36] upgrade to min pep517 and py3.9 compatible dependency
 versions

---
 poetry.lock    | 379 ++++++++++++++++++++++++++++++++-----------------
 pyproject.toml |  12 +-
 2 files changed, 252 insertions(+), 139 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6c88cd2c..1464a754 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -641,63 +641,89 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.1.2"
+version = "3.3.3"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
 files = [
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-    {file = "matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2d6ab54015a7c0d727c33e36f85f5c5e4172059efdd067f7527f6e5d16ad01aa"},
-    {file = "matplotlib-3.1.2-cp36-cp36m-win32.whl", hash = "sha256:819d4860315468b482f38f1afe45a5437f60f03eaede495d5ff89f2eeac89500"},
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 python-dateutil = ">=2.1"
 
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 threadpoolctl = ">=2.0.0"
 
 [package.extras]
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 [package.dependencies]
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 [[package]]
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-    {file = "statsmodels-0.10.2.tar.gz", hash = "sha256:9cd2194c6642a8754e85f9a6e6912cdf996bebf6ff715d3cc67f65dadfd37cc9"},
+    {file = "statsmodels-0.12.1-cp36-cp36m-macosx_10_13_x86_64.whl", hash = "sha256:3b482ab9759b89cc1c4777b71c1ccf272e868a7551fc6b74da300557407d8379"},
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+    {file = "statsmodels-0.12.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:142eacd5a1bd8728358ff48101ee0e51ca3d42a93f6e5cb61fcfacf613977bcf"},
+    {file = "statsmodels-0.12.1-cp36-none-win32.whl", hash = "sha256:ef3a54b3594f4c49c295388de1fdd840a8c63a857a5252125aaf92a03ea1e3a6"},
+    {file = "statsmodels-0.12.1-cp36-none-win_amd64.whl", hash = "sha256:830d59d94841332429edf735430180031ad5dc660de26728d723e347f414c59d"},
+    {file = "statsmodels-0.12.1-cp37-cp37m-macosx_10_13_x86_64.whl", hash = "sha256:aa964ca1d65f066b9b096c94fe298aab1441e11731ce6b154ffb5f8d4a4e9ccf"},
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+    {file = "statsmodels-0.12.1-cp37-none-win_amd64.whl", hash = "sha256:e5e426fb962f41d58a07a7d2f7daf32f83e911ff578368caddbcdd1886887ed1"},
+    {file = "statsmodels-0.12.1-cp38-cp38-macosx_10_13_x86_64.whl", hash = "sha256:3582c0a497a9cda473470b4dd59ecd103739e3cfef1eb2e20d48dd1a2239f2e4"},
+    {file = "statsmodels-0.12.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:02679bf39d35a2aceb2d9f6d332b4e1cda1797157df792fe867b45f2a14d20d3"},
+    {file = "statsmodels-0.12.1-cp38-none-win32.whl", hash = "sha256:a652d8bfb4ec430b706a69e3fcbdac1cdf930823e3f9b8468e3e179d47097bbb"},
+    {file = "statsmodels-0.12.1-cp38-none-win_amd64.whl", hash = "sha256:74c6c863d6f8a1f021d42f965b1b97eeea05293d3b18e3690c46eac0cf6d64d9"},
+    {file = "statsmodels-0.12.1-cp39-cp39-macosx_10_15_x86_64.whl", hash = "sha256:62be4dd5b4a254d59b7feb8093623ba6158080aa6758c2eb19105609da4b40fb"},
+    {file = "statsmodels-0.12.1-cp39-cp39-manylinux1_i686.whl", hash = "sha256:630b9d938b0388488c66394597500dfba877e3b53da536369393a9a840b8f2a0"},
+    {file = "statsmodels-0.12.1-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:f585c02b716c161f00e6a2d10f9f3497f57191183dbd6ae7eaa988707023b1ee"},
+    {file = "statsmodels-0.12.1-cp39-none-win32.whl", hash = "sha256:3dd59b7cd35843f4764b8a1476be20cf959d3da700327975f7cd2bf2a1b630b2"},
+    {file = "statsmodels-0.12.1-cp39-none-win_amd64.whl", hash = "sha256:78813784f5fa612b4399c4963414799fbbb031188f1ad630a501c6b2af7e94e0"},
+    {file = "statsmodels-0.12.1.tar.gz", hash = "sha256:a271b4ccec190148dccda25f0cbdcbf871f408fc1394a10a7dc1af4a62b91c8e"},
 ]
 
 [package.dependencies]
-numpy = ">=1.11"
-pandas = ">=0.19"
-patsy = ">=0.4.0"
-scipy = ">=0.18"
+numpy = ">=1.15"
+pandas = ">=0.21"
+patsy = ">=0.5"
+scipy = ">=1.1"
 
 [package.extras]
-build = ["cython (>=0.24)"]
-develop = ["cython (>=0.24)"]
+build = ["cython (>=0.29)"]
+develop = ["cython (>=0.29)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
@@ -1413,4 +1526,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "48ddd87493343d4facb25131c725d156dc3c77163534021c5f0d1f17ef70a17d"
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..3700ca67 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,13 +21,13 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2",
-    "numpy>=1.17.3",
+    "matplotlib>=3.3.3",
+    "numpy>=1.19.3",
     "pandas>=1.2.0",
-    "pysam>=0.15.4",
-    "scikit-learn>=0.23.1",
-    "scipy>=1.3.3",
-    "statsmodels>=0.10.2",
+    "pysam>=0.17.0",
+    "scikit-learn>=0.24.0",
+    "scipy>=1.5.4",
+    "statsmodels>=0.12.1",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From 8a0fc1019a431c1daeba7ba97e0a733a61b10045 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 23 Jan 2025 17:17:49 +0000
Subject: [PATCH 08/36] revert to previous min dependency versions

---
 poetry.lock    |  2 +-
 pyproject.toml | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 1464a754..a4f843d1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1526,4 +1526,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "48ddd87493343d4facb25131c725d156dc3c77163534021c5f0d1f17ef70a17d"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index 3700ca67..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,13 +21,13 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.3.3",
-    "numpy>=1.19.3",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
     "pandas>=1.2.0",
-    "pysam>=0.17.0",
-    "scikit-learn>=0.24.0",
-    "scipy>=1.5.4",
-    "statsmodels>=0.12.1",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From f651f002c5a0705f72d7e16b492f4a484da8eafa Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 18:38:39 +0000
Subject: [PATCH 09/36] try to include both lowest versions and py3.9 versions

---
 poetry.lock    | 367 +++++++++++++++++++++++++++++++++++++++----------
 pyproject.toml |  21 ++-
 2 files changed, 310 insertions(+), 78 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a4f843d1..ca353409 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -639,6 +639,37 @@ files = [
     {file = "MarkupSafe-2.1.3.tar.gz", hash = "sha256:af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad"},
 ]
 
+[[package]]
+name = "matplotlib"
+version = "3.1.2"
+description = "Python plotting package"
+optional = false
+python-versions = ">=3.6"
+groups = ["main"]
+markers = "python_version <= \"3.8\""
+files = [
+    {file = "matplotlib-3.1.2-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:98c2ffeab8b79a4e3a0af5dd9939f92980eb6e3fec10f7f313df5f35a84dacab"},
+    {file = "matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2d6ab54015a7c0d727c33e36f85f5c5e4172059efdd067f7527f6e5d16ad01aa"},
+    {file = "matplotlib-3.1.2-cp36-cp36m-win32.whl", hash = "sha256:819d4860315468b482f38f1afe45a5437f60f03eaede495d5ff89f2eeac89500"},
+    {file = "matplotlib-3.1.2-cp36-cp36m-win_amd64.whl", hash = "sha256:08ccc8922eb4792b91c652d3e6d46b1c99073f1284d1b6705155643e8046463a"},
+    {file = "matplotlib-3.1.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:1f9e885bfa1b148d16f82a6672d043ecf11197f6c71ae222d0546db706e52eb2"},
+    {file = "matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:8cc0e44905c2c8fda5637cad6f311eb9517017515a034247ab93d0cf99f8bb7a"},
+    {file = "matplotlib-3.1.2-cp37-cp37m-win32.whl", hash = "sha256:161dcd807c0c3232f4dcd4a12a382d52004a498174cbfafd40646106c5bcdcc8"},
+    {file = "matplotlib-3.1.2-cp37-cp37m-win_amd64.whl", hash = "sha256:ee59b7bb9eb75932fe3787e54e61c99b628155b0cedc907864f24723ba55b309"},
+    {file = "matplotlib-3.1.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:5d2e408a2813abf664bd79431107543ecb449136912eb55bb312317edecf597e"},
+    {file = "matplotlib-3.1.2-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:d59bb0e82002ac49f4152963f8a1079e66794a4f454457fd2f0dcc7bf0797d30"},
+    {file = "matplotlib-3.1.2-cp38-cp38-win32.whl", hash = "sha256:61c8b740a008218eb604de518eb411c4953db0cb725dd0b32adf8a81771cab9e"},
+    {file = "matplotlib-3.1.2-cp38-cp38-win_amd64.whl", hash = "sha256:80f10af8378fccc136da40ea6aa4a920767476cdfb3241acb93ef4f0465dbf57"},
+    {file = "matplotlib-3.1.2.tar.gz", hash = "sha256:8e8e2c2fe3d873108735c6ee9884e6f36f467df4a143136209cff303b183bada"},
+]
+
+[package.dependencies]
+cycler = ">=0.10"
+kiwisolver = ">=1.0.1"
+numpy = ">=1.11"
+pyparsing = ">=2.0.1,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
+python-dateutil = ">=2.1"
+
 [[package]]
 name = "matplotlib"
 version = "3.3.3"
@@ -646,6 +677,7 @@ description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version > \"3.8\""
 files = [
     {file = "matplotlib-3.3.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b2a5e1f637a92bb6f3526cc54cc8af0401112e81ce5cba6368a1b7908f9e18bc"},
     {file = "matplotlib-3.3.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:c586ac1d64432f92857c3cf4478cfb0ece1ae18b740593f8a39f2f0b27c7fda5"},
@@ -682,6 +714,38 @@ pillow = ">=6.2.0"
 pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
 python-dateutil = ">=2.1"
 
+[[package]]
+name = "numpy"
+version = "1.17.3"
+description = "NumPy is the fundamental package for array computing with Python."
+optional = false
+python-versions = ">=3.5"
+groups = ["main"]
+markers = "python_version <= \"3.8\""
+files = [
+    {file = "numpy-1.17.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:4dd830a11e8724c9c9379feed1d1be43113f8bcce55f47ea7186d3946769ce26"},
+    {file = "numpy-1.17.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:30c84e3a62cfcb9e3066f25226e131451312a044f1fe2040e69ce792cb7de418"},
+    {file = "numpy-1.17.3-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:9395b0a41e8b7e9a284e3be7060db9d14ad80273841c952c83a5afc241d2bd98"},
+    {file = "numpy-1.17.3-cp35-cp35m-win32.whl", hash = "sha256:9e37c35fc4e9410093b04a77d11a34c64bf658565e30df7cbe882056088a91c1"},
+    {file = "numpy-1.17.3-cp35-cp35m-win_amd64.whl", hash = "sha256:de2b1c20494bdf47f0160bd88ed05f5e48ae5dc336b8de7cfade71abcc95c0b9"},
+    {file = "numpy-1.17.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:669795516d62f38845c7033679c648903200980d68935baaa17ac5c7ae03ae0c"},
+    {file = "numpy-1.17.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:4650d94bb9c947151737ee022b934b7d9a845a7c76e476f3e460f09a0c8c6f39"},
+    {file = "numpy-1.17.3-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:4f2a2b279efde194877aff1f76cf61c68e840db242a5c7169f1ff0fd59a2b1e2"},
+    {file = "numpy-1.17.3-cp36-cp36m-win32.whl", hash = "sha256:ffca69e29079f7880c5392bf675eb8b4146479d976ae1924d01cd92b04cccbcc"},
+    {file = "numpy-1.17.3-cp36-cp36m-win_amd64.whl", hash = "sha256:2e418f0a59473dac424f888dd57e85f77502a593b207809211c76e5396ae4f5c"},
+    {file = "numpy-1.17.3-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:75fcd60d682db3e1f8fbe2b8b0c6761937ad56d01c1dc73edf4ef2748d5b6bc4"},
+    {file = "numpy-1.17.3-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:28b1180c758abf34a5c3fea76fcee66a87def1656724c42bb14a6f9717a5bdf7"},
+    {file = "numpy-1.17.3-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:dd0667f5be56fb1b570154c2c0516a528e02d50da121bbbb2cbb0b6f87f59bc2"},
+    {file = "numpy-1.17.3-cp37-cp37m-win32.whl", hash = "sha256:25ffe71f96878e1da7e014467e19e7db90ae7d4e12affbc73101bcf61785214e"},
+    {file = "numpy-1.17.3-cp37-cp37m-win_amd64.whl", hash = "sha256:0b0dd8f47fb177d00fa6ef2d58783c4f41ad3126b139c91dd2f7c4b3fdf5e9a5"},
+    {file = "numpy-1.17.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:62d22566b3e3428dfc9ec972014c38ed9a4db4f8969c78f5414012ccd80a149e"},
+    {file = "numpy-1.17.3-cp38-cp38-manylinux1_i686.whl", hash = "sha256:26efd7f7d755e6ca966a5c0ac5a930a87dbbaab1c51716ac26a38f42ecc9bc4b"},
+    {file = "numpy-1.17.3-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:b46554ad4dafb2927f88de5a1d207398c5385edbb5c84d30b3ef187c4a3894d8"},
+    {file = "numpy-1.17.3-cp38-cp38-win32.whl", hash = "sha256:c867eeccd934920a800f65c6068acdd6b87e80d45cd8c8beefff783b23cdc462"},
+    {file = "numpy-1.17.3-cp38-cp38-win_amd64.whl", hash = "sha256:f1df7b2b7740dd777571c732f98adb5aad5450aee32772f1b39249c8a50386f6"},
+    {file = "numpy-1.17.3.zip", hash = "sha256:a0678793096205a4d784bd99f32803ba8100f639cf3b932dc63b21621390ea7e"},
+]
+
 [[package]]
 name = "numpy"
 version = "1.19.3"
@@ -689,6 +753,7 @@ description = "NumPy is the fundamental package for array computing with Python.
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version > \"3.8\""
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 python-versions = "*"
 groups = ["main"]
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 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
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+numpy = ">=1.13.3"
+scipy = ">=0.19.1"
+threadpoolctl = ">=2.0.0"
+
+[package.extras]
+alldeps = ["numpy (>=1.13.3)", "scipy (>=0.19.1)"]
+
 [[package]]
 name = "scikit-learn"
 version = "0.24.0"
@@ -1105,6 +1246,7 @@ description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version > \"3.8\""
 files = [
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@@ -1145,6 +1287,41 @@ docs = ["Pillow (>=7.1.2)", "matplotlib (>=2.1.1)", "memory-profiler (>=0.57.0)"
 examples = ["matplotlib (>=2.1.1)", "pandas (>=0.25.0)", "scikit-image (>=0.13)", "seaborn (>=0.9.0)"]
 tests = ["flake8 (>=3.8.2)", "matplotlib (>=2.1.1)", "mypy (>=0.770)", "pandas (>=0.25.0)", "pyamg (>=4.0.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "scikit-image (>=0.13)"]
 
+[[package]]
+name = "scipy"
+version = "1.3.3"
+description = "SciPy: Scientific Library for Python"
+optional = false
+python-versions = ">=3.5"
+groups = ["main"]
+markers = "python_version <= \"3.9\""
+files = [
+    {file = "scipy-1.3.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:a70308bb065562afb936c963780deab359966d71ab4f230368b154dde3136ea4"},
+    {file = "scipy-1.3.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:7be424ee09bed7ced36c9457f99c826ce199fd0c0f5b272cf3d098ff7b29e3ae"},
+    {file = "scipy-1.3.3-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:f5d47351aeb1cb6bda14a8908e56648926a6b2d714f89717c71f7ada41282141"},
+    {file = "scipy-1.3.3-cp35-cp35m-win32.whl", hash = "sha256:4ba2ce1a58fe117e993cf316a149cf9926c7c5000c0cdc4bc7c56ae8325612f6"},
+    {file = "scipy-1.3.3-cp35-cp35m-win_amd64.whl", hash = "sha256:c008f1b58f99f1d1cc546957b3effe448365e0a217df1f1894e358906e91edad"},
+    {file = "scipy-1.3.3-cp36-cp36m-macosx_10_6_intel.whl", hash = "sha256:bb0899d3f8b9fe8ef95b79210cf0deb6709542889fadaa438eeb3a28001e09e7"},
+    {file = "scipy-1.3.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:18ad034be955df046b5a27924cdb3db0e8e1d76aaa22c635403fe7aee17f1482"},
+    {file = "scipy-1.3.3-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2f690ba68ed7caa7c30b6dc48c1deed22c78f3840fa4736083ef4f2bd8baa19e"},
+    {file = "scipy-1.3.3-cp36-cp36m-win32.whl", hash = "sha256:b7b8cf45f9a48f23084f19deb9384a1cccb5e92fbc879b12f97dc4d56fb2eb92"},
+    {file = "scipy-1.3.3-cp36-cp36m-win_amd64.whl", hash = "sha256:0b8c9dc042b9a47912b18b036b4844029384a5b8d89b64a4901ac3e06876e5f6"},
+    {file = "scipy-1.3.3-cp37-cp37m-macosx_10_6_intel.whl", hash = "sha256:225d0b5e140bb66df23d438c7b535303ce8e533f94454f4e5bde5f8d109103ea"},
+    {file = "scipy-1.3.3-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:884e619821f47eccd42979488d10fa1e15dbe9f3b7660b1c8c928d203bd3c1a3"},
+    {file = "scipy-1.3.3-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:583f2ccd6a112656c9feb2345761d2b19e9213a094cfced4e7d2c1cae4173272"},
+    {file = "scipy-1.3.3-cp37-cp37m-win32.whl", hash = "sha256:dfcb0f0a2d8e958611e0b56536285bb435f03746b6feac0e29f045f7c6caf164"},
+    {file = "scipy-1.3.3-cp37-cp37m-win_amd64.whl", hash = "sha256:b01ea5e4cf95a93dc335089f8fbe97852f56fdb74afff238cbdf09793103b6b7"},
+    {file = "scipy-1.3.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:cfee99d085d562a7e3c4afe51ac1fe9b434363489e565a130459307f30077973"},
+    {file = "scipy-1.3.3-cp38-cp38-manylinux1_i686.whl", hash = "sha256:a42b0d02150ef4747e225c31c976a304de5dc8202ec35a27111b7bb8176e5f13"},
+    {file = "scipy-1.3.3-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:869465c7ff89fc0a1e2ea1642b0c65f1b3c05030f3a4c0d53d6a57b2dba7c242"},
+    {file = "scipy-1.3.3-cp38-cp38-win32.whl", hash = "sha256:4b8746f4a755bdb2eeb39d6e253a60481e165cfd74fdfb54d27394bd2c9ec8ac"},
+    {file = "scipy-1.3.3-cp38-cp38-win_amd64.whl", hash = "sha256:546f0dc020b155b8711159d53c87b36591d31f3327c47974a4fb6b50d91589c2"},
+    {file = "scipy-1.3.3.tar.gz", hash = "sha256:64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a"},
+]
+
+[package.dependencies]
+numpy = ">=1.13.3"
+
 [[package]]
 name = "scipy"
 version = "1.5.4"
@@ -1152,6 +1329,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version > \"3.9\""
 files = [
     {file = "scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4f12d13ffbc16e988fa40809cbbd7a8b45bc05ff6ea0ba8e3e41f6f4db3a9e47"},
     {file = "scipy-1.5.4-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:a254b98dbcc744c723a838c03b74a8a34c0558c9ac5c86d5561703362231107d"},
@@ -1409,6 +1587,52 @@ files = [
 lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
+[[package]]
+name = "statsmodels"
+version = "0.10.2"
+description = "Statistical computations and models for Python"
+optional = false
+python-versions = "*"
+groups = ["main"]
+markers = "python_version <= \"3.8\""
+files = [
+    {file = "statsmodels-0.10.2-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:e67e244ae4ca988b40783db7e1bac0de5b7f9f91062cdc0c93e219b189700388"},
+    {file = "statsmodels-0.10.2-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:65f08024ef9a0bd40b63c455d02da34394658c53c16e3494dd6171e86e639f9b"},
+    {file = "statsmodels-0.10.2-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:9c9de647fa3ed058635e6a1b1bb2d3d2396f103cb1dcd00d5e70c36d8137639d"},
+    {file = "statsmodels-0.10.2-cp27-none-win32.whl", hash = "sha256:6cb8395c820eda886721ec2e0db41ffebb2c5a090b27ef9bf51f64e9ab1486af"},
+    {file = "statsmodels-0.10.2-cp27-none-win_amd64.whl", hash = "sha256:a7e6d67d986ef9776b80d30fba4dca1db534986ee2023bab121d70bd78d06c49"},
+    {file = "statsmodels-0.10.2-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:4d1c4b4ecdff539c7fea788f919ed25f25fdc50189a5c0b1a1a966bf04f3a2b8"},
+    {file = "statsmodels-0.10.2-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:75d8e36693d3e7459df9d4e5e4761b0277dd1c9d028a60ef6876e8299f8b9cd7"},
+    {file = "statsmodels-0.10.2-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:7db46146a5e773c9905d914735fabc1e7b3b1027adc98e42060ad8e61460e647"},
+    {file = "statsmodels-0.10.2-cp35-none-win32.whl", hash = "sha256:938dcf95b37fdd6404e0c1f2035b51de0cfd63a63faa9048751176ea55cb4ce9"},
+    {file = "statsmodels-0.10.2-cp35-none-win_amd64.whl", hash = "sha256:be0436f7ea14c277f30e3175dd463d2a26226d8fd360d06bb1c7cd1d9bbedafc"},
+    {file = "statsmodels-0.10.2-cp36-cp36m-macosx_10_6_intel.whl", hash = "sha256:ede6c56ae5d67bf068c4486f970f24b10b952d85dab0b44e7761749159a90d7f"},
+    {file = "statsmodels-0.10.2-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:81c1a0a9dcc46713f47a5b69b1e7d74041ed85f774009302deedad11786beee0"},
+    {file = "statsmodels-0.10.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:8954e9f1659e99a6684167432d36e25bf4e739bb3ae99709a021490f11992fed"},
+    {file = "statsmodels-0.10.2-cp36-none-win32.whl", hash = "sha256:f797eada017668ca4c8c50664ff44437c461dc20233da0e12ff81327a13877fd"},
+    {file = "statsmodels-0.10.2-cp36-none-win_amd64.whl", hash = "sha256:eb0589fae351e123d8dbf0a8fbfd9e9cc033622b0e9f6e81684aa692be48688d"},
+    {file = "statsmodels-0.10.2-cp37-cp37m-macosx_10_6_intel.whl", hash = "sha256:c84625b8746ee7e613752334bfb9ff60dffb91d22f19b7f08b8c387776dc42c1"},
+    {file = "statsmodels-0.10.2-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:172d947a1a8542eefe7155f73ead951f6748782846e8e97e73b8ebf6483d5820"},
+    {file = "statsmodels-0.10.2-cp37-none-win32.whl", hash = "sha256:a8848b368838a62d06c9f0995bdc6f5e82e09f55440bd85c2c13c58777813ebc"},
+    {file = "statsmodels-0.10.2-cp37-none-win_amd64.whl", hash = "sha256:1d61edd4b73f1f4ef983007cd0d797e6cafd9e7de0125584761d93f79675cdd2"},
+    {file = "statsmodels-0.10.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:3b22ed234b80cd9d38988fba487da89cae484a4c2b9088b3e7783c0a937a4568"},
+    {file = "statsmodels-0.10.2-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:e3d36ff3653b50554d9ad2c95556224d1882a5db328eea8a9aa32a0eb08e4e80"},
+    {file = "statsmodels-0.10.2-cp38-none-win32.whl", hash = "sha256:f9271b4ff7430f63e6c20c28afacb75e97a384fafb336fe336985da80bcd8a49"},
+    {file = "statsmodels-0.10.2-cp38-none-win_amd64.whl", hash = "sha256:adb5e524be26842c867f7dfdd74d7cfb2078fe2a6159b948e2f7ccf0e3d92002"},
+    {file = "statsmodels-0.10.2.tar.gz", hash = "sha256:9cd2194c6642a8754e85f9a6e6912cdf996bebf6ff715d3cc67f65dadfd37cc9"},
+]
+
+[package.dependencies]
+numpy = ">=1.11"
+pandas = ">=0.19"
+patsy = ">=0.4.0"
+scipy = ">=0.18"
+
+[package.extras]
+build = ["cython (>=0.24)"]
+develop = ["cython (>=0.24)"]
+docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
+
 [[package]]
 name = "statsmodels"
 version = "0.12.1"
@@ -1416,6 +1640,7 @@ description = "Statistical computations and models for Python"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version > \"3.8\""
 files = [
     {file = "statsmodels-0.12.1-cp36-cp36m-macosx_10_13_x86_64.whl", hash = "sha256:3b482ab9759b89cc1c4777b71c1ccf272e868a7551fc6b74da300557407d8379"},
     {file = "statsmodels-0.12.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:33c6cbed74f075b8816cec37e5c7853ed31dcacebfdbbc3af898b4907911544e"},
@@ -1526,4 +1751,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "30b0a74a3e9d0834453bbdbd608999529abdacaed679048a603c53a8050e2035"
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..484b5e37 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,13 +21,20 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2",
-    "numpy>=1.17.3",
-    "pandas>=1.2.0",
-    "pysam>=0.15.4",
-    "scikit-learn>=0.23.1",
-    "scipy>=1.3.3",
-    "statsmodels>=0.10.2",
+    "matplotlib>=3.1.2 ; python_version <= '3.8'",
+    "matplotlib==3.3.3 ; python_version > '3.8'",
+    "numpy>=1.17.3 ; python_version <= '3.8'",
+    "numpy==1.19.3 ; python_version > '3.8'",
+    "pandas>=1.2.0 ; python_version <= '3.8'",
+    "pandas==1.2.0 ; python_version > '3.8'",
+    "pysam>=0.15.4 ; python_version <= '3.8'",
+    "pysam==0.17.0 ; python_version > '3.8'",
+    "scikit-learn>=0.23.1 ; python_version <= '3.8'",
+    "scikit-learn==0.24.0 ; python_version > '3.8'",
+    "scipy>=1.3.3 ; python_version <= '3.8'",
+    "scipy==1.5.4 ; python_version > '3.9'",
+    "statsmodels>=0.10.2 ; python_version <= '3.8'",
+    "statsmodels==0.12.1 ; python_version > '3.8'",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From bbc0ad454fd6b36491338067a2ae86e3dbb6ec99 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 18:39:23 +0000
Subject: [PATCH 10/36] revert noxfile

---
 noxfile.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 1c35c8fa..c6609fb6 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -21,6 +21,21 @@
 ]
 
 
+
+def install_handle_python(session):
+    """
+    handle incompatibilities between python and other packages
+    see https://github.com/cjolowicz/nox-poetry/issues/1116
+    """
+    # install the latest versions of all dependencies for py3.10+
+    # but install the locked versions for <= py3.9 to ensure some stability in the CI and
+    # help us understand when we need to bump our version constraints
+    if session._session.python in ("3.10", "3.11", "3.12"):
+        session._session.install(".")
+    else:
+        session.install(".")
+
+
 # detect whether conda/mamba is installed
 if os.getenv("CONDA_EXE"):
     conda_cmd = "conda"
@@ -42,7 +57,7 @@ def tests(session: Session) -> None:
             "pytest-cov",
             channel="conda-forge",
         )
-        session.install(".")
+        install_handle_python(".")
         session.run(
            "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )
@@ -54,7 +69,7 @@ def tests(session: Session) -> None:
     def tests(session: Session) -> None:
         """Run the test suite."""
         session.install("pytest", "pytest-cov")
-        session.install(".")
+        install_handle_python(".")
         session.run(
             "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )

From a7dd8846e1b976506207087cc60961b687f45304 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 18:48:57 +0000
Subject: [PATCH 11/36] manually edit lock file hash to sync with pyproject

---
 poetry.lock    |  2 +-
 pyproject.toml | 21 +++++++--------------
 2 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index ca353409..99e19b28 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1751,4 +1751,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "30b0a74a3e9d0834453bbdbd608999529abdacaed679048a603c53a8050e2035"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index 484b5e37..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,20 +21,13 @@ requires-python = ">=3.7.1"
 dependencies = [
     "importlib-metadata>=3.0.0 ; python_version < '3.8'",
     "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2 ; python_version <= '3.8'",
-    "matplotlib==3.3.3 ; python_version > '3.8'",
-    "numpy>=1.17.3 ; python_version <= '3.8'",
-    "numpy==1.19.3 ; python_version > '3.8'",
-    "pandas>=1.2.0 ; python_version <= '3.8'",
-    "pandas==1.2.0 ; python_version > '3.8'",
-    "pysam>=0.15.4 ; python_version <= '3.8'",
-    "pysam==0.17.0 ; python_version > '3.8'",
-    "scikit-learn>=0.23.1 ; python_version <= '3.8'",
-    "scikit-learn==0.24.0 ; python_version > '3.8'",
-    "scipy>=1.3.3 ; python_version <= '3.8'",
-    "scipy==1.5.4 ; python_version > '3.9'",
-    "statsmodels>=0.10.2 ; python_version <= '3.8'",
-    "statsmodels==0.12.1 ; python_version > '3.8'",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
+    "pandas>=1.2.0",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
     "pyfaidx>=0.5.6",
     "pgenlib>=0.90.1",
 ]

From 6d58b11a8773d401484726bace226a233f48cb9f Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 18:50:26 +0000
Subject: [PATCH 12/36] continue to revert noxfile - fix typos

---
 noxfile.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index c6609fb6..05f2a3b6 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -21,7 +21,6 @@
 ]
 
 
-
 def install_handle_python(session):
     """
     handle incompatibilities between python and other packages
@@ -57,7 +56,7 @@ def tests(session: Session) -> None:
             "pytest-cov",
             channel="conda-forge",
         )
-        install_handle_python(".")
+        install_handle_python(session)
         session.run(
            "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )
@@ -69,7 +68,7 @@ def tests(session: Session) -> None:
     def tests(session: Session) -> None:
         """Run the test suite."""
         session.install("pytest", "pytest-cov")
-        install_handle_python(".")
+        install_handle_python(session)
         session.run(
             "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )

From e26ffc880d75fe804328bd41276e739e85c3b12d Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 19:08:11 +0000
Subject: [PATCH 13/36] try again to lock all versions

---
 poetry.lock    | 650 +++++++++++++++++++++++++++++++++----------------
 pyproject.toml |  29 ++-
 2 files changed, 460 insertions(+), 219 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 99e19b28..e3d22fe0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -32,126 +32,128 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2025.1.31"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"},
+    {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"},
 ]
 
 [[package]]
 name = "charset-normalizer"
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+    {file = "charset_normalizer-3.4.1.tar.gz", hash = "sha256:44251f18cd68a75b56585dd00dae26183e102cd5e0f9f1466e6df5da2ed64ea3"},
 ]
 
 [[package]]
 name = "click"
-version = "8.1.7"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
-    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
+    {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
 ]
 
 [package.dependencies]
@@ -272,11 +274,29 @@ description = "Composable style cycles"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
     {file = "cycler-0.11.0-py3-none-any.whl", hash = "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3"},
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 ]
 
+[[package]]
+name = "cycler"
+version = "0.12.1"
+description = "Composable style cycles"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
+    {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
+    {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
+]
+
+[package.extras]
+docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+
 [[package]]
 name = "cyvcf2"
 version = "0.30.27"
@@ -334,15 +354,15 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
 markers = "python_version < \"3.11\""
 files = [
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-    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
 ]
 
 [package.extras]
@@ -366,16 +386,19 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 groups = ["docs"]
 files = [
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-    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
@@ -390,25 +413,23 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.7.0"
+version = "3.0.0"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 groups = ["main", "tests"]
 markers = "python_version < \"3.8\""
 files = [
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-    {file = "importlib_metadata-6.7.0.tar.gz", hash = "sha256:1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4"},
+    {file = "importlib_metadata-3.0.0-py2.py3-none-any.whl", hash = "sha256:fc3b3f9697703d3833d2803162d60cbe8b9f57b5da5e6496ac81e3cb82bd8d9c"},
+    {file = "importlib_metadata-3.0.0.tar.gz", hash = "sha256:d582eb5c35b2f16c78e365e0f89e369f36af38fdaad0146208aa973c693ba247"},
 ]
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+docs = ["rst.linker", "sphinx"]
+testing = ["importlib-resources (>=1.3)", "packaging", "pep517"]
 
 [[package]]
 name = "iniconfig"
@@ -424,14 +445,14 @@ files = [
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.5"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
 files = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+    {file = "jinja2-3.1.5-py3-none-any.whl", hash = "sha256:aba0f4dc9ed8013c424088f68a5c226f7d6097ed89b246d7749c2ec4175c6adb"},
+    {file = "jinja2-3.1.5.tar.gz", hash = "sha256:8fefff8dc3034e27bb80d67c671eb8a9bc424c0ef4c0826edbff304cceff43bb"},
 ]
 
 [package.dependencies]
@@ -447,11 +468,25 @@ description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
     {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"},
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 ]
 
+[[package]]
+name = "joblib"
+version = "1.4.2"
+description = "Lightweight pipelining with Python functions"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
+    {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
+    {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
+]
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.5"
@@ -459,6 +494,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
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@@ -569,74 +605,199 @@ files = [
 [package.dependencies]
 typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 
+[[package]]
+name = "kiwisolver"
+version = "1.4.7"
+description = "A fast implementation of the Cassowary constraint solver"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
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+    {file = "MarkupSafe-2.1.5-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:5049256f536511ee3f7e1b3f87d1d1209d327e818e6ae1365e8653d7e3abb6a6"},
+    {file = "MarkupSafe-2.1.5-cp39-cp39-win32.whl", hash = "sha256:00e046b6dd71aa03a41079792f8473dc494d564611a8f89bbbd7cb93295ebdcf"},
+    {file = "MarkupSafe-2.1.5-cp39-cp39-win_amd64.whl", hash = "sha256:fa173ec60341d6bb97a89f5ea19c85c5643c1e7dedebc22f5181eb73573142c5"},
+    {file = "MarkupSafe-2.1.5.tar.gz", hash = "sha256:d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"},
 ]
 
 [[package]]
@@ -793,14 +954,14 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "23.2"
+version = "24.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs", "tests"]
 files = [
-    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
-    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
+    {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
+    {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
 ]
 
 [[package]]
@@ -840,19 +1001,18 @@ test = ["hypothesis (>=3.58)", "pytest (>=5.0.1)", "pytest-xdist"]
 
 [[package]]
 name = "patsy"
-version = "0.5.4"
+version = "1.0.1"
 description = "A Python package for describing statistical models and for building design matrices."
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 groups = ["main"]
 files = [
-    {file = "patsy-0.5.4-py2.py3-none-any.whl", hash = "sha256:0486413077a527db51ddea8fa94a5234d0feb17a4f4dc01b59b6086c58a70f80"},
-    {file = "patsy-0.5.4.tar.gz", hash = "sha256:7dabc527597308de0e8f188faa20af7e06a89bdaa306756dfc7783693ea16af4"},
+    {file = "patsy-1.0.1-py2.py3-none-any.whl", hash = "sha256:751fb38f9e97e62312e921a1954b81e1bb2bcda4f5eeabaf94db251ee791509c"},
+    {file = "patsy-1.0.1.tar.gz", hash = "sha256:e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4"},
 ]
 
 [package.dependencies]
 numpy = ">=1.4"
-six = "*"
 
 [package.extras]
 test = ["pytest", "pytest-cov", "scipy"]
@@ -1019,14 +1179,31 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.1"
+version = "3.1.4"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
-    {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
-    {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
+    {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
+    {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
+]
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
+
+[[package]]
+name = "pyparsing"
+version = "3.2.1"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
+    {file = "pyparsing-3.2.1-py3-none-any.whl", hash = "sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1"},
+    {file = "pyparsing-3.2.1.tar.gz", hash = "sha256:61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a"},
 ]
 
 [package.extras]
@@ -1046,17 +1223,20 @@ files = [
 
 [[package]]
 name = "pyreadline3"
-version = "3.4.1"
+version = "3.5.4"
 description = "A python implementation of GNU readline."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 groups = ["main"]
 markers = "sys_platform == \"win32\" and python_version >= \"3.8\""
 files = [
-    {file = "pyreadline3-3.4.1-py3-none-any.whl", hash = "sha256:b0efb6516fd4fb07b45949053826a62fa4cb353db5be2bbb4a7aa1fdd1e345fb"},
-    {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"},
+    {file = "pyreadline3-3.5.4-py3-none-any.whl", hash = "sha256:eaf8e6cc3c49bcccf145fc6067ba8643d1df34d604a1ec0eccbf7a18e6d3fae6"},
+    {file = "pyreadline3-3.5.4.tar.gz", hash = "sha256:8d57d53039a1c75adba8e50dd3d992b28143480816187ea5efbd5c78e6c885b7"},
 ]
 
+[package.extras]
+dev = ["build", "flake8", "mypy", "pytest", "twine"]
+
 [[package]]
 name = "pysam"
 version = "0.15.4"
@@ -1112,14 +1292,14 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "7.4.3"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
 files = [
-    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
-    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
+    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
+    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
 ]
 
 [package.dependencies]
@@ -1155,14 +1335,14 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
 files = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
 
 [package.dependencies]
@@ -1170,14 +1350,14 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.3.post1"
+version = "2025.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 groups = ["main", "docs"]
 files = [
-    {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
-    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
+    {file = "pytz-2025.1-py2.py3-none-any.whl", hash = "sha256:89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57"},
+    {file = "pytz-2025.1.tar.gz", hash = "sha256:c2db42be2a2518b28e65f9207c4d05e6ff547d1efa4086469ef855e4ab70178e"},
 ]
 markers = {docs = "python_version < \"3.9\""}
 
@@ -1294,7 +1474,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
-markers = "python_version <= \"3.9\""
+markers = "python_version <= \"3.8\""
 files = [
     {file = "scipy-1.3.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:a70308bb065562afb936c963780deab359966d71ab4f230368b154dde3136ea4"},
     {file = "scipy-1.3.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:7be424ee09bed7ced36c9457f99c826ce199fd0c0f5b272cf3d098ff7b29e3ae"},
@@ -1361,6 +1541,46 @@ files = [
 [package.dependencies]
 numpy = ">=1.14.5"
 
+[[package]]
+name = "scipy"
+version = "1.9.3"
+description = "Fundamental algorithms for scientific computing in Python"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.8\" and python_version <= \"3.9\""
+files = [
+    {file = "scipy-1.9.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1884b66a54887e21addf9c16fb588720a8309a57b2e258ae1c7986d4444d3bc0"},
+    {file = "scipy-1.9.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:83b89e9586c62e787f5012e8475fbb12185bafb996a03257e9675cd73d3736dd"},
+    {file = "scipy-1.9.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1a72d885fa44247f92743fc20732ae55564ff2a519e8302fb7e18717c5355a8b"},
+    {file = "scipy-1.9.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d01e1dd7b15bd2449c8bfc6b7cc67d630700ed655654f0dfcf121600bad205c9"},
+    {file = "scipy-1.9.3-cp310-cp310-win_amd64.whl", hash = "sha256:68239b6aa6f9c593da8be1509a05cb7f9efe98b80f43a5861cd24c7557e98523"},
+    {file = "scipy-1.9.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:b41bc822679ad1c9a5f023bc93f6d0543129ca0f37c1ce294dd9d386f0a21096"},
+    {file = "scipy-1.9.3-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:90453d2b93ea82a9f434e4e1cba043e779ff67b92f7a0e85d05d286a3625df3c"},
+    {file = "scipy-1.9.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:83c06e62a390a9167da60bedd4575a14c1f58ca9dfde59830fc42e5197283dab"},
+    {file = "scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:abaf921531b5aeaafced90157db505e10345e45038c39e5d9b6c7922d68085cb"},
+    {file = "scipy-1.9.3-cp311-cp311-win_amd64.whl", hash = "sha256:06d2e1b4c491dc7d8eacea139a1b0b295f74e1a1a0f704c375028f8320d16e31"},
+    {file = "scipy-1.9.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:5a04cd7d0d3eff6ea4719371cbc44df31411862b9646db617c99718ff68d4840"},
+    {file = "scipy-1.9.3-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:545c83ffb518094d8c9d83cce216c0c32f8c04aaf28b92cc8283eda0685162d5"},
+    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0d54222d7a3ba6022fdf5773931b5d7c56efe41ede7f7128c7b1637700409108"},
+    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cff3a5295234037e39500d35316a4c5794739433528310e117b8a9a0c76d20fc"},
+    {file = "scipy-1.9.3-cp38-cp38-win_amd64.whl", hash = "sha256:2318bef588acc7a574f5bfdff9c172d0b1bf2c8143d9582e05f878e580a3781e"},
+    {file = "scipy-1.9.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:d644a64e174c16cb4b2e41dfea6af722053e83d066da7343f333a54dae9bc31c"},
+    {file = "scipy-1.9.3-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:da8245491d73ed0a994ed9c2e380fd058ce2fa8a18da204681f2fe1f57f98f95"},
+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4db5b30849606a95dcf519763dd3ab6fe9bd91df49eba517359e450a7d80ce2e"},
+    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c68db6b290cbd4049012990d7fe71a2abd9ffbe82c0056ebe0f01df8be5436b0"},
+    {file = "scipy-1.9.3-cp39-cp39-win_amd64.whl", hash = "sha256:5b88e6d91ad9d59478fafe92a7c757d00c59e3bdc3331be8ada76a4f8d683f58"},
+    {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
+]
+
+[package.dependencies]
+numpy = ">=1.18.5,<1.26.0"
+
+[package.extras]
+dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
+doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
+test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "setuptools"
 version = "68.0.0"
@@ -1380,14 +1600,14 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
 files = [
-    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
-    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
 [[package]]
@@ -1682,11 +1902,25 @@ description = "threadpoolctl"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version <= \"3.8\""
 files = [
     {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"},
     {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"},
 ]
 
+[[package]]
+name = "threadpoolctl"
+version = "3.5.0"
+description = "threadpoolctl"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.8\""
+files = [
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
+]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -1706,7 +1940,7 @@ version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 optional = false
 python-versions = ">=3.7"
-groups = ["main", "tests"]
+groups = ["main"]
 markers = "python_version < \"3.8\""
 files = [
     {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
@@ -1751,4 +1985,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "b99949a45a38fcdd813b4730f6eb5a9ac4a33410a3c163cc7d6e8a1b78ce8ac6"
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..d266fcd6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,17 +19,24 @@ classifiers = [
 ]
 requires-python = ">=3.7.1"
 dependencies = [
-    "importlib-metadata>=3.0.0 ; python_version < '3.8'",
-    "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2",
-    "numpy>=1.17.3",
-    "pandas>=1.2.0",
-    "pysam>=0.15.4",
-    "scikit-learn>=0.23.1",
-    "scipy>=1.3.3",
-    "statsmodels>=0.10.2",
-    "pyfaidx>=0.5.6",
-    "pgenlib>=0.90.1",
+    "importlib-metadata==3.0.0 ; python_version < '3.8'",
+    "cyvcf2==0.30.27",
+    "matplotlib==3.1.2 ; python_version <= '3.8'",
+    "matplotlib==3.3.3 ; python_version > '3.8'",
+    "numpy==1.17.3 ; python_version <= '3.8'",
+    "numpy==1.19.3 ; python_version > '3.8'",
+    "pandas==1.2.0 ; python_version <= '3.8'",
+    "pandas==1.2.0 ; python_version > '3.8'",
+    "pysam==0.15.4 ; python_version <= '3.8'",
+    "pysam==0.17.0 ; python_version > '3.8'",
+    "scikit-learn==0.23.1 ; python_version <= '3.8'",
+    "scikit-learn==0.24.0 ; python_version > '3.8'",
+    "scipy==1.3.3 ; python_version <= '3.8'",
+    "scipy==1.5.4 ; python_version > '3.9'",
+    "statsmodels==0.10.2 ; python_version <= '3.8'",
+    "statsmodels==0.12.1 ; python_version > '3.8'",
+    "pyfaidx==0.5.6",
+    "pgenlib==0.90.1",
 ]
 
 [project.urls]

From 896200727a131cbc85e5464c68fdaf0c264f54fc Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 19:08:41 +0000
Subject: [PATCH 14/36] manually edit lock file hash to sync with pyproject

---
 poetry.lock    |  2 +-
 pyproject.toml | 29 +++++++++++------------------
 2 files changed, 12 insertions(+), 19 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index e3d22fe0..dd0c78bc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1985,4 +1985,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "b99949a45a38fcdd813b4730f6eb5a9ac4a33410a3c163cc7d6e8a1b78ce8ac6"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index d266fcd6..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,24 +19,17 @@ classifiers = [
 ]
 requires-python = ">=3.7.1"
 dependencies = [
-    "importlib-metadata==3.0.0 ; python_version < '3.8'",
-    "cyvcf2==0.30.27",
-    "matplotlib==3.1.2 ; python_version <= '3.8'",
-    "matplotlib==3.3.3 ; python_version > '3.8'",
-    "numpy==1.17.3 ; python_version <= '3.8'",
-    "numpy==1.19.3 ; python_version > '3.8'",
-    "pandas==1.2.0 ; python_version <= '3.8'",
-    "pandas==1.2.0 ; python_version > '3.8'",
-    "pysam==0.15.4 ; python_version <= '3.8'",
-    "pysam==0.17.0 ; python_version > '3.8'",
-    "scikit-learn==0.23.1 ; python_version <= '3.8'",
-    "scikit-learn==0.24.0 ; python_version > '3.8'",
-    "scipy==1.3.3 ; python_version <= '3.8'",
-    "scipy==1.5.4 ; python_version > '3.9'",
-    "statsmodels==0.10.2 ; python_version <= '3.8'",
-    "statsmodels==0.12.1 ; python_version > '3.8'",
-    "pyfaidx==0.5.6",
-    "pgenlib==0.90.1",
+    "importlib-metadata>=3.0.0 ; python_version < '3.8'",
+    "cyvcf2>=0.30.27",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
+    "pandas>=1.2.0",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
+    "pyfaidx>=0.5.6",
+    "pgenlib>=0.90.1",
 ]
 
 [project.urls]

From fb55dea26badc40165a678e76f3b938aade8620e Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 19:17:39 +0000
Subject: [PATCH 15/36] oops try again to lock all versions with correct py
 marker for scipy

---
 poetry.lock    | 44 ++------------------------------------------
 pyproject.toml | 29 ++++++++++++++++++-----------
 2 files changed, 20 insertions(+), 53 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index dd0c78bc..f765c5db 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1509,7 +1509,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.9\""
+markers = "python_version > \"3.8\""
 files = [
     {file = "scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4f12d13ffbc16e988fa40809cbbd7a8b45bc05ff6ea0ba8e3e41f6f4db3a9e47"},
     {file = "scipy-1.5.4-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:a254b98dbcc744c723a838c03b74a8a34c0558c9ac5c86d5561703362231107d"},
@@ -1541,46 +1541,6 @@ files = [
 [package.dependencies]
 numpy = ">=1.14.5"
 
-[[package]]
-name = "scipy"
-version = "1.9.3"
-description = "Fundamental algorithms for scientific computing in Python"
-optional = false
-python-versions = ">=3.8"
-groups = ["main"]
-markers = "python_version > \"3.8\" and python_version <= \"3.9\""
-files = [
-    {file = "scipy-1.9.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1884b66a54887e21addf9c16fb588720a8309a57b2e258ae1c7986d4444d3bc0"},
-    {file = "scipy-1.9.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:83b89e9586c62e787f5012e8475fbb12185bafb996a03257e9675cd73d3736dd"},
-    {file = "scipy-1.9.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1a72d885fa44247f92743fc20732ae55564ff2a519e8302fb7e18717c5355a8b"},
-    {file = "scipy-1.9.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d01e1dd7b15bd2449c8bfc6b7cc67d630700ed655654f0dfcf121600bad205c9"},
-    {file = "scipy-1.9.3-cp310-cp310-win_amd64.whl", hash = "sha256:68239b6aa6f9c593da8be1509a05cb7f9efe98b80f43a5861cd24c7557e98523"},
-    {file = "scipy-1.9.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:b41bc822679ad1c9a5f023bc93f6d0543129ca0f37c1ce294dd9d386f0a21096"},
-    {file = "scipy-1.9.3-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:90453d2b93ea82a9f434e4e1cba043e779ff67b92f7a0e85d05d286a3625df3c"},
-    {file = "scipy-1.9.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:83c06e62a390a9167da60bedd4575a14c1f58ca9dfde59830fc42e5197283dab"},
-    {file = "scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:abaf921531b5aeaafced90157db505e10345e45038c39e5d9b6c7922d68085cb"},
-    {file = "scipy-1.9.3-cp311-cp311-win_amd64.whl", hash = "sha256:06d2e1b4c491dc7d8eacea139a1b0b295f74e1a1a0f704c375028f8320d16e31"},
-    {file = "scipy-1.9.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:5a04cd7d0d3eff6ea4719371cbc44df31411862b9646db617c99718ff68d4840"},
-    {file = "scipy-1.9.3-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:545c83ffb518094d8c9d83cce216c0c32f8c04aaf28b92cc8283eda0685162d5"},
-    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0d54222d7a3ba6022fdf5773931b5d7c56efe41ede7f7128c7b1637700409108"},
-    {file = "scipy-1.9.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cff3a5295234037e39500d35316a4c5794739433528310e117b8a9a0c76d20fc"},
-    {file = "scipy-1.9.3-cp38-cp38-win_amd64.whl", hash = "sha256:2318bef588acc7a574f5bfdff9c172d0b1bf2c8143d9582e05f878e580a3781e"},
-    {file = "scipy-1.9.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:d644a64e174c16cb4b2e41dfea6af722053e83d066da7343f333a54dae9bc31c"},
-    {file = "scipy-1.9.3-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:da8245491d73ed0a994ed9c2e380fd058ce2fa8a18da204681f2fe1f57f98f95"},
-    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4db5b30849606a95dcf519763dd3ab6fe9bd91df49eba517359e450a7d80ce2e"},
-    {file = "scipy-1.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c68db6b290cbd4049012990d7fe71a2abd9ffbe82c0056ebe0f01df8be5436b0"},
-    {file = "scipy-1.9.3-cp39-cp39-win_amd64.whl", hash = "sha256:5b88e6d91ad9d59478fafe92a7c757d00c59e3bdc3331be8ada76a4f8d683f58"},
-    {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
-]
-
-[package.dependencies]
-numpy = ">=1.18.5,<1.26.0"
-
-[package.extras]
-dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
-doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
-test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
-
 [[package]]
 name = "setuptools"
 version = "68.0.0"
@@ -1985,4 +1945,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "417a013cfda0e86783e51a3b19f3ff958c2e0c799afece671f60fddcc21d5c19"
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..93c962cd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,17 +19,24 @@ classifiers = [
 ]
 requires-python = ">=3.7.1"
 dependencies = [
-    "importlib-metadata>=3.0.0 ; python_version < '3.8'",
-    "cyvcf2>=0.30.27",
-    "matplotlib>=3.1.2",
-    "numpy>=1.17.3",
-    "pandas>=1.2.0",
-    "pysam>=0.15.4",
-    "scikit-learn>=0.23.1",
-    "scipy>=1.3.3",
-    "statsmodels>=0.10.2",
-    "pyfaidx>=0.5.6",
-    "pgenlib>=0.90.1",
+    "importlib-metadata==3.0.0 ; python_version < '3.8'",
+    "cyvcf2==0.30.27",
+    "matplotlib==3.1.2 ; python_version <= '3.8'",
+    "matplotlib==3.3.3 ; python_version > '3.8'",
+    "numpy==1.17.3 ; python_version <= '3.8'",
+    "numpy==1.19.3 ; python_version > '3.8'",
+    "pandas==1.2.0 ; python_version <= '3.8'",
+    "pandas==1.2.0 ; python_version > '3.8'",
+    "pysam==0.15.4 ; python_version <= '3.8'",
+    "pysam==0.17.0 ; python_version > '3.8'",
+    "scikit-learn==0.23.1 ; python_version <= '3.8'",
+    "scikit-learn==0.24.0 ; python_version > '3.8'",
+    "scipy==1.3.3 ; python_version <= '3.8'",
+    "scipy==1.5.4 ; python_version > '3.8'",
+    "statsmodels==0.10.2 ; python_version <= '3.8'",
+    "statsmodels==0.12.1 ; python_version > '3.8'",
+    "pyfaidx==0.5.6",
+    "pgenlib==0.90.1",
 ]
 
 [project.urls]

From a78be1bbcad2609489c9b4eb4de35eb8f2351720 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 19:19:23 +0000
Subject: [PATCH 16/36] manually edit lock file hash to sync with pyproject

---
 poetry.lock    |  2 +-
 pyproject.toml | 29 +++++++++++------------------
 2 files changed, 12 insertions(+), 19 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f765c5db..59fd8786 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1945,4 +1945,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "417a013cfda0e86783e51a3b19f3ff958c2e0c799afece671f60fddcc21d5c19"
+content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
diff --git a/pyproject.toml b/pyproject.toml
index 93c962cd..44a9a705 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,24 +19,17 @@ classifiers = [
 ]
 requires-python = ">=3.7.1"
 dependencies = [
-    "importlib-metadata==3.0.0 ; python_version < '3.8'",
-    "cyvcf2==0.30.27",
-    "matplotlib==3.1.2 ; python_version <= '3.8'",
-    "matplotlib==3.3.3 ; python_version > '3.8'",
-    "numpy==1.17.3 ; python_version <= '3.8'",
-    "numpy==1.19.3 ; python_version > '3.8'",
-    "pandas==1.2.0 ; python_version <= '3.8'",
-    "pandas==1.2.0 ; python_version > '3.8'",
-    "pysam==0.15.4 ; python_version <= '3.8'",
-    "pysam==0.17.0 ; python_version > '3.8'",
-    "scikit-learn==0.23.1 ; python_version <= '3.8'",
-    "scikit-learn==0.24.0 ; python_version > '3.8'",
-    "scipy==1.3.3 ; python_version <= '3.8'",
-    "scipy==1.5.4 ; python_version > '3.8'",
-    "statsmodels==0.10.2 ; python_version <= '3.8'",
-    "statsmodels==0.12.1 ; python_version > '3.8'",
-    "pyfaidx==0.5.6",
-    "pgenlib==0.90.1",
+    "importlib-metadata>=3.0.0 ; python_version < '3.8'",
+    "cyvcf2>=0.30.27",
+    "matplotlib>=3.1.2",
+    "numpy>=1.17.3",
+    "pandas>=1.2.0",
+    "pysam>=0.15.4",
+    "scikit-learn>=0.23.1",
+    "scipy>=1.3.3",
+    "statsmodels>=0.10.2",
+    "pyfaidx>=0.5.6",
+    "pgenlib>=0.90.1",
 ]
 
 [project.urls]

From 95be6764670769113826df57751db6882b08881b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 21:11:26 +0000
Subject: [PATCH 17/36] revert macos-13 ci test to py3.8

---
 .github/workflows/tests.yml | 2 +-
 pyproject.toml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0b71b842..4452372d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -21,7 +21,7 @@ jobs:
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
           # - { python: "3.11", os: "windows-latest", session: "tests" }
-          - { python: "3.9", os: "macos-13", session: "tests" }
+          - { python: "3.8", os: "macos-13", session: "tests" }
           - { python: "3.9", os: "macos-latest", session: "tests" }
           - { python: "3.9", os: "ubuntu-latest", session: "size" }
           - { python: "3.9", os: "ubuntu-latest", session: "coverage" }
diff --git a/pyproject.toml b/pyproject.toml
index 44a9a705..531cb332 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["poetry-core>=2.0.1"]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [project]

From 08f258006d31e1b5f60b8c2e6b47101cb476d083 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 31 Jan 2025 21:31:29 +0000
Subject: [PATCH 18/36] oops try latest for macos

---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 4452372d..1e157be4 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -20,9 +20,9 @@ jobs:
           - { python: "3.10", os: "ubuntu-latest", session: "tests" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
-          # - { python: "3.11", os: "windows-latest", session: "tests" }
-          - { python: "3.8", os: "macos-13", session: "tests" }
-          - { python: "3.9", os: "macos-latest", session: "tests" }
+          # - { python: "3.12", os: "windows-latest", session: "tests" }
+          - { python: "3.9", os: "macos-13", session: "tests" }
+          - { python: "3.12", os: "macos-latest", session: "tests" }
           - { python: "3.9", os: "ubuntu-latest", session: "size" }
           - { python: "3.9", os: "ubuntu-latest", session: "coverage" }
 

From 54118799d6f03c6bd38c086124342c6c19e88f36 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 16:15:43 +0000
Subject: [PATCH 19/36] use strategy in
 https://github.com/orgs/python-poetry/discussions/10142#discussioncomment-12050625

---
 poetry.lock    | 57 ++++++++++++++++++++++++++++----------------------
 pyproject.toml | 42 +++++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+), 25 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 59fd8786..d60a6ca0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -274,7 +274,7 @@ description = "Composable style cycles"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "cycler-0.11.0-py3-none-any.whl", hash = "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3"},
     {file = "cycler-0.11.0.tar.gz", hash = "sha256:9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f"},
@@ -287,7 +287,7 @@ description = "Composable style cycles"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -468,7 +468,7 @@ description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"},
     {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"},
@@ -481,7 +481,7 @@ description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
     {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
@@ -494,7 +494,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:05703cf211d585109fcd72207a31bb170a0f22144d68298dc5e61b3c946518af"},
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:146d14bebb7f1dc4d5fbf74f8a6cb15ac42baadee8912eb84ac0b3b2a3dc6ac3"},
@@ -612,7 +612,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8a9c83f75223d5e48b0bc9cb1bf2776cf01563e00ade8775ffe13b0b6e1af3a6"},
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58370b1ffbd35407444d57057b57da5d6549d2d854fa30249771775c63b5fe17"},
@@ -807,7 +807,7 @@ description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "matplotlib-3.1.2-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:98c2ffeab8b79a4e3a0af5dd9939f92980eb6e3fec10f7f313df5f35a84dacab"},
     {file = "matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:2d6ab54015a7c0d727c33e36f85f5c5e4172059efdd067f7527f6e5d16ad01aa"},
@@ -838,7 +838,7 @@ description = "Python plotting package"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "matplotlib-3.3.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b2a5e1f637a92bb6f3526cc54cc8af0401112e81ce5cba6368a1b7908f9e18bc"},
     {file = "matplotlib-3.3.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:c586ac1d64432f92857c3cf4478cfb0ece1ae18b740593f8a39f2f0b27c7fda5"},
@@ -882,7 +882,7 @@ description = "NumPy is the fundamental package for array computing with Python.
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "numpy-1.17.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:4dd830a11e8724c9c9379feed1d1be43113f8bcce55f47ea7186d3946769ce26"},
     {file = "numpy-1.17.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:30c84e3a62cfcb9e3066f25226e131451312a044f1fe2040e69ce792cb7de418"},
@@ -914,7 +914,7 @@ description = "NumPy is the fundamental package for array computing with Python.
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "numpy-1.19.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:942d2cdcb362739908c26ce8dd88db6e139d3fa829dd7452dd9ff02cba6b58b2"},
     {file = "numpy-1.19.3-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:efd656893171bbf1331beca4ec9f2e74358fc732a2084f664fd149cc4b3441d2"},
@@ -971,6 +971,7 @@ description = "Powerful data structures for data analysis, time series, and stat
 optional = false
 python-versions = ">=3.7.1"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "pandas-1.2.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:cba93d4fd3b0a42858b2b599495aff793fb5d94587979f45a14177d1217ba446"},
     {file = "pandas-1.2.0-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:9e18631d996fe131de6cb31a8bdae18965cc8f39eb23fdfbbf42808ecc63dabf"},
@@ -1006,6 +1007,7 @@ description = "A Python package for describing statistical models and for buildi
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "patsy-1.0.1-py2.py3-none-any.whl", hash = "sha256:751fb38f9e97e62312e921a1954b81e1bb2bcda4f5eeabaf94db251ee791509c"},
     {file = "patsy-1.0.1.tar.gz", hash = "sha256:e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4"},
@@ -1024,6 +1026,7 @@ description = "Python wrapper for pgenlib's basic reader and writer."
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "Pgenlib-0.90.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0c5823a8f3bb558c2d60243eb19ca6220cc2d5c759fc50139e5c09b179353b68"},
     {file = "Pgenlib-0.90.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:758b3927228029bb10758a28a8ded86a71844da973d6196b44913c4765cdf23d"},
@@ -1044,7 +1047,7 @@ description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "pillow-11.1.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:e1abe69aca89514737465752b4bcaf8016de61b3be1397a8fc260ba33321b3a8"},
     {file = "pillow-11.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c640e5a06869c75994624551f45e5506e4256562ead981cce820d5ab39ae2192"},
@@ -1153,6 +1156,7 @@ description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "pyfaidx-0.5.6.tar.gz", hash = "sha256:2b6ab4212158ccf8f8490ae33f21a162a5c5f7ab2717f227c30013ed7a6c40e8"},
 ]
@@ -1184,7 +1188,7 @@ description = "pyparsing module - Classes and methods to define and execute pars
 optional = false
 python-versions = ">=3.6.8"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
     {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
@@ -1200,7 +1204,7 @@ description = "pyparsing module - Classes and methods to define and execute pars
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "pyparsing-3.2.1-py3-none-any.whl", hash = "sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1"},
     {file = "pyparsing-3.2.1.tar.gz", hash = "sha256:61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a"},
@@ -1244,7 +1248,7 @@ description = "pysam"
 optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "pysam-0.15.4-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:0b0f407ad96b3bd492017ee82a317ac0fc68dc858ecba9119e4ae69b1cda9910"},
     {file = "pysam-0.15.4-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:5b6a2258e326204ee94bf4d482d9a137ce8cbb3f3cefada42c7f26802d15b95d"},
@@ -1273,7 +1277,7 @@ description = "pysam"
 optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "pysam-0.17.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:c4a8099cf474067eaf5e270b5e71433a9ea0e97af90262143a655528eb756cd9"},
     {file = "pysam-0.17.0-cp36-cp36m-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:4d0a35dec9194bacbde0647ddf32ebf805a6724b0192758039c031fce849f01f"},
@@ -1340,6 +1344,7 @@ description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
@@ -1359,7 +1364,7 @@ files = [
     {file = "pytz-2025.1-py2.py3-none-any.whl", hash = "sha256:89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57"},
     {file = "pytz-2025.1.tar.gz", hash = "sha256:c2db42be2a2518b28e65f9207c4d05e6ff547d1efa4086469ef855e4ab70178e"},
 ]
-markers = {docs = "python_version < \"3.9\""}
+markers = {main = "python_version <= \"3.9\"", docs = "python_version < \"3.9\""}
 
 [[package]]
 name = "requests"
@@ -1390,7 +1395,7 @@ description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "scikit-learn-0.23.1.tar.gz", hash = "sha256:e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8"},
     {file = "scikit_learn-0.23.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:058d213092de4384710137af1300ed0ff030b8c40459a6c6f73c31ccd274cc39"},
@@ -1426,7 +1431,7 @@ description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "scikit-learn-0.24.0.tar.gz", hash = "sha256:076369634ee72b5a5941440661e2f306ff4ac30903802dc52031c7e9199ac640"},
     {file = "scikit_learn-0.24.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:890d7d588f65acb0c4f6c083347c9076916bda5e6bd8400f06244b1afc1009af"},
@@ -1474,7 +1479,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "scipy-1.3.3-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:a70308bb065562afb936c963780deab359966d71ab4f230368b154dde3136ea4"},
     {file = "scipy-1.3.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:7be424ee09bed7ced36c9457f99c826ce199fd0c0f5b272cf3d098ff7b29e3ae"},
@@ -1509,7 +1514,7 @@ description = "SciPy: Scientific Library for Python"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "scipy-1.5.4-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4f12d13ffbc16e988fa40809cbbd7a8b45bc05ff6ea0ba8e3e41f6f4db3a9e47"},
     {file = "scipy-1.5.4-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:a254b98dbcc744c723a838c03b74a8a34c0558c9ac5c86d5561703362231107d"},
@@ -1552,6 +1557,7 @@ files = [
     {file = "setuptools-68.0.0-py3-none-any.whl", hash = "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f"},
     {file = "setuptools-68.0.0.tar.gz", hash = "sha256:baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235"},
 ]
+markers = {main = "python_version <= \"3.9\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
@@ -1565,6 +1571,7 @@ description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
+markers = "python_version <= \"3.9\""
 files = [
     {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
@@ -1774,7 +1781,7 @@ description = "Statistical computations and models for Python"
 optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "statsmodels-0.10.2-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:e67e244ae4ca988b40783db7e1bac0de5b7f9f91062cdc0c93e219b189700388"},
     {file = "statsmodels-0.10.2-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:65f08024ef9a0bd40b63c455d02da34394658c53c16e3494dd6171e86e639f9b"},
@@ -1820,7 +1827,7 @@ description = "Statistical computations and models for Python"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "statsmodels-0.12.1-cp36-cp36m-macosx_10_13_x86_64.whl", hash = "sha256:3b482ab9759b89cc1c4777b71c1ccf272e868a7551fc6b74da300557407d8379"},
     {file = "statsmodels-0.12.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:33c6cbed74f075b8816cec37e5c7853ed31dcacebfdbbc3af898b4907911544e"},
@@ -1862,7 +1869,7 @@ description = "threadpoolctl"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.8\""
+markers = "python_version < \"3.9\""
 files = [
     {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"},
     {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"},
@@ -1875,7 +1882,7 @@ description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version > \"3.8\""
+markers = "python_version == \"3.9\""
 files = [
     {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
     {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
@@ -1945,4 +1952,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "debba75e8de6735d90f2da978c222fd978bd0aa1514183a035cd5e1fe16ee7cd"
+content-hash = "acad38c84c0c02b3f79a0d44107214804d6c5db6b46e00e16ee48e154f2ad455"
diff --git a/pyproject.toml b/pyproject.toml
index 531cb332..47c8a419 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,6 +32,48 @@ dependencies = [
     "pgenlib>=0.90.1",
 ]
 
+[tool.poetry.dependencies]
+importlib-metadata = [
+    { version = "3.0.0" , markers = "python_version < '3.8'" },
+]
+cyvcf2 = [
+    { version = "0.30.27" },
+]
+matplotlib = [
+    { version = "3.1.2" , markers = "python_version < '3.9'" },
+    { version = "3.3.3" , markers = "python_version == '3.9'" },
+]
+numpy = [
+    { version = "1.17.3" , markers = "python_version < '3.9'" },
+    { version = "1.19.3" , markers = "python_version == '3.9'" },
+]
+pandas = [
+    { version = "1.2.0" , markers = "python_version <= '3.9'" },
+    { version = "1.2.0" , markers = "python_version == '3.9'" },
+]
+pysam = [
+    { version = "0.15.4" , markers = "python_version < '3.9'" },
+    { version = "0.17.0" , markers = "python_version == '3.9'" },
+]
+scikit-learn = [
+    { version = "0.23.1" , markers = "python_version < '3.9'" },
+    { version = "0.24.0" , markers = "python_version == '3.9'" },
+]
+scipy = [
+    { version = "1.3.3" , markers = "python_version < '3.9'" },
+    { version = "1.5.4" , markers = "python_version == '3.9'" },
+]
+statsmodels = [
+    { version = "0.10.2" , markers = "python_version < '3.9'" },
+    { version = "0.12.1" , markers = "python_version == '3.9'" },
+]
+pyfaidx = [
+    { version = "0.5.6" , markers = "python_version <= '3.9'" },
+]
+pgenlib = [
+    { version = "0.90.1" , markers = "python_version <= '3.9'" },
+]
+
 [project.urls]
 repository = "https://github.com/gymrek-lab/trtools"
 homepage = "https://trtools.readthedocs.org"

From 1846334c6d732c155579da01f9d1cb6a7c331382 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 16:16:03 +0000
Subject: [PATCH 20/36] also lock for 3.10+

---
 .devcontainer.json |  16 +-
 poetry.lock        | 690 +++++++++++++++++++++++++++++++++++++++++++--
 pyproject.toml     |   9 +
 3 files changed, 693 insertions(+), 22 deletions(-)

diff --git a/.devcontainer.json b/.devcontainer.json
index 3467fd4d..0164ad46 100644
--- a/.devcontainer.json
+++ b/.devcontainer.json
@@ -15,23 +15,31 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "mamba env create -n trtools -f dev-env.yml && conda run -n trtools poetry install",
+	"postCreateCommand": "mamba env create -n trtools -f dev-env.yml && conda run -n trtools poetry config virtualenvs.in-project true && conda run -n trtools poetry install",
 
 	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"extensions": [
 				"ms-python.python",
-				"ms-vscode.live-server"
+				"ms-vscode.live-server",
+				"GitHub.vscode-github-actions"
 			],
 			"settings": {
 				"python.condaPath": "/opt/conda/condabin/conda",
 				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"],
+				"python.venvPath": "/workspaces/trtools/.venv",
+				"python.defaultInterpreterPath": "/workspaces/trtools/.venv/bin/python",
+				"python.testing.pytestEnabled": true,
+				"python.testing.unittestEnabled": false,
 				"terminal.integrated.environmentChangesRelaunch": true,
-				"terminal.integrated.hideOnStartup": "always"
+				"terminal.integrated.hideOnStartup": "always",
+				"files.eol": "\n",
+				"git.autofetch": true,
+				"git.enableSmartCommit": true,
+				"git.confirmSync": false
 			}
 		}
 	}
diff --git a/poetry.lock b/poetry.lock
index d60a6ca0..8a60804e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -7,6 +7,7 @@ description = "A configurable sidebar-enabled Sphinx theme"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
@@ -19,6 +20,7 @@ description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
     {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
@@ -37,6 +39,7 @@ description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"},
     {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"},
@@ -49,6 +52,7 @@ description = "The Real First Universal Charset Detector. Open, modern and activ
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "charset_normalizer-3.4.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:91b36a978b5ae0ee86c394f5a54d6ef44db1de0815eb43de826d41d21e4af3de"},
     {file = "charset_normalizer-3.4.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:7461baadb4dc00fd9e0acbe254e3d7d2112e7f92ced2adc96e54ef6501c5f176"},
@@ -151,6 +155,7 @@ description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
     {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
@@ -171,7 +176,7 @@ files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
-markers = {main = "platform_system == \"Windows\"", docs = "sys_platform == \"win32\"", tests = "sys_platform == \"win32\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Windows\"", docs = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\"", tests = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\""}
 
 [[package]]
 name = "coloredlogs"
@@ -180,6 +185,7 @@ description = "Colored terminal output for Python's logging module"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coloredlogs-15.0.1-py2.py3-none-any.whl", hash = "sha256:612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934"},
     {file = "coloredlogs-15.0.1.tar.gz", hash = "sha256:7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0"},
@@ -191,6 +197,81 @@ humanfriendly = ">=9.1"
 [package.extras]
 cron = ["capturer (>=2.4)"]
 
+[[package]]
+name = "contourpy"
+version = "1.3.1"
+description = "Python library for calculating contours of 2D quadrilateral grids"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
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+    {file = "contourpy-1.3.1-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:44a29502ca9c7b5ba389e620d44f2fbe792b1fb5734e8b931ad307071ec58c53"},
+    {file = "contourpy-1.3.1.tar.gz", hash = "sha256:dfd97abd83335045a913e3bcc4a09c0ceadbe66580cf573fe961f4a825efa699"},
+]
+
+[package.dependencies]
+numpy = ">=1.23"
+
+[package.extras]
+bokeh = ["bokeh", "selenium"]
+docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.11.1)", "types-Pillow"]
+test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
+
 [[package]]
 name = "coverage"
 version = "7.2.7"
@@ -198,6 +279,7 @@ description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coverage-7.2.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d39b5b4f2a66ccae8b7263ac3c8170994b65266797fb96cbbfd3fb5b23921db8"},
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@@ -287,7 +369,7 @@ description = "Composable style cycles"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -304,6 +386,7 @@ description = "fast vcf parsing with cython + htslib"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "cyvcf2-0.30.27-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ab4cc28e7adbad5459dfa0c90fb7693cf7f04680a5e21455f9aa52ef64f30a79"},
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@@ -347,6 +430,7 @@ description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"},
     {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
@@ -368,6 +452,81 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "fonttools"
+version = "4.55.8"
+description = "Tools to manipulate font files"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
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+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
+graphite = ["lz4 (>=1.7.4.2)"]
+interpolatable = ["munkres", "pycairo", "scipy"]
+lxml = ["lxml (>=4.0)"]
+pathops = ["skia-pathops (>=0.5.0)"]
+plot = ["matplotlib"]
+repacker = ["uharfbuzz (>=0.23.0)"]
+symfont = ["sympy"]
+type1 = ["xattr"]
+ufo = ["fs (>=2.2.0,<3)"]
+unicode = ["unicodedata2 (>=15.1.0)"]
+woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+
 [[package]]
 name = "humanfriendly"
 version = "10.0"
@@ -375,6 +534,7 @@ description = "Human friendly output for text interfaces using Python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -391,6 +551,7 @@ description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -406,6 +567,7 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -418,11 +580,11 @@ description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.6"
 groups = ["main", "tests"]
-markers = "python_version < \"3.8\""
 files = [
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 ]
+markers = {main = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\" or python_version < \"3.8\"", tests = "python_version < \"3.8\""}
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -438,6 +600,7 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -450,6 +613,7 @@ description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -481,7 +645,7 @@ description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -612,7 +776,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -737,6 +901,7 @@ description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -875,6 +1040,65 @@ pillow = ">=6.2.0"
 pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
 python-dateutil = ">=2.1"
 
+[[package]]
+name = "matplotlib"
+version = "3.10.0"
+description = "Python plotting package"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
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 [[package]]
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 version = "1.17.3"
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 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
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 version = "24.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
-groups = ["docs", "tests"]
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 [[package]]
 name = "pandas"
@@ -1000,6 +1291,94 @@ pytz = ">=2017.3"
 [package.extras]
 test = ["hypothesis (>=3.58)", "pytest (>=5.0.1)", "pytest-xdist"]
 
+[[package]]
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 [[package]]
 name = "patsy"
 version = "1.0.1"
@@ -1007,7 +1386,7 @@ description = "A Python package for describing statistical models and for buildi
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.9\""
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1040,6 +1419,28 @@ files = [
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+python-versions = ">=3.5"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
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 [[package]]
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 version = "11.1.0"
@@ -1047,7 +1448,7 @@ description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1137,6 +1538,7 @@ description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
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@@ -1165,6 +1567,23 @@ files = [
 setuptools = ">=0.7"
 six = "*"
 
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+description = "pyfaidx: efficient pythonic random access to fasta subsequences"
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+[package.dependencies]
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+packaging = "*"
+
 [[package]]
 name = "pygments"
 version = "2.17.2"
@@ -1172,6 +1591,7 @@ description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1232,7 +1652,7 @@ description = "A python implementation of GNU readline."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "sys_platform == \"win32\" and python_version >= \"3.8\""
+markers = "sys_platform == \"win32\" and python_version >= \"3.8\" and (python_version <= \"3.11\" or python_version >= \"3.12\")"
 files = [
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 ]
 
+[[package]]
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+version = "0.22.1"
+description = "Package for reading, manipulating, and writing genomic data"
+optional = false
+python-versions = ">=3.6"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
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 version = "7.4.4"
@@ -1301,6 +1759,7 @@ description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
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@@ -1325,6 +1784,7 @@ description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
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 [[package]]
 name = "requests"
@@ -1373,6 +1833,7 @@ description = "Python HTTP for Humans."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
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+
 [[package]]
 name = "scipy"
 version = "1.3.3"
@@ -1546,6 +2063,65 @@ files = [
 [package.dependencies]
 numpy = ">=1.14.5"
 
+[[package]]
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+
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+
 [[package]]
 name = "setuptools"
 version = "68.0.0"
@@ -1557,7 +2133,7 @@ files = [
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 ]
-markers = {main = "python_version <= \"3.9\""}
+markers = {main = "python_version <= \"3.9\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
@@ -1571,7 +2147,7 @@ description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
-markers = "python_version <= \"3.9\""
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1584,6 +2160,7 @@ description = "This package provides 29 stemmers for 28 languages generated from
 optional = false
 python-versions = "*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1596,6 +2173,7 @@ description = "Python documentation generator"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 groups = ["docs"]
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 files = [
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@@ -1671,6 +2251,7 @@ description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1719,6 +2302,7 @@ description = "Extension to include jQuery on newer Sphinx releases"
 optional = false
 python-versions = ">=2.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1734,6 +2318,7 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1749,6 +2334,7 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1765,6 +2351,7 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -1862,6 +2449,59 @@ build = ["cython (>=0.29)"]
 develop = ["cython (>=0.29)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
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+description = "Statistical computations and models for Python"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+    {file = "statsmodels-0.14.4-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:b5a24f5d2c22852d807d2b42daf3a61740820b28d8381daaf59dcb7055bf1a79"},
+    {file = "statsmodels-0.14.4-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:df4f7864606fa843d7e7c0e6af288f034a2160dba14e6ccc09020a3cf67cb092"},
+    {file = "statsmodels-0.14.4-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:91341cbde9e8bea5fb419a76e09114e221567d03f34ca26e6d67ae2c27d8fe3c"},
+    {file = "statsmodels-0.14.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1322286a7bfdde2790bf72d29698a1b76c20b8423a55bdcd0d457969d0041f72"},
+    {file = "statsmodels-0.14.4-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:e31b95ac603415887c9f0d344cb523889cf779bc52d68e27e2d23c358958fec7"},
+    {file = "statsmodels-0.14.4-cp313-cp313-win_amd64.whl", hash = "sha256:81030108d27aecc7995cac05aa280cf8c6025f6a6119894eef648997936c2dd0"},
+    {file = "statsmodels-0.14.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:4793b01b7a5f5424f5a1dbcefc614c83c7608aa2b035f087538253007c339d5d"},
+    {file = "statsmodels-0.14.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:d330da34f59f1653c5193f9fe3a3a258977c880746db7f155fc33713ea858db5"},
+    {file = "statsmodels-0.14.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6e9ddefba1d4e1107c1f20f601b0581421ea3ad9fd75ce3c2ba6a76b6dc4682c"},
+    {file = "statsmodels-0.14.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6f43da7957e00190104c5dd0f661bfc6dfc68b87313e3f9c4dbd5e7d222e0aeb"},
+    {file = "statsmodels-0.14.4-cp39-cp39-win_amd64.whl", hash = "sha256:8286f69a5e1d0e0b366ffed5691140c83d3efc75da6dbf34a3d06e88abfaaab6"},
+    {file = "statsmodels-0.14.4.tar.gz", hash = "sha256:5d69e0f39060dc72c067f9bb6e8033b6dccdb0bae101d76a7ef0bcc94e898b67"},
+]
+
+[package.dependencies]
+numpy = ">=1.22.3,<3"
+packaging = ">=21.3"
+pandas = ">=1.4,<2.1.0 || >2.1.0"
+patsy = ">=0.5.6"
+scipy = ">=1.8,<1.9.2 || >1.9.2"
+
+[package.extras]
+build = ["cython (>=3.0.10)"]
+develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"]
+docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
+
 [[package]]
 name = "threadpoolctl"
 version = "3.1.0"
@@ -1882,7 +2522,7 @@ description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
     {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
@@ -1914,6 +2554,19 @@ files = [
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
+[[package]]
+name = "tzdata"
+version = "2025.1"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
+    {file = "tzdata-2025.1-py2.py3-none-any.whl", hash = "sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639"},
+    {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"},
+]
+
 [[package]]
 name = "urllib3"
 version = "2.0.7"
@@ -1921,6 +2574,7 @@ description = "HTTP library with thread-safe connection pooling, file post, and
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
     {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
@@ -1939,11 +2593,11 @@ description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.7"
 groups = ["main", "tests"]
-markers = "python_version < \"3.8\""
 files = [
     {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
     {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
 ]
+markers = {main = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\" or python_version < \"3.8\"", tests = "python_version < \"3.8\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
@@ -1952,4 +2606,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "acad38c84c0c02b3f79a0d44107214804d6c5db6b46e00e16ee48e154f2ad455"
+content-hash = "a05500b6265f50222bbacbed8d6fdb3a326d399d1610c1747324838fcdff46d8"
diff --git a/pyproject.toml b/pyproject.toml
index 47c8a419..bf011d78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,36 +42,45 @@ cyvcf2 = [
 matplotlib = [
     { version = "3.1.2" , markers = "python_version < '3.9'" },
     { version = "3.3.3" , markers = "python_version == '3.9'" },
+    { version = "3.10.0" , markers = "python_version > '3.9'" },
 ]
 numpy = [
     { version = "1.17.3" , markers = "python_version < '3.9'" },
     { version = "1.19.3" , markers = "python_version == '3.9'" },
+    { version = "2.2.2" , markers = "python_version > '3.9'" },
 ]
 pandas = [
     { version = "1.2.0" , markers = "python_version <= '3.9'" },
     { version = "1.2.0" , markers = "python_version == '3.9'" },
+    { version = "2.2.3" , markers = "python_version > '3.9'" },
 ]
 pysam = [
     { version = "0.15.4" , markers = "python_version < '3.9'" },
     { version = "0.17.0" , markers = "python_version == '3.9'" },
+    { version = "0.22.1" , markers = "python_version > '3.9'" },
 ]
 scikit-learn = [
     { version = "0.23.1" , markers = "python_version < '3.9'" },
     { version = "0.24.0" , markers = "python_version == '3.9'" },
+    { version = "1.6.1" , markers = "python_version > '3.9'" },
 ]
 scipy = [
     { version = "1.3.3" , markers = "python_version < '3.9'" },
     { version = "1.5.4" , markers = "python_version == '3.9'" },
+    { version = "1.15.1" , markers = "python_version > '3.9'" },
 ]
 statsmodels = [
     { version = "0.10.2" , markers = "python_version < '3.9'" },
     { version = "0.12.1" , markers = "python_version == '3.9'" },
+    { version = "0.14.4" , markers = "python_version > '3.9'" },
 ]
 pyfaidx = [
     { version = "0.5.6" , markers = "python_version <= '3.9'" },
+    { version = "0.8.1.3" , markers = "python_version > '3.9'" },
 ]
 pgenlib = [
     { version = "0.90.1" , markers = "python_version <= '3.9'" },
+    { version = "0.92.0" , markers = "python_version > '3.9'" },
 ]
 
 [project.urls]

From 44563cf2729579dc9d6381722e12a0ca96c5966f Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 16:39:53 +0000
Subject: [PATCH 21/36] remove conda defaults from tests.yml

---
 .devcontainer.json          | 1 -
 .github/workflows/tests.yml | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer.json b/.devcontainer.json
index 0164ad46..9ffad751 100644
--- a/.devcontainer.json
+++ b/.devcontainer.json
@@ -27,7 +27,6 @@
 			],
 			"settings": {
 				"python.condaPath": "/opt/conda/condabin/conda",
-				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
 				"python.venvPath": "/workspaces/trtools/.venv",
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 1e157be4..e5172649 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -39,6 +39,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: trtools
+          conda-remove-defaults: true
           auto-activate-base: false
           miniforge-version: latest
           use-mamba: true

From f416839bc6fe57ff235d5aa1b8a80385810e1c5c Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 08:49:43 -0800
Subject: [PATCH 22/36] use locked dependencies in noxfile

---
 noxfile.py | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 05f2a3b6..1c35c8fa 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -21,20 +21,6 @@
 ]
 
 
-def install_handle_python(session):
-    """
-    handle incompatibilities between python and other packages
-    see https://github.com/cjolowicz/nox-poetry/issues/1116
-    """
-    # install the latest versions of all dependencies for py3.10+
-    # but install the locked versions for <= py3.9 to ensure some stability in the CI and
-    # help us understand when we need to bump our version constraints
-    if session._session.python in ("3.10", "3.11", "3.12"):
-        session._session.install(".")
-    else:
-        session.install(".")
-
-
 # detect whether conda/mamba is installed
 if os.getenv("CONDA_EXE"):
     conda_cmd = "conda"
@@ -56,7 +42,7 @@ def tests(session: Session) -> None:
             "pytest-cov",
             channel="conda-forge",
         )
-        install_handle_python(session)
+        session.install(".")
         session.run(
            "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )
@@ -68,7 +54,7 @@ def tests(session: Session) -> None:
     def tests(session: Session) -> None:
         """Run the test suite."""
         session.install("pytest", "pytest-cov")
-        install_handle_python(session)
+        session.install(".")
         session.run(
             "python", "-m", "pytest", *cov_cli_args, *session.posargs
         )

From 27b95afd4c3a1ebd64878a9b11a7dd2b2a1a6a9e Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 16:58:24 +0000
Subject: [PATCH 23/36] clarify how to lock dependencies now

---
 doc/index.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/index.rst b/doc/index.rst
index f1d9dfcb..82bd851d 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -172,8 +172,8 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 #. Make your changes. 
 #. If you need to add a dependency or update the version of a dependency, you can use the :code:`poetry add` command.
 
-    * You should specify a `version constraint <https://python-poetry.org/docs/master/dependency-specification#version-constraints>`_ when adding a dependency. Use the oldest version compatible with your code. For example, to specify a version of :code:`numpy>=1.23.0`, you can run :code:`poetry add 'numpy>=1.23.0'`. Note: For most cases, a version constraint operator of :code:`>=` `is better than <https://iscinumpy.dev/post/bound-version-constraints>`_ poetry's default of :code:`^`.
-    * Afterward, double-check that the :code:`poetry.lock` file contains 1.23.0 in it. **All of our dependencies should be locked to their minimum versions at all times.** To downgrade to a specific version of :code:`numpy` in our lock file, you can explicitly add the version via :code:`poetry add 'numpy==1.23.0'`, manually edit the pyproject.toml file to use a :code:`>=` sign in front of the version number, and then run :code:`poetry lock`.
+    * You should specify a `version constraint <https://python-poetry.org/docs/master/dependency-specification#version-constraints>`_ when adding a dependency. Use the oldest version compatible with your code. For example, to specify a version of :code:`numpy>=1.23.0`, you can run :code:`poetry add 'numpy>=1.23.0'`.
+    * Afterward, double-check that the :code:`poetry.lock` file contains 1.23.0 in it. **All of our dependencies should be locked to their minimum versions at all times.** To downgrade to a specific version of a package in our lock file, you can `explicitly add the version <https://python-poetry.org/docs/dependency-specification/#projectdependencies-and-toolpoetrydependencies>`_ to the :code:`tool.poetry.dependencies` of our pyproject.toml file and then run :code:`poetry lock`.
     * Only PyPI packages can be added to our pyproject.toml file. So if a dependency is only available on conda, then you can add it to our :code:`dev-env.yml` file instead. Please note that anyone who installs TRTools from PyPI will not be guaranteed to have your dependency installed, so you should design your code accordingly. 
     * Any changes to our dependencies must also added to our bioconda recipe at the time of publication. See `PUBLISHING.rst <https://github.com/gymrek-lab/TRTools/blob/master/PUBLISHING.rst>`_ for more details.
 

From 3bb0173416f51ded7a953c1b00fec0650092f765 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 4 Feb 2025 17:56:38 +0000
Subject: [PATCH 24/36] lock at a version of cyvcf2 which is compatible with
 numpy 2

---
 doc/index.rst  |  2 +-
 poetry.lock    | 52 ++++++++++++++++++++++++++++++++++++++++++++++++--
 pyproject.toml |  3 ++-
 3 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/doc/index.rst b/doc/index.rst
index 82bd851d..e29fbfa1 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -27,7 +27,7 @@ If you use TRTools in your work, please cite: Nima Mousavi, Jonathan Margoliash,
 Install
 -------
 
-Note: TRTools supports Python versions 3.8 and up. We do not officially support python version 3.7 as it is `end of life <https://devguide.python.org/versions/#status-of-python-versions>`_, but we believe TRTools likely works with it from previous testing results.
+Note: TRTools supports Python versions 3.9 and up. We do not officially support python version 3.7 or 3.8 as they are `end of life <https://devguide.python.org/versions/#status-of-python-versions>`_, but we believe TRTools likely works with them from previous testing results.
 
 With conda
 ^^^^^^^^^^
diff --git a/poetry.lock b/poetry.lock
index 8a60804e..ac18335f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -386,7 +386,7 @@ description = "fast vcf parsing with cython + htslib"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version <= \"3.9\""
 files = [
     {file = "cyvcf2-0.30.27-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ab4cc28e7adbad5459dfa0c90fb7693cf7f04680a5e21455f9aa52ef64f30a79"},
     {file = "cyvcf2-0.30.27-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40a95e00cdb7e4766aa33d81bc35b95e44deb3315e642cccc55d102a3000b2d1"},
@@ -423,6 +423,54 @@ click = "*"
 coloredlogs = "*"
 numpy = "*"
 
+[[package]]
+name = "cyvcf2"
+version = "0.31.1"
+description = "fast vcf parsing with cython + htslib"
+optional = false
+python-versions = ">=3.7"
+groups = ["main"]
+markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+files = [
+    {file = "cyvcf2-0.31.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5345e952a37a0fc227a81a3b3ecf61449d6f2cbd7f862bcc8d80bda13be683ea"},
+    {file = "cyvcf2-0.31.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6ac78c7fff3ad173cb6dfa7e394ce14c645c43fa7bb1ef3bd4ddc45fba11d025"},
+    {file = "cyvcf2-0.31.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0b37e6ef23965f0efc5f3119ce3eea9d71d0fbfeb3376ef5723dac3aa391f0b4"},
+    {file = "cyvcf2-0.31.1-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:054ee5fddfac0da12adf5ae5c86d0627615c97a6488ba700d45c46d6c93f9c83"},
+    {file = "cyvcf2-0.31.1-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:f39a37c2358ea7cee996d238b64e957b87ed5d0ccf4a0cec4a34e78efc37c47f"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:142eaa5614d984e290ef84accf46b64b6fe15e89aa19a0045a346cb0b45ea1d0"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:cfe331698cf3f844be3a3332f8a5dbcb38330509c1683daa9b0441a9261ed774"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b06ed66c304f84bb959777859e4065730b067204c7cec3cc29ee3665e884ac4f"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:ce48c485ecc3391e384ed1f815d8ae0a34ea8867caa1925608fef9bdab6720f5"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:fbe63f75854880044e2bfaa06afc92d6e60aa7b1e35013e43fac3c4e930830ed"},
+    {file = "cyvcf2-0.31.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:2dd9f8afc80c3204bf69d0f24a8cf45353438a93aa82bbbdac136c3b6e7d318a"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:75993f0ef2eca17b618c946bf43eb2e0b932b76f4d3e086b5a580a271d13d2d8"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:dda34f22ae7d609355120a39577e0519fb6ec8746ca45d99e78c4b318a0721ea"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc16c9016581550310d605141550f0aaaca6bd19adec75426c8271da769721e4"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:0691c075ee73c8c0fe45144929c3b22a53060c666928444996e4b487233ff948"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:f0830744b6efb9084230e21a6032cb69836abad80790d7890378db3079a32248"},
+    {file = "cyvcf2-0.31.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:4c376ac3f54d48537ca3fd93f4bb1be2c9e5688d7aa75cfeefb4ce4c9a6fcf06"},
+    {file = "cyvcf2-0.31.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:93acb8d221db3af315defcf2cd8f88b41803afd32b1682252d4969c04a1968b7"},
+    {file = "cyvcf2-0.31.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:517103732f922f15f3f01c009376913922f838e3873c77ab50be7988abcbe959"},
+    {file = "cyvcf2-0.31.1-cp37-cp37m-manylinux_2_28_aarch64.whl", hash = "sha256:c34cde3785148907e1143f6df9cb6d77d1f6e5b4fe588ec9760b8168b92e5758"},
+    {file = "cyvcf2-0.31.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:7d4a1222ac9ce3c7f726ab8105536d0e6a00ee451e9851e6028448040ea9c567"},
+    {file = "cyvcf2-0.31.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:94e82feb4750db1167a0c8a91ca191b8a3fb721c8d8ab48f5836e99399626a3f"},
+    {file = "cyvcf2-0.31.1-cp38-cp38-manylinux_2_28_aarch64.whl", hash = "sha256:851040cd272f6afbaacb3267851597e893e9a75935dca99ff1c08a65c13b79a5"},
+    {file = "cyvcf2-0.31.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:55ce92d58cbc18d4bd7e56d62031909bb88cd4262f081d3df04c569048cf0fa9"},
+    {file = "cyvcf2-0.31.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:996db8d4c901f7496d9be61786e5a68218d92d26dcdc14c8e0eedf52cce7d459"},
+    {file = "cyvcf2-0.31.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d63c2b29d011303ef7e2c1388950b3a7c94193fa628bbae7a3b4caba1949276c"},
+    {file = "cyvcf2-0.31.1-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:701fe8eb8479dc71f05dfa36eb6b2125357e8b38b52dda4c4eab5c328191b799"},
+    {file = "cyvcf2-0.31.1-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:5372665990a7b67f0b39c9a19310900ae58e9b410dc128dc3ee49afca0dd2c5b"},
+    {file = "cyvcf2-0.31.1-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:fc0b33b39b2b20b35d61bd49636ac1d3e212835b96d4da5a8e03d4798f3cb7c4"},
+    {file = "cyvcf2-0.31.1-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6bde2b1b62b46ce332241a1930a4585b11b078e7e2fae556e3e4c65350b5a131"},
+    {file = "cyvcf2-0.31.1-pp310-pypy310_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:fc2943f5645698eb2a5e0596badf65ef3a5f6907ce6927b0770b1c00aeb148ed"},
+    {file = "cyvcf2-0.31.1.tar.gz", hash = "sha256:00bd0e09a3719d29fbc02bc8a40a690ac2c475e91744648750907d1816558fc5"},
+]
+
+[package.dependencies]
+click = "*"
+coloredlogs = "*"
+numpy = ">=1.16.0"
+
 [[package]]
 name = "docutils"
 version = "0.17.1"
@@ -2606,4 +2654,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "a05500b6265f50222bbacbed8d6fdb3a326d399d1610c1747324838fcdff46d8"
+content-hash = "aa49ca32479d49920519e2934698b7b791aa1bebe8d620ba0743aeac6cb87c84"
diff --git a/pyproject.toml b/pyproject.toml
index bf011d78..34a401d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,8 @@ importlib-metadata = [
     { version = "3.0.0" , markers = "python_version < '3.8'" },
 ]
 cyvcf2 = [
-    { version = "0.30.27" },
+    { version = "0.30.27" , markers = "python_version <= '3.9'" },
+    { version = "0.31.1" , markers = "python_version > '3.9'" },
 ]
 matplotlib = [
     { version = "3.1.2" , markers = "python_version < '3.9'" },

From 04ea60e2a9f3393c7b6d6b3c1e097a4cb27d7fa5 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 20:12:40 +0000
Subject: [PATCH 25/36] ensure proper venv is used in devcontainer

---
 .devcontainer.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.devcontainer.json b/.devcontainer.json
index 9ffad751..8ad1cc33 100644
--- a/.devcontainer.json
+++ b/.devcontainer.json
@@ -4,18 +4,17 @@
 	"name": "Ubuntu",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
 	"image": "mcr.microsoft.com/devcontainers/base:jammy",
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
 	"features": {
 		"ghcr.io/rocker-org/devcontainer-features/miniforge:2": {}
 	},
 
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "mamba env create -n trtools -f dev-env.yml && conda run -n trtools poetry config virtualenvs.in-project true && conda run -n trtools poetry install",
+	"postCreateCommand": "mamba env create -y -n trtools -f dev-env.yml && conda run -n trtools poetry config virtualenvs.in-project true && conda run -n trtools poetry install",
 
 	// Configure tool-specific properties.
 	"customizations": {
@@ -26,11 +25,12 @@
 				"GitHub.vscode-github-actions"
 			],
 			"settings": {
+				"python.analysis.typeCheckingMode": "off",
 				"python.condaPath": "/opt/conda/condabin/conda",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.venvPath": "/workspaces/trtools/.venv",
-				"python.defaultInterpreterPath": "/workspaces/trtools/.venv/bin/python",
+				"python.venvPath": "/opt/conda/envs/trtools",
+				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/bin/python",
 				"python.testing.pytestEnabled": true,
 				"python.testing.unittestEnabled": false,
 				"terminal.integrated.environmentChangesRelaunch": true,

From ba07b97b1f941c3018f52213f23f139a9e2e44e7 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 20:13:02 +0000
Subject: [PATCH 26/36] update to newest pysam in lock file

---
 poetry.lock    | 62 +++++++++++++++++++++++++++-----------------------
 pyproject.toml |  2 +-
 2 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index ac18335f..7f9503b1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1764,40 +1764,44 @@ files = [
 
 [[package]]
 name = "pysam"
-version = "0.22.1"
+version = "0.23.0"
 description = "Package for reading, manipulating, and writing genomic data"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
 markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
-    {file = "pysam-0.22.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f18e72013ef2db9a9bb7e8ac421934d054427f6c03e66ce8abc39b09c846ba72"},
-    {file = "pysam-0.22.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:79cd94eeb96541385fa99e759a8f83d21428e092c8b577d50b4eee5823e757cd"},
-    {file = "pysam-0.22.1-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:c71ea45461ee596949061f321a799a97c418164485fdd7e8db89aea2ff979092"},
-    {file = "pysam-0.22.1-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:ab3343f221994d163e1ba2691430ce0f6e7da13762473e0d7f9a2d5db3bec235"},
-    {file = "pysam-0.22.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:503c833e6cf348d87aec9113b1386d5c85c031d64deb914c29f5ad1792d103e6"},
-    {file = "pysam-0.22.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4447fdc2630519a00b6bf598995f1440e6f398eb0c084a7c141db026990ae07a"},
-    {file = "pysam-0.22.1-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:1be663a73cf56ddd1d309b91d314a0c94c9bf352eaa3c6eda30cef12699843f0"},
-    {file = "pysam-0.22.1-cp311-cp311-manylinux_2_28_x86_64.whl", hash = "sha256:aeb31472365014fd8b37da4a88af758094b5872a8a16a25635a52cf8ceff5a9f"},
-    {file = "pysam-0.22.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:e72e129d245574801125029a5892c9e18d2956b13c4203ea585cbd64ccde9351"},
-    {file = "pysam-0.22.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:f8f00bb1fb977fc33c87cf5fe9023eefc2ba3d43d30ab4875a1765827018c949"},
-    {file = "pysam-0.22.1-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:c0e051fda433c1c7ff94532f60477bb83b97f4bb183567a0ae23f340e1c200b4"},
-    {file = "pysam-0.22.1-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:860c7c78ddb1539b83d5476502ba14c8b4e8435810dc7a5b715196da3dfb86b6"},
-    {file = "pysam-0.22.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:18d886d50d75d8f853057fbbb284f0f0e98afad1f76b1a6f55660ea167d31c17"},
-    {file = "pysam-0.22.1-cp36-cp36m-manylinux_2_28_aarch64.whl", hash = "sha256:44420290a619c02da48ca0956548eb82a1665ae97b6ee69c094f9da5a6206431"},
-    {file = "pysam-0.22.1-cp36-cp36m-manylinux_2_28_x86_64.whl", hash = "sha256:acff506c921af36f364c5a87f3a30b3c105ebeb270d0e821c2ca571eaf60ca20"},
-    {file = "pysam-0.22.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:098e0bf12d8b0399613065843310c91ba31a02d014b1f6b4e9d7f2d0d1254ff8"},
-    {file = "pysam-0.22.1-cp37-cp37m-manylinux_2_28_aarch64.whl", hash = "sha256:cd9d457063272df16136640515183ea501bf3371f140a134b2f0a42f425a37d9"},
-    {file = "pysam-0.22.1-cp37-cp37m-manylinux_2_28_x86_64.whl", hash = "sha256:af9fb53157ba2431b7b20a550c0223f4a039304c9f180d8da98ea9d2d3ef3fbf"},
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 ]
 
 [[package]]
@@ -2654,4 +2658,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "aa49ca32479d49920519e2934698b7b791aa1bebe8d620ba0743aeac6cb87c84"
+content-hash = "fec6f4f800955ffccd984b806a5256998a0552acb6ea03e1d6404fe45d468b8f"
diff --git a/pyproject.toml b/pyproject.toml
index 34a401d9..5a491df5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ pandas = [
 pysam = [
     { version = "0.15.4" , markers = "python_version < '3.9'" },
     { version = "0.17.0" , markers = "python_version == '3.9'" },
-    { version = "0.22.1" , markers = "python_version > '3.9'" },
+    { version = "0.23.0" , markers = "python_version > '3.9'" },
 ]
 scikit-learn = [
     { version = "0.23.1" , markers = "python_version < '3.9'" },

From 37c5dbcea562ea600dbe71d21796a5d936045096 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 20:14:18 +0000
Subject: [PATCH 27/36] add py3.13 ci test

---
 .github/workflows/tests.yml | 1 +
 noxfile.py                  | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e5172649..dd1fc774 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -20,6 +20,7 @@ jobs:
           - { python: "3.10", os: "ubuntu-latest", session: "tests" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
+          - { python: "3.13", os: "ubuntu-latest", session: "tests" }
           # - { python: "3.12", os: "windows-latest", session: "tests" }
           - { python: "3.9", os: "macos-13", session: "tests" }
           - { python: "3.12", os: "macos-latest", session: "tests" }
diff --git a/noxfile.py b/noxfile.py
index 1c35c8fa..10f6eca1 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -8,7 +8,7 @@
 
 
 package = "trtools"
-python_versions = ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+python_versions = ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 nox.needs_version = ">= 2022.11.21"
 nox.options.sessions = (
     "tests",

From 5af870d81793b824f00e7482f0b1cfdca4675f46 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 12:18:12 -0800
Subject: [PATCH 28/36] remove py3.13 ci test

pip can't retrieve the wheel for some reason
---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index dd1fc774..81da6730 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -20,8 +20,8 @@ jobs:
           - { python: "3.10", os: "ubuntu-latest", session: "tests" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.13", os: "ubuntu-latest", session: "tests" }
-          # - { python: "3.12", os: "windows-latest", session: "tests" }
+          # - { python: "3.13", os: "ubuntu-latest", session: "tests" }
+          # - { python: "3.13", os: "windows-latest", session: "tests" }
           - { python: "3.9", os: "macos-13", session: "tests" }
           - { python: "3.12", os: "macos-latest", session: "tests" }
           - { python: "3.9", os: "ubuntu-latest", session: "size" }

From 44e4f9a70f349eb1cbc555060a36127903632d7b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 12:33:28 -0800
Subject: [PATCH 29/36] add use-only-tar-bz2 to make caching work better
 hopefully

---
 .github/workflows/tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 81da6730..c346bd11 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -39,6 +39,7 @@ jobs:
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
           activate-environment: trtools
           conda-remove-defaults: true
           auto-activate-base: false

From f54b8e5bb5c45be9a2040b338909b7bfed806d38 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 5 Feb 2025 13:23:14 -0800
Subject: [PATCH 30/36] revert use-only-tar-bz2 bc it broke everything

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c346bd11..bcb9cbff 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -39,7 +39,7 @@ jobs:
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
           activate-environment: trtools
           conda-remove-defaults: true
           auto-activate-base: false

From 27c43beb4dabd05da5dd3829f3f381d25b6106fe Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sat, 15 Feb 2025 16:09:16 +0000
Subject: [PATCH 31/36] upgrade to newest poetry

---
 .github/workflows/release.yml | 2 +-
 dev-env.yml                   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 769c5573..3cf26e76 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -37,7 +37,7 @@ jobs:
       - name: Install Poetry
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          pip install 'poetry==2.0.1' # keep version in sync with dev-env.yml
+          pip install 'poetry==2.1.0' # keep version in sync with dev-env.yml
           poetry --version
 
       - name: Build package
diff --git a/dev-env.yml b/dev-env.yml
index e3814fbb..7bf1f450 100644
--- a/dev-env.yml
+++ b/dev-env.yml
@@ -7,10 +7,10 @@ dependencies:
   - conda-forge::pip==24.3.1
   - bioconda::bcftools==1.21
   - bioconda::art==2016.06.05
-  - conda-forge::poetry==2.0.1 # keep in sync with release.yml
+  - conda-forge::poetry==2.1.0 # keep in sync with release.yml
   - conda-forge::nox==2024.10.9
   - conda-forge::poetry-plugin-export==1.9.0
   - pip:
-    - nox-poetry==1.0.3
+    - nox-poetry==1.1.0
     - poetry-conda==0.1.4
     - poetry-plugin-shell==1.0.1

From aa8b064e3911ae95bf4e32d004ddfeec81351374 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 16 Feb 2025 17:36:19 +0000
Subject: [PATCH 32/36] relock with newest poetry

---
 poetry.lock | 122 +++++++++++++++++++---------------------------------
 1 file changed, 44 insertions(+), 78 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7f9503b1..459807d5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.0 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -7,7 +7,6 @@ description = "A configurable sidebar-enabled Sphinx theme"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
@@ -20,7 +19,6 @@ description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
     {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
@@ -39,7 +37,6 @@ description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"},
     {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"},
@@ -52,7 +49,6 @@ description = "The Real First Universal Charset Detector. Open, modern and activ
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "charset_normalizer-3.4.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:91b36a978b5ae0ee86c394f5a54d6ef44db1de0815eb43de826d41d21e4af3de"},
     {file = "charset_normalizer-3.4.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:7461baadb4dc00fd9e0acbe254e3d7d2112e7f92ced2adc96e54ef6501c5f176"},
@@ -155,7 +151,6 @@ description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
     {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
@@ -176,7 +171,7 @@ files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Windows\"", docs = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\"", tests = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\""}
+markers = {main = "platform_system == \"Windows\"", docs = "sys_platform == \"win32\"", tests = "sys_platform == \"win32\""}
 
 [[package]]
 name = "coloredlogs"
@@ -185,7 +180,6 @@ description = "Colored terminal output for Python's logging module"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coloredlogs-15.0.1-py2.py3-none-any.whl", hash = "sha256:612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934"},
     {file = "coloredlogs-15.0.1.tar.gz", hash = "sha256:7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0"},
@@ -204,7 +198,7 @@ description = "Python library for calculating contours of 2D quadrilateral grids
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "contourpy-1.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a045f341a77b77e1c5de31e74e966537bba9f3c4099b35bf4c2e3939dd54cdab"},
     {file = "contourpy-1.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:500360b77259914f7805af7462e41f9cb7ca92ad38e9f94d6c8641b089338124"},
@@ -279,7 +273,6 @@ description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coverage-7.2.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d39b5b4f2a66ccae8b7263ac3c8170994b65266797fb96cbbfd3fb5b23921db8"},
     {file = "coverage-7.2.7-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d040ef7c9859bb11dfeb056ff5b3872436e3b5e401817d87a31e1750b9ae2fb"},
@@ -347,7 +340,7 @@ files = [
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-toml = ["tomli"]
+toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
 [[package]]
 name = "cycler"
@@ -369,7 +362,7 @@ description = "Composable style cycles"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -430,7 +423,7 @@ description = "fast vcf parsing with cython + htslib"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "cyvcf2-0.31.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5345e952a37a0fc227a81a3b3ecf61449d6f2cbd7f862bcc8d80bda13be683ea"},
     {file = "cyvcf2-0.31.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6ac78c7fff3ad173cb6dfa7e394ce14c645c43fa7bb1ef3bd4ddc45fba11d025"},
@@ -478,7 +471,6 @@ description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"},
     {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
@@ -507,7 +499,7 @@ description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "fonttools-4.55.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d11600f5343092697d7434f3bf77a393c7ae74be206fe30e577b9a195fd53165"},
     {file = "fonttools-4.55.8-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c96f2506ce1a0beeaa9595f9a8b7446477eb133f40c0e41fc078744c28149f80"},
@@ -562,18 +554,18 @@ files = [
 ]
 
 [package.extras]
-all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
+all = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\"", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0) ; python_version <= \"3.12\"", "xattr ; sys_platform == \"darwin\"", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "pycairo", "scipy"]
+interpolatable = ["munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\""]
 lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
-type1 = ["xattr"]
+type1 = ["xattr ; sys_platform == \"darwin\""]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=15.1.0)"]
-woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+unicode = ["unicodedata2 (>=15.1.0) ; python_version <= \"3.12\""]
+woff = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "humanfriendly"
@@ -582,7 +574,6 @@ description = "Human friendly output for text interfaces using Python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477"},
     {file = "humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc"},
@@ -599,7 +590,6 @@ description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
     {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
@@ -615,7 +605,6 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -632,14 +621,14 @@ files = [
     {file = "importlib_metadata-3.0.0-py2.py3-none-any.whl", hash = "sha256:fc3b3f9697703d3833d2803162d60cbe8b9f57b5da5e6496ac81e3cb82bd8d9c"},
     {file = "importlib_metadata-3.0.0.tar.gz", hash = "sha256:d582eb5c35b2f16c78e365e0f89e369f36af38fdaad0146208aa973c693ba247"},
 ]
-markers = {main = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\" or python_version < \"3.8\"", tests = "python_version < \"3.8\""}
+markers = {main = "python_version < \"3.8\" or python_version > \"3.9\"", tests = "python_version < \"3.8\""}
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
 docs = ["rst.linker", "sphinx"]
-testing = ["importlib-resources (>=1.3)", "packaging", "pep517"]
+testing = ["importlib-resources (>=1.3) ; python_version < \"3.9\"", "packaging", "pep517"]
 
 [[package]]
 name = "iniconfig"
@@ -648,7 +637,6 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
@@ -661,7 +649,6 @@ description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jinja2-3.1.5-py3-none-any.whl", hash = "sha256:aba0f4dc9ed8013c424088f68a5c226f7d6097ed89b246d7749c2ec4175c6adb"},
     {file = "jinja2-3.1.5.tar.gz", hash = "sha256:8fefff8dc3034e27bb80d67c671eb8a9bc424c0ef4c0826edbff304cceff43bb"},
@@ -693,7 +680,7 @@ description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
     {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
@@ -824,7 +811,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8a9c83f75223d5e48b0bc9cb1bf2776cf01563e00ade8775ffe13b0b6e1af3a6"},
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58370b1ffbd35407444d57057b57da5d6549d2d854fa30249771775c63b5fe17"},
@@ -949,7 +936,6 @@ description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a17a92de5231666cfbe003f0e4b9b3a7ae3afb1ec2845aadc2bacc93ff85febc"},
     {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:72b6be590cc35924b02c78ef34b467da4ba07e4e0f0454a2c5907f473fc50ce5"},
@@ -1095,7 +1081,7 @@ description = "Python plotting package"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "matplotlib-3.10.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2c5829a5a1dd5a71f0e31e6e8bb449bc0ee9dbfb05ad28fc0c6b55101b3a4be6"},
     {file = "matplotlib-3.10.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a2a43cbefe22d653ab34bb55d42384ed30f611bcbdea1f8d7f431011a2e1c62e"},
@@ -1231,7 +1217,7 @@ description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "numpy-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7079129b64cb78bdc8d611d1fd7e8002c0a2565da6a47c4df8062349fee90e3e"},
     {file = "numpy-2.2.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2ec6c689c61df613b783aeb21f945c4cbe6c51c28cb70aae8430577ab39f163e"},
@@ -1301,7 +1287,7 @@ files = [
     {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
     {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
 ]
-markers = {main = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", tests = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "python_version > \"3.9\""}
 
 [[package]]
 name = "pandas"
@@ -1346,7 +1332,7 @@ description = "Powerful data structures for data analysis, time series, and stat
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1948ddde24197a0f7add2bdc4ca83bf2b1ef84a1bc8ccffd95eda17fd836ecb5"},
     {file = "pandas-2.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:381175499d3802cde0eabbaf6324cce0c4f5d52ca6f8c377c29ad442f50f6348"},
@@ -1434,7 +1420,6 @@ description = "A Python package for describing statistical models and for buildi
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "patsy-1.0.1-py2.py3-none-any.whl", hash = "sha256:751fb38f9e97e62312e921a1954b81e1bb2bcda4f5eeabaf94db251ee791509c"},
     {file = "patsy-1.0.1.tar.gz", hash = "sha256:e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4"},
@@ -1474,7 +1459,7 @@ description = "Python wrapper for pgenlib's basic reader and writer."
 optional = false
 python-versions = ">=3.5"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "Pgenlib-0.92.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:56cc9715c3464f2d5559f0779cf671922c7651ed2aff3b851974968b86c167f7"},
     {file = "Pgenlib-0.92.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1875f05956d08217adbf8750598dc564741ad6bda1d8f724f45dda9b740ecf66"},
@@ -1496,7 +1481,7 @@ description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "pillow-11.1.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:e1abe69aca89514737465752b4bcaf8016de61b3be1397a8fc260ba33321b3a8"},
     {file = "pillow-11.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c640e5a06869c75994624551f45e5506e4256562ead981cce820d5ab39ae2192"},
@@ -1576,7 +1561,7 @@ docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage (>=7.4.2)", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout", "trove-classifiers (>=2024.10.12)"]
-typing = ["typing-extensions"]
+typing = ["typing-extensions ; python_version < \"3.10\""]
 xmp = ["defusedxml"]
 
 [[package]]
@@ -1586,7 +1571,6 @@ description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
     {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
@@ -1622,7 +1606,7 @@ description = "pyfaidx: efficient pythonic random access to fasta subsequences"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "pyfaidx-0.8.1.3-py3-none-any.whl", hash = "sha256:044abb9b7b03fef1cc393ae6831ece80df5c1a4dff295fa33808c6f63a81cdc4"},
     {file = "pyfaidx-0.8.1.3.tar.gz", hash = "sha256:feb599f8dfd192cf68bdb24969a5fd8f46772a7bd75d059e764bfd86b888e9b2"},
@@ -1639,14 +1623,13 @@ description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
     {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
 ]
 
 [package.extras]
-plugins = ["importlib-metadata"]
+plugins = ["importlib-metadata ; python_version < \"3.8\""]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -1672,7 +1655,7 @@ description = "pyparsing module - Classes and methods to define and execute pars
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "pyparsing-3.2.1-py3-none-any.whl", hash = "sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1"},
     {file = "pyparsing-3.2.1.tar.gz", hash = "sha256:61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a"},
@@ -1700,7 +1683,7 @@ description = "A python implementation of GNU readline."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "sys_platform == \"win32\" and python_version >= \"3.8\" and (python_version <= \"3.11\" or python_version >= \"3.12\")"
+markers = "sys_platform == \"win32\" and python_version >= \"3.8\""
 files = [
     {file = "pyreadline3-3.5.4-py3-none-any.whl", hash = "sha256:eaf8e6cc3c49bcccf145fc6067ba8643d1df34d604a1ec0eccbf7a18e6d3fae6"},
     {file = "pyreadline3-3.5.4.tar.gz", hash = "sha256:8d57d53039a1c75adba8e50dd3d992b28143480816187ea5efbd5c78e6c885b7"},
@@ -1769,7 +1752,7 @@ description = "Package for reading, manipulating, and writing genomic data"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "pysam-0.23.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9ee2ef5f3452bc84834163a881269efed56d1be5045865b5af74d010aee4b44c"},
     {file = "pysam-0.23.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a061857f8bd723f0f223ec986b0b955f28ddea3b330a767f3c39daaca5908e39"},
@@ -1811,7 +1794,6 @@ description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
     {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
@@ -1836,7 +1818,6 @@ description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
     {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
@@ -1856,7 +1837,6 @@ description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
@@ -1876,7 +1856,7 @@ files = [
     {file = "pytz-2025.1-py2.py3-none-any.whl", hash = "sha256:89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57"},
     {file = "pytz-2025.1.tar.gz", hash = "sha256:c2db42be2a2518b28e65f9207c4d05e6ff547d1efa4086469ef855e4ab70178e"},
 ]
-markers = {main = "python_version <= \"3.11\" or python_version >= \"3.12\"", docs = "python_version < \"3.9\""}
+markers = {docs = "python_version < \"3.9\""}
 
 [[package]]
 name = "requests"
@@ -1885,7 +1865,6 @@ description = "Python HTTP for Humans."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
     {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
@@ -1992,7 +1971,7 @@ description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "scikit_learn-1.6.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d056391530ccd1e501056160e3c9673b4da4805eb67eb2bdf4e983e1f9c9204e"},
     {file = "scikit_learn-1.6.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:0c8d036eb937dbb568c6242fa598d551d88fb4399c0344d95c001980ec1c7d36"},
@@ -2122,7 +2101,7 @@ description = "Fundamental algorithms for scientific computing in Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "scipy-1.15.1-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:c64ded12dcab08afff9e805a67ff4480f5e69993310e093434b10e85dc9d43e1"},
     {file = "scipy-1.15.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:5b190b935e7db569960b48840e5bef71dc513314cc4e79a1b7d14664f57fd4ff"},
@@ -2172,7 +2151,7 @@ numpy = ">=1.23.5,<2.5"
 [package.extras]
 dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
 doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.16.5)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.0.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
-test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "setuptools"
@@ -2185,11 +2164,11 @@ files = [
     {file = "setuptools-68.0.0-py3-none-any.whl", hash = "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f"},
     {file = "setuptools-68.0.0.tar.gz", hash = "sha256:baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235"},
 ]
-markers = {main = "python_version <= \"3.9\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "python_version <= \"3.9\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov ; platform_python_implementation != \"PyPy\"", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\"", "pytest-perf", "pytest-ruff ; sys_platform != \"cygwin\"", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -2199,7 +2178,6 @@ description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
@@ -2212,7 +2190,6 @@ description = "This package provides 29 stemmers for 28 languages generated from
 optional = false
 python-versions = "*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
     {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
@@ -2225,7 +2202,6 @@ description = "Python documentation generator"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "Sphinx-4.3.2-py3-none-any.whl", hash = "sha256:6a11ea5dd0bdb197f9c2abc2e0ce73e01340464feaece525e64036546d24c851"},
     {file = "Sphinx-4.3.2.tar.gz", hash = "sha256:0a8836751a68306b3fe97ecbe44db786f8479c3bf4b80e3a7f5c838657b4698c"},
@@ -2253,7 +2229,7 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
 lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.920)", "types-pkg-resources", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"]
+test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast ; python_version < \"3.8\""]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
@@ -2262,7 +2238,6 @@ description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx_autodoc_typehints-1.17.1-py3-none-any.whl", hash = "sha256:f16491cad05a13f4825ecdf9ee4ff02925d9a3b1cf103d4d02f2f81802cce653"},
     {file = "sphinx_autodoc_typehints-1.17.1.tar.gz", hash = "sha256:844d7237d3f6280b0416f5375d9556cfd84df1945356fcc34b82e8aaacab40f3"},
@@ -2273,7 +2248,7 @@ Sphinx = ">=4"
 
 [package.extras]
 testing = ["covdefaults (>=2)", "coverage (>=6)", "diff-cover (>=6.4)", "nptyping (>=1,<2)", "pytest (>=6)", "pytest-cov (>=3)", "sphobjinv (>=2)", "typing-extensions (>=3.5)"]
-type-comments = ["typed-ast (>=1.4.0)"]
+type-comments = ["typed-ast (>=1.4.0) ; python_version < \"3.8\""]
 
 [[package]]
 name = "sphinx-rtd-theme"
@@ -2282,7 +2257,6 @@ description = "Read the Docs theme for Sphinx"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl", hash = "sha256:46ddef89cc2416a81ecfbeaceab1881948c014b1b6e4450b815311a89fb977b0"},
     {file = "sphinx_rtd_theme-1.3.0.tar.gz", hash = "sha256:590b030c7abb9cf038ec053b95e5380b5c70d61591eb0b552063fbe7c41f0931"},
@@ -2303,7 +2277,6 @@ description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
     {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
@@ -2320,7 +2293,6 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
     {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
@@ -2337,7 +2309,6 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h
 optional = false
 python-versions = ">=3.6"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-htmlhelp-2.0.0.tar.gz", hash = "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"},
     {file = "sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl", hash = "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07"},
@@ -2354,7 +2325,6 @@ description = "Extension to include jQuery on newer Sphinx releases"
 optional = false
 python-versions = ">=2.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"},
     {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"},
@@ -2370,7 +2340,6 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -2386,7 +2355,6 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
     {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
@@ -2403,7 +2371,6 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
     {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
@@ -2508,7 +2475,7 @@ description = "Statistical computations and models for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "statsmodels-0.14.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7a62f1fc9086e4b7ee789a6f66b3c0fc82dd8de1edda1522d30901a0aa45e42b"},
     {file = "statsmodels-0.14.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:46ac7ddefac0c9b7b607eed1d47d11e26fe92a1bc1f4d9af48aeed4e21e87981"},
@@ -2551,7 +2518,7 @@ scipy = ">=1.8,<1.9.2 || >1.9.2"
 
 [package.extras]
 build = ["cython (>=3.0.10)"]
-develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"]
+develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty ; os_name == \"nt\"", "setuptools-scm[toml] (>=8.0,<9.0)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
@@ -2574,7 +2541,7 @@ description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version >= \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version >= \"3.9\""
 files = [
     {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
     {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
@@ -2587,7 +2554,7 @@ description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.7"
 groups = ["tests"]
-markers = "python_full_version <= \"3.11.0a6\""
+markers = "python_version < \"3.11\""
 files = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -2613,7 +2580,7 @@ description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 groups = ["main"]
-markers = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\""
+markers = "python_version > \"3.9\""
 files = [
     {file = "tzdata-2025.1-py2.py3-none-any.whl", hash = "sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639"},
     {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"},
@@ -2626,14 +2593,13 @@ description = "HTTP library with thread-safe connection pooling, file post, and
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
     {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
 secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -2649,11 +2615,11 @@ files = [
     {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
     {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
 ]
-markers = {main = "python_version > \"3.9\" and python_version <= \"3.11\" or python_version >= \"3.12\" or python_version < \"3.8\"", tests = "python_version < \"3.8\""}
+markers = {main = "python_version < \"3.8\" or python_version > \"3.9\"", tests = "python_version < \"3.8\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8 ; python_version < \"3.12\"", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\""]
 
 [metadata]
 lock-version = "2.1"

From 9d66e3b653f0b35c6afc9f102f9b4416ac147b79 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 16 Feb 2025 18:00:07 +0000
Subject: [PATCH 33/36] explain the new locking strategy in the docs

---
 doc/index.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/index.rst b/doc/index.rst
index e29fbfa1..22d69a34 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -173,7 +173,8 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 #. If you need to add a dependency or update the version of a dependency, you can use the :code:`poetry add` command.
 
     * You should specify a `version constraint <https://python-poetry.org/docs/master/dependency-specification#version-constraints>`_ when adding a dependency. Use the oldest version compatible with your code. For example, to specify a version of :code:`numpy>=1.23.0`, you can run :code:`poetry add 'numpy>=1.23.0'`.
-    * Afterward, double-check that the :code:`poetry.lock` file contains 1.23.0 in it. **All of our dependencies should be locked to their minimum versions at all times.** To downgrade to a specific version of a package in our lock file, you can `explicitly add the version <https://python-poetry.org/docs/dependency-specification/#projectdependencies-and-toolpoetrydependencies>`_ to the :code:`tool.poetry.dependencies` of our pyproject.toml file and then run :code:`poetry lock`.
+    * Afterward, double-check that the :code:`pyproject.toml` file has been changed appropriately. Our minimum version constraints should be listed in the `[project.dependencies]` section and the locked versions should appear in the `[tool.poetry.dependencies]` section. Ideally, the `[tool.poetry.dependencies]` section should contain at least the minimum supported version and the latest version of each dependency at all times.
+    * We try to keep the oldest version of python that is not `end-of-life <https://devguide.python.org/versions>`_ in our development environment (:code:`dev-env.yml` file), so that developers do not inadvertently make any changes that break support for that version of python. If, at any time, the minimum supported version of a dependency does not work with the version of python in our development environment, then you should also add the minimum working version of that dependency to our `[tool.poetry.dependencies]` section. See `this discussion thread <https://github.com/orgs/python-poetry/discussions/10142#discussioncomment-12050625>`_ for an example.
     * Only PyPI packages can be added to our pyproject.toml file. So if a dependency is only available on conda, then you can add it to our :code:`dev-env.yml` file instead. Please note that anyone who installs TRTools from PyPI will not be guaranteed to have your dependency installed, so you should design your code accordingly. 
     * Any changes to our dependencies must also added to our bioconda recipe at the time of publication. See `PUBLISHING.rst <https://github.com/gymrek-lab/TRTools/blob/master/PUBLISHING.rst>`_ for more details.
 

From 3203542b86e91a023b81d7dcdbe4013a9bf550e8 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 16 Feb 2025 10:07:42 -0800
Subject: [PATCH 34/36] docs: explain when to run poetry lock

---
 doc/index.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/index.rst b/doc/index.rst
index 22d69a34..c763b56c 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -173,8 +173,8 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 #. If you need to add a dependency or update the version of a dependency, you can use the :code:`poetry add` command.
 
     * You should specify a `version constraint <https://python-poetry.org/docs/master/dependency-specification#version-constraints>`_ when adding a dependency. Use the oldest version compatible with your code. For example, to specify a version of :code:`numpy>=1.23.0`, you can run :code:`poetry add 'numpy>=1.23.0'`.
-    * Afterward, double-check that the :code:`pyproject.toml` file has been changed appropriately. Our minimum version constraints should be listed in the `[project.dependencies]` section and the locked versions should appear in the `[tool.poetry.dependencies]` section. Ideally, the `[tool.poetry.dependencies]` section should contain at least the minimum supported version and the latest version of each dependency at all times.
-    * We try to keep the oldest version of python that is not `end-of-life <https://devguide.python.org/versions>`_ in our development environment (:code:`dev-env.yml` file), so that developers do not inadvertently make any changes that break support for that version of python. If, at any time, the minimum supported version of a dependency does not work with the version of python in our development environment, then you should also add the minimum working version of that dependency to our `[tool.poetry.dependencies]` section. See `this discussion thread <https://github.com/orgs/python-poetry/discussions/10142#discussioncomment-12050625>`_ for an example.
+    * Afterward, double-check that the :code:`pyproject.toml` file has been changed appropriately. Our minimum version constraints should be listed in the `[project.dependencies]` section and the locked versions should appear in the `[tool.poetry.dependencies]` section. Ideally, the `[tool.poetry.dependencies]` section should contain at least the minimum supported version and the latest version of each dependency at all times. After making any changes to the :code:`pyproject.toml` file, you must run the :code:`poetry lock` command to sync with the :code:`poetry.lock` file.
+    * We try to keep the oldest version of python that is not `end-of-life <https://devguide.python.org/versions>`_ in our development environment (:code:`dev-env.yml` file), so that developers do not inadvertently make any changes that break support for that version of python. If, at any time, the minimum supported version of a dependency does not work with the version of python in our development environment, then you should also add the minimum working version of that dependency to our locked versions in the `[tool.poetry.dependencies]` section. See `this discussion thread <https://github.com/orgs/python-poetry/discussions/10142#discussioncomment-12050625>`_ for an example.
     * Only PyPI packages can be added to our pyproject.toml file. So if a dependency is only available on conda, then you can add it to our :code:`dev-env.yml` file instead. Please note that anyone who installs TRTools from PyPI will not be guaranteed to have your dependency installed, so you should design your code accordingly. 
     * Any changes to our dependencies must also added to our bioconda recipe at the time of publication. See `PUBLISHING.rst <https://github.com/gymrek-lab/TRTools/blob/master/PUBLISHING.rst>`_ for more details.
 

From 2e8d57a136c270bb7f68c270614f8b1cfbae3664 Mon Sep 17 00:00:00 2001
From: Aarushi Sehgal <suzy20159@gmail.com>
Date: Tue, 18 Feb 2025 12:05:43 -0800
Subject: [PATCH 35/36] Update pyproject.toml

Co-authored-by: Arya Massarat <23412689+aryarm@users.noreply.github.com>
---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5a491df5..4fd35105 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,7 +52,6 @@ numpy = [
 ]
 pandas = [
     { version = "1.2.0" , markers = "python_version <= '3.9'" },
-    { version = "1.2.0" , markers = "python_version == '3.9'" },
     { version = "2.2.3" , markers = "python_version > '3.9'" },
 ]
 pysam = [

From 8b251ecdc5bdc52b367acbcad89d8f751fa490d3 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 18 Feb 2025 20:11:33 +0000
Subject: [PATCH 36/36] relock after changes to pyproject

---
 poetry.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 459807d5..6f12bb6d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2624,4 +2624,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.7.1"
-content-hash = "fec6f4f800955ffccd984b806a5256998a0552acb6ea03e1d6404fe45d468b8f"
+content-hash = "d09883ff5b4e3f0b581c7f892790cf5079a8bd958e85e73f050efbd012a38477"