docs: drop support for py 3.8 and update to poetry 2 in our CI

.devcontainer.json

@@ -4,34 +4,41 @@
 	"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 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": {
 		"vscode": {
 			"extensions": [
 				"ms-python.python",
-				"ms-vscode.live-server"
+				"ms-vscode.live-server",
+				"GitHub.vscode-github-actions"
 			],
 			"settings": {
+				"python.analysis.typeCheckingMode": "off",
 				"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": "/opt/conda/envs/trtools",
+				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/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
 			}
 		}
 	}

.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

.github/workflows/tests.yml

@@ -20,11 +20,12 @@ 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: "3.8", os: "ubuntu-latest", session: "size" }
-          - { python: "3.8", os: "ubuntu-latest", session: "coverage" }
+          # - { 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" }
+          - { python: "3.9", os: "ubuntu-latest", session: "coverage" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -38,7 +39,9 @@ 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
           miniforge-version: latest
           use-mamba: true

.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

dev-env.yml

@@ -3,13 +3,14 @@ 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-plugin-export==1.8.0
+  - conda-forge::poetry==2.0.1 # 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
-    - poetry-conda==0.1.1
+    - poetry-conda==0.1.4
+    - poetry-plugin-shell==1.0.1

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
 ^^^^^^^^^^
@@ -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 --no-update`. The :code:`--no-update` is important because otherwise, poetry will try to update other dependencies in the lock file.
+    * 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.
 

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",
@@ -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
         )