feat: fix Binding DB assay html encoding, polars_canonical_smiles_wo_salt, ci and mkdocs (#2)

Author: kiyoon

.github/workflows/deploy-mkdocs-on-latest.yml

@@ -0,0 +1,14 @@
+name: Deploy MkDocs on latest commit
+
+on:
+  push:
+    branches:
+      - main
+      - master
+
+jobs:
+  deploy-mkdocs:
+    uses: deargen/workflows/.github/workflows/deploy-mkdocs.yml@master
+    with:
+      deploy-type: latest
+      requirements-file: deps/lock/x86_64-manylinux_2_28/requirements_docs.txt

README.md

@@ -1,5 +1,6 @@
 # bio-data-to-db: make Uniprot PostgreSQL database
 
+
 [![image](https://img.shields.io/pypi/v/bio-data-to-db.svg)](https://pypi.python.org/pypi/bio-data-to-db)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/bio-data-to-db)](https://pypi.python.org/pypi/bio-data-to-db)
 [![image](https://img.shields.io/pypi/l/bio-data-to-db.svg)](https://pypi.python.org/pypi/bio-data-to-db)
@@ -19,6 +20,8 @@ Written in Rust, thus equipped with extremely fast parsers. Packaged for python,
 
 So far, there is only one function implemented: **convert uniprot data to postgresql**. This package focuses more on parsing the data and inserting it into the database, rather than curating the data.
 
+[📚 Documentation](https://deargen.github.io/bio-data-to-db/)
+
 ## 🛠️ Installation
 
 ```bash
@@ -29,6 +32,8 @@ pip install bio-data-to-db
 
 You can use the command line interface or the python API.
 
+### Uniprot
+
 ```bash
 # It will create a db 'uniprot' and a table named 'public.uniprot_info' in the database.
 # If you want another name, you can optionally pass it as the last argument.
@@ -61,6 +66,49 @@ create_accession_to_pk_id_table("postgresql://user:password@localhost:5432/unipr
 keywords_tsv_to_postgresql("~/Downloads/keywords_all_2024_06_26.tsv", "postgresql://user:password@localhost:5432/uniprot")
 ```
 
+### BindingDB
+
+```bash
+# Decode HTML entities and strip the strings in the `assay` table (column: description and assay_name).
+# Currently, only assay table is supported.
+bio-data-to-db bindingdb fix-table assay 'mysql://username:password@localhost/bind'
+```
+
+```python
+from bio_data_to_db.bindingdb.fix_tables import fix_assay_table
+
+fix_assay_table("mysql://username:password@localhost/bind")
+```
+
+### PostgreSQL Helpers, SMILES, Polars utils and more
+
+```python
+Some useful functions to work with PostgreSQL.
+
+```python
+from bio_data_to_db.utils.postgresql import (
+    create_db_if_not_exists,
+    create_schema_if_not_exists,
+    set_column_as_primary_key,
+    make_columns_unique,
+    make_large_columns_unique,
+    split_column_str_to_list,
+    polars_write_database,
+)
+
+from bio_data_to_db.utils.smiles import (
+    canonical_smiles_wo_salt,
+    polars_canonical_smiles_wo_salt,
+)
+
+from bio_data_to_db.utils.polars import (
+    w_pbar,
+)
+```
+
+You can find the usage in the [📚 documentation](https://deargen.github.io/bio-data-to-db/).
+
+
 ## 👨‍💻️ Maintenance Notes
 
 ### Install from source
@@ -72,10 +120,14 @@ bash scripts/install.sh
 uv pip install -r deps/requirements_dev.in
 ```
 
-### Compile requirements (generate lockfiles)
+### Generate lockfiles
 
 Use GitHub Actions: `apply-pip-compile.yml`. Manually launch the workflow and it will make a commit with the updated lockfiles.
 
+### Publish a new version to PyPI
+
+Use GitHub Actions: `deploy.yml`. Manually launch the workflow and it will compile on all architectures and publish the new version to PyPI.
+
 ### About sqlx
 
 Sqlx offline mode should be configured so you can compile the code without a database present.

deps/lock/aarch64-apple-darwin/.requirements.in.sha256

@@ -1 +1 @@
-816025c3ff73af3261b082ee7e0c71954aa6b20922e17344cfb2f29636733488  requirements.in
+2f65dd8deb2842edfead23a6aafb4f4f0b9e9e98982e39216069787d16327901  requirements.in

deps/lock/aarch64-apple-darwin/.requirements_docs.in.sha256

@@ -0,0 +1 @@
+f0f530946f38443ec95d76ac402dc3e3045fe8f7c26220e46b575aa56649503d  requirements_docs.in

deps/lock/aarch64-apple-darwin/requirements.txt

@@ -2,16 +2,23 @@
 #    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements.txt --python-platform aarch64-apple-darwin --python-version 3.10
 click==8.1.7
     # via typer
+connectorx==0.3.3
+    # via -r requirements.in
 markdown-it-py==3.0.0
     # via rich
 mdurl==0.1.2
     # via markdown-it-py
-numpy==2.0.0
+mysqlclient==2.2.4
+    # via -r requirements.in
+numpy==1.26.4
     # via
     #   pandas
     #   pyarrow
+    #   rdkit
 pandas==2.2.2
     # via -r requirements.in
+pillow==10.4.0
+    # via rdkit
 polars==1.2.0
     # via -r requirements.in
 psycopg==3.2.1
@@ -26,6 +33,8 @@ python-dateutil==2.9.0.post0
     # via pandas
 pytz==2024.1
     # via pandas
+rdkit==2024.3.3
+    # via -r requirements.in
 rich==13.7.1
     # via typer
 shellingham==1.5.4
@@ -34,6 +43,8 @@ six==1.16.0
     # via python-dateutil
 sqlalchemy==2.0.31
     # via -r requirements.in
+tqdm==4.66.4
+    # via -r requirements.in
 typer==0.12.3
     # via -r requirements.in
 typing-extensions==4.12.2

deps/lock/aarch64-apple-darwin/requirements_dev.txt

@@ -6,6 +6,8 @@ charset-normalizer==3.3.2
     # via requests
 click==8.1.7
     # via typer
+connectorx==0.3.3
+    # via -r requirements.in
 exceptiongroup==1.2.2
     # via pytest
 filelock==3.15.4
@@ -24,13 +26,16 @@ maturin==1.7.0
     # via -r requirements_dev.in
 mdurl==0.1.2
     # via markdown-it-py
+mysqlclient==2.2.4
+    # via -r requirements.in
 networkx==3.3
     # via -r requirements_dev.in
-numpy==2.0.0
+numpy==1.26.4
     # via
     #   -r requirements_dev.in
     #   pandas
     #   pyarrow
+    #   rdkit
     #   scipy
     #   trimesh
 packaging==24.1
@@ -39,6 +44,8 @@ packaging==24.1
     #   pytest
 pandas==2.2.2
     # via -r requirements.in
+pillow==10.4.0
+    # via rdkit
 pluggy==1.5.0
     # via pytest
 polars==1.2.0
@@ -59,6 +66,8 @@ pytz==2024.1
     # via pandas
 pyyaml==6.0.1
     # via huggingface-hub
+rdkit==2024.3.3
+    # via -r requirements.in
 requests==2.32.3
     # via huggingface-hub
 rich==13.7.1
@@ -82,7 +91,9 @@ tomli==2.0.1
     #   maturin
     #   pytest
 tqdm==4.66.4
-    # via huggingface-hub
+    # via
+    #   -r requirements.in
+    #   huggingface-hub
 trimesh==4.4.3
     # via -r requirements_dev.in
 typer==0.12.3

deps/lock/aarch64-apple-darwin/requirements_docs.txt

@@ -0,0 +1,156 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements_docs.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements_docs.txt --python-platform aarch64-apple-darwin --python-version 3.10
+babel==2.15.0
+    # via mkdocs-material
+backports-strenum==1.3.1
+    # via griffe
+cairocffi==1.7.1
+    # via cairosvg
+cairosvg==2.7.1
+    # via mkdocs-material
+certifi==2024.7.4
+    # via requests
+cffi==1.16.0
+    # via cairocffi
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via
+    #   mkdocs
+    #   mkdocstrings
+colorama==0.4.6
+    # via
+    #   griffe
+    #   mkdocs-material
+cssselect2==0.7.0
+    # via cairosvg
+defusedxml==0.7.1
+    # via cairosvg
+ghp-import==2.1.0
+    # via mkdocs
+griffe==0.48.0
+    # via mkdocstrings-python
+idna==3.7
+    # via requests
+importlib-metadata==8.2.0
+    # via mike
+importlib-resources==6.4.0
+    # via mike
+jinja2==3.1.4
+    # via
+    #   mike
+    #   mkdocs
+    #   mkdocs-material
+    #   mkdocstrings
+markdown==3.6
+    # via
+    #   mkdocs
+    #   mkdocs-autorefs
+    #   mkdocs-material
+    #   mkdocstrings
+    #   pymdown-extensions
+markupsafe==2.1.5
+    # via
+    #   jinja2
+    #   mkdocs
+    #   mkdocs-autorefs
+    #   mkdocstrings
+mergedeep==1.3.4
+    # via
+    #   mkdocs
+    #   mkdocs-get-deps
+mike==2.1.2
+    # via -r requirements_docs.in
+mkdocs==1.6.0
+    # via
+    #   -r requirements_docs.in
+    #   mike
+    #   mkdocs-autorefs
+    #   mkdocs-coverage
+    #   mkdocs-gen-files
+    #   mkdocs-literate-nav
+    #   mkdocs-material
+    #   mkdocstrings
+mkdocs-autorefs==1.0.1
+    # via
+    #   -r requirements_docs.in
+    #   mkdocstrings
+mkdocs-coverage==1.1.0
+    # via -r requirements_docs.in
+mkdocs-gen-files==0.5.0
+    # via -r requirements_docs.in
+mkdocs-get-deps==0.2.0
+    # via mkdocs
+mkdocs-literate-nav==0.6.1
+    # via -r requirements_docs.in
+mkdocs-material==9.5.30
+    # via -r requirements_docs.in
+mkdocs-material-extensions==1.3.1
+    # via
+    #   -r requirements_docs.in
+    #   mkdocs-material
+mkdocstrings==0.25.2
+    # via
+    #   -r requirements_docs.in
+    #   mkdocstrings-python
+mkdocstrings-python==1.10.7
+    # via -r requirements_docs.in
+packaging==24.1
+    # via mkdocs
+paginate==0.5.6
+    # via mkdocs-material
+pathspec==0.12.1
+    # via mkdocs
+pillow==10.4.0
+    # via
+    #   cairosvg
+    #   mkdocs-material
+platformdirs==4.2.2
+    # via
+    #   mkdocs-get-deps
+    #   mkdocstrings
+pycparser==2.22
+    # via cffi
+pygments==2.18.0
+    # via mkdocs-material
+pymdown-extensions==10.9
+    # via
+    #   mkdocs-material
+    #   mkdocstrings
+pyparsing==3.1.2
+    # via mike
+python-dateutil==2.9.0.post0
+    # via ghp-import
+pyyaml==6.0.1
+    # via
+    #   mike
+    #   mkdocs
+    #   mkdocs-get-deps
+    #   pymdown-extensions
+    #   pyyaml-env-tag
+pyyaml-env-tag==0.1
+    # via
+    #   mike
+    #   mkdocs
+regex==2024.7.24
+    # via mkdocs-material
+requests==2.32.3
+    # via mkdocs-material
+six==1.16.0
+    # via python-dateutil
+tinycss2==1.3.0
+    # via
+    #   cairosvg
+    #   cssselect2
+urllib3==2.2.2
+    # via requests
+verspec==0.1.0
+    # via mike
+watchdog==4.0.1
+    # via mkdocs
+webencodings==0.5.1
+    # via
+    #   cssselect2
+    #   tinycss2
+zipp==3.19.2
+    # via importlib-metadata

deps/lock/x86_64-apple-darwin/.requirements.in.sha256

@@ -1 +1 @@
-816025c3ff73af3261b082ee7e0c71954aa6b20922e17344cfb2f29636733488  requirements.in
+2f65dd8deb2842edfead23a6aafb4f4f0b9e9e98982e39216069787d16327901  requirements.in

deps/lock/x86_64-apple-darwin/.requirements_docs.in.sha256

@@ -0,0 +1 @@
+f0f530946f38443ec95d76ac402dc3e3045fe8f7c26220e46b575aa56649503d  requirements_docs.in