Merge pull request #12 from monarch-initiative/formatted-code

Format code using `tox`

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/monarch-initiative/monarch-project-template/",
-  "commit": "0fce395fe859618d3feb3ac9ebd2f8b94d743b2b",
+  "commit": "e5f758215fa58b92093e71b632f804569fde9dba",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/deploy-docs.yml

@@ -10,7 +10,7 @@ jobs:
       uses: actions/checkout@v3.0.2
       with:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-    
+
     - name: Set up Python 3.
       uses: actions/setup-python@v3
       with:
@@ -21,8 +21,8 @@ jobs:
 
     - name: Install dependencies.
       run: |
-        poetry install -E docs
-        
+        poetry install --with docs
+
     - name: Build documentation.
       run: |
         echo ${{ secrets.GH_TOKEN }} >> src/curate_gpt/token.txt
@@ -31,8 +31,8 @@ jobs:
         cd docs/
         poetry run sphinx-apidoc -o . ../src/curate_gpt/ --ext-autodoc -f
         poetry run sphinx-build -b html . _build
-        cp -r _build/html/* ../gh-pages/
-    
+        cp -r _build/* ../gh-pages/
+
     - name: Deploy documentation.
       if: ${{ github.event_name == 'push' }}
       uses: JamesIves/github-pages-deploy-action@v4.4.1

.github/workflows/pypi-publish.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   release:
     types: [created]
-    
+
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
@@ -20,7 +20,7 @@ jobs:
 
       - name: Install Poetry
         run: pip install poetry poetry-dynamic-versioning
-    
+
       - name: Install dependencies
         run: poetry install --no-interaction
 
@@ -32,5 +32,3 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-
-

.github/workflows/qc.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: [ "3.8", "3.11" ]
 
     steps:
       - uses: actions/checkout@v3.0.2
@@ -26,8 +26,11 @@ jobs:
       - name: Install dependencies
         run: poetry install --no-interaction
 
+      - name: Check common spelling errors
+        run: poetry run tox -e codespell
+
       - name: Check code quality with flake8
-        run: poetry run tox -e flake8
+        run: poetry run tox -e lint
 
       - name: Test with pytest and generate coverage file
         run: poetry run tox -e py

.gitignore

@@ -135,4 +135,8 @@ dmypy.json
 .pyre/
 
 # User defined
-stagedb/*
+!tests/input/dbs/go-nucleus-chroma/*.sqlite3
+stagedb/*
+*.rej
+tests/input/dbs/go-nucleus-chroma/*/*.bin
+tests/output/*

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-toml
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
+  hooks:
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli

CONTRIBUTING.md

@@ -29,4 +29,24 @@ Note: All the development must be done on a branch on your fork.
 
 ALSO NOTE: github.com lets you create a pull request from the main branch, automating the steps above.
 
-> A code review (which happens with both the contributor and the reviewer present) is required for contributing.
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.
+
+### How to write a great issue
+
+Please review GitHub's overview article,
+["Tracking Your Work with Issues"][about-issues].
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request
+
+Please review GitHub's article, ["About Pull Requests"][about-pulls],
+and make your changes on a [new branch][about-branches].
+
+[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
+[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
+[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
+[issues]: https://github.com/monarch-initiative/curate-gpt/issues/
+[pulls]: https://github.com/monarch-initiative/curate-gpt/pulls/
+
+We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)

docs/conf.py

@@ -1,5 +1,4 @@
-# Configuration file for the Sphinx documentation builder.
-#
+"""Configuration file for the Sphinx documentation builder."""
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
@@ -47,13 +46,13 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.