Merge pull request #73 from bobleesj/scikit-package

Apply `scikit-package` v0.1.0 to `cifkit` - autoamtic docformatter, prettier, codespell

.codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  status:
+    project: # more options at https://docs.codecov.com/docs/commit-status
+      default:
+        target: auto # use the coverage from the base commit, fail if coverage is lower
+        threshold: 0% # allow the coverage to drop by
+
+comment:
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
+  hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,20 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; indide is chemical name
+indide
+
+;; used as a date
+nd
+
+;; chemical
+te

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -6,15 +6,55 @@ labels: "release"
 assignees: ""
 ---
 
-### Release checklist for GitHub contributors
+### PyPI/GitHub rc-release preparation checklist:
 
 - [ ] All PRs/issues attached to the release are merged.
 - [ ] All the badges on the README are passing.
+- [ ] License information is verified as correct. If you are unsure, please
+      comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including
-      API references (check no modules are missing), tutorials, and other human
-      written text is up-to-date with any changes in the code.
-- [ ] Installation instructions in the README, documentation and on the website
-      are updated and tested
-- [ ] Successfully run any tutorial examples or do functional testing in some
-      other way.
-- [ ] Grammar and writing quality have been checked (no typos).
+      API references (check no modules are missing), tutorials, and other
+      human-written text is up-to-date with any changes in the code.
+- [ ] Installation instructions in the README, documentation, and the website
+      (e.g., diffpy.org) are updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the
+      latest Python version.
+- [ ] Grammar and writing quality are checked (no typos).
+- [ ] Install `pip install build twine`, run `python -m build` and
+      `twine check dist/*` to ensure that the package can be built and is
+      correctly formatted for PyPI release.
+
+Please mention @bobleesj here when you are ready for PyPI/GitHub release.
+Include any additional comments necessary, such as version information and
+details about the pre-release here:
+
+### PyPI/GitHub full-release preparation checklist:
+
+- [ ] Create a new conda environment and install the rc from PyPI
+      (`pip install <package-name>==??`)
+- [ ] License information on PyPI is correct.
+- [ ] Docs are deployed successfully to `https://www.diffpy.org/<package-name>`.
+- [ ] Successfully run all tests, tutorial examples or do functional testing.
+
+Please let @bobleesj know that all checks are done and the package is ready for
+full release.
+
+### conda-forge release preparation checklist:
+
+<!-- After @bobleesj releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+
+- [ ] Ensure that the full release has appeared on PyPI successfully.
+- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to
+      `meta.yaml` in the feedstock.
+- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have
+      questions.
+- [ ] Tag @bobleesj for conda-forge release.
+
+### Post-release checklist
+
+<!-- Before closing this issue, please complete the following: -->
+
+- [ ] Run tutorial examples and conduct functional testing using the
+      installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, tutorials, API references, and websites) is
+      deployed without broken links or missing figures.

.github/workflows/build-wheel-release-upload.yml

@@ -1,18 +1,18 @@
-name: Release (GitHub/PyPI)
+name: Release (GitHub/PyPI) and Deploy Docs
 
 on:
   workflow_dispatch:
   push:
     tags:
-      - '*'
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
   release:
-    permissions:
-      contents: write
-    uses: bobleesj/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: cifkit
+      c_extension: false
+      github_admin_username: bobleesj
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/check-news-item.yml

@@ -2,9 +2,11 @@ name: Check for News
 
 on:
   pull_request_target:
+    branches:
+      - main
 
 jobs:
-  build:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@{{ VERSION/v0 }}
+  check-news-item:
+    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: cifkit

.github/workflows/tests-on-pr.yml

@@ -12,29 +12,27 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Create virtual environment and install dependencies
-      run: |
-        python -m venv venv
-        source venv/bin/activate
-        pip install .
-
-    - name: Test with pytest and generate coverage report
-      run: |
-        source venv/bin/activate
-        pip install pytest pytest-cov
-        python -m pytest -m "not pyvista" --cov=./ --cov-report=xml
-
-    - name: Upload coverage reports to Codecov
-      uses: codecov/[email protected]
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Create virtual environment and install dependencies
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+          pip install .
+      - name: Test with pytest and generate coverage report
+        run: |
+          source venv/bin/activate
+          pip install pytest pytest-cov
+          python -m pytest -m "not pyvista" --cov=./ --cov-report=xml
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -2,21 +2,13 @@
 __pycache__/
 *.py[cod]
 *$py.class
-.DS_Store
-
-
-# Test file
-test.ipynb
 
 # C extensions
 *.so
 
-nodemon.json
-debug/
-.ruff_cache
-
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -28,12 +20,14 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
+venv/
 *.egg-info/
 .installed.cfg
 *.egg
+bin/
+temp/
+tags/
+errors.err
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -44,89 +38,55 @@ share/python-wheels/
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+MANIFEST
 
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*.cover
-*.py,cover
+*,cover
 .hypothesis/
-.pytest_cache/
-cover/
 
 # Translations
 *.mo
 *.pot
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
 # Django stuff:
 *.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
 
 # PyBuilder
 target/
 
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
+# Editor files
+# mac
+.DS_Store
+*~
 
-# pytype static type analyzer
-.pytype/
+# vim
+*.swp
+*.swo
 
-# Cython debug symbols
-cython_debug/
+# pycharm
+.idea/
 
-# VS Code settings
+# VSCode
 .vscode/
+
+# Ipython Notebook
+.ipynb_checkpoints

.isort.cfg

@@ -0,0 +1,5 @@
+[settings]
+# Keep import statement below line_length character limit
+line_length = 90
+multi_line_output = 3
+include_trailing_comma = True