PyScaffold migration: error-free installation on Windows/Linux for Py 3.8+ and .md instead of .rst

.coveragerc

@@ -0,0 +1,28 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = science_jubilee
+# omit = bad_file.py
+
+[paths]
+source =
+    src/
+    */site-packages/
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -12,7 +12,7 @@ body:
     label: Steps to reproduce this bug
     description: Include a simple code snippet that demonstrates the problem if relevant, along with any errors produced. If this isn't possible, then simply describe the issue as best you can!
     value: "### Steps:
-    
+
     1.
 
     2.
@@ -23,12 +23,12 @@ body:
 
 
     ### Snippet:
-    
+
 
     ```python
 
 
-      // Paste your code here :) 
+      // Paste your code here :)
 
 
     ```"

.github/pull_request_template.md

@@ -15,4 +15,3 @@ Resolves #[Add issue number here]
 -->
 
 - [ ] [Inline documentation] is included / updated
-

.github/workflows/ci.yml

@@ -0,0 +1,126 @@
+# GitHub Actions configuration **EXAMPLE**,
+# MODIFY IT ACCORDING TO YOUR NEEDS!
+# Reference: https://docs.github.com/en/actions
+
+name: tests
+
+on:
+  push:
+    # Avoid using all the resources/limits available by checking only
+    # relevant branches and tags. Other branches can be checked via PRs.
+    branches: [main]
+    tags: ['v[0-9]*', '[0-9]+.[0-9]+*']  # Match tags that resemble a version
+  pull_request:  # Run in every PR
+  workflow_dispatch:  # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: '0 0 1,16 * *'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      wheel-distribution: ${{ steps.wheel-distribution.outputs.path }}
+    steps:
+      - uses: actions/checkout@v3
+        with: {fetch-depth: 0}  # deep clone for setuptools-scm
+      - uses: actions/setup-python@v4
+        id: setup-python
+        with: {python-version: "3.11"}
+      - name: Run static analysis and format checkers
+        run: pipx run pre-commit run --all-files --show-diff-on-failure
+      - name: Build package distribution files
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox -e clean,build
+      - name: Record the path of wheel distribution
+        id: wheel-distribution
+        run: echo "path=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
+      - name: Store the distribution files for use in other stages
+        # `tests` and `publish` will use the same pre-built distributions,
+        # so we make sure to release the exact same package that was tested
+        uses: actions/upload-artifact@v3
+        with:
+          name: python-distribution-files
+          path: dist/
+          retention-days: 1
+
+  test:
+    needs: prepare
+    strategy:
+      matrix:
+        python:
+        - "3.8"  # oldest Python supported by PSF
+        - "3.11"  # newest Python that is stable
+        platform:
+        - ubuntu-latest
+        # - macos-latest
+        # - windows-latest
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Retrieve pre-built distribution files
+        uses: actions/download-artifact@v3
+        with: {name: python-distribution-files, path: dist/}
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox --installpkg '${{ needs.prepare.outputs.wheel-distribution }}'
+          -- -rFEx --durations 10 --color yes  # pytest args
+      # - name: Generate coverage report
+      #   run: pipx run coverage lcov -o coverage.lcov
+      # - name: Upload partial coverage report
+      #   uses: coverallsapp/github-action@master
+      #   with:
+      #     path-to-lcov: coverage.lcov
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     flag-name: ${{ matrix.platform }} - py${{ matrix.python }}
+      #     parallel: true
+
+  # finalize: # TODO: revisit coverage
+  #   needs: test
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Finalize coverage report
+  #       uses: coverallsapp/github-action@master
+  #       with:
+  #         github-token: ${{ secrets.GITHUB_TOKEN }}
+  #         parallel-finished: true
+
+  publish:
+    # needs: finalize # TODO: revisit coverage
+    needs: test
+    if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with: {python-version: "3.11"}
+      - name: Retrieve pre-built distribution files
+        uses: actions/download-artifact@v3
+        with: {name: python-distribution-files, path: dist/}
+      - name: Publish Package
+        env:
+          # TODO: Set your PYPI_TOKEN as a secret using GitHub UI
+          # - https://pypi.org/help/#apitoken
+          # - https://docs.github.com/en/actions/security-guides/encrypted-secrets
+          TWINE_REPOSITORY: pypi
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: pipx run tox -e publish

.gitignore

@@ -1,7 +1,55 @@
-.venv/
-.ipynb_checkpoints
-__pycache__/
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
 .DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
 *.egg-info
-integration-tests/*
-docs/build/*
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+.python-version
+tool_library/OT2_pipette/designs/OT_post_base.3mf

.isort.cfg

@@ -0,0 +1,3 @@
+[settings]
+profile = black
+known_first_party = science_jubilee

.pre-commit-config.yaml

@@ -0,0 +1,69 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+    args: ['--maxkb=5000']
+    # exclude: ^(docs/_static/robot-loop.gif)$
+  - id: check-ast
+  # - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+## If you want to automatically "modernize" your Python code:
+# - repo: https://github.com/asottile/pyupgrade
+#   rev: v3.7.0
+#   hooks:
+#   - id: pyupgrade
+#     args: ['--py37-plus']
+
+## If you want to avoid flake8 errors due to unused vars or imports:
+# - repo: https://github.com/PyCQA/autoflake
+#   rev: v2.1.1
+#   hooks:
+#   - id: autoflake
+#     args: [
+#       --in-place,
+#       --remove-all-unused-imports,
+#       --remove-unused-variables,
+#     ]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 24.4.2
+  hooks:
+  - id: black
+    language_version: python3
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+# - repo: https://github.com/PyCQA/flake8
+#   rev: 7.0.0
+#   hooks:
+#   - id: flake8
+#   ## You can add flake8 plugins via `additional_dependencies`:
+#   #  additional_dependencies: [flake8-bugbear]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell