User cloning

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e1ad02ce3592def18a437f1884177507
+tags: 645f666f9bcd5a90fca523b33c5a78b7

.github/workflows/publish-docs.yml

@@ -0,0 +1,53 @@
+on: [push, pull_request]
+
+name: "Documentation Status"
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-publish:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+
+    timeout-minutes: 10
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+
+    - name: Session information
+      run: |
+        python --version
+
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs.prefer-active-python: true
+
+    - name: 🔩 list Poetry settings
+      run: poetry config --list
+
+    - name: 🔩 Install with Poetry
+      run: poetry install --all-extras --with docs
+
+    - name: Build documentation
+      run: |
+        cd docs
+        poetry run bash autogen_docs.sh
+        poetry run make html
+
+    - name: Deploy to GitHub pages 🚀
+      # Deploy only when master changes
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+      uses: JamesIves/[email protected]
+      with:
+        clean: false
+        branch: gh-pages
+        folder: docs/_build/html

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -2,32 +2,32 @@ name: Tests & Coverage
 on:
   push:
     branches:
-      - '**'
-      - '!master'   # excludes master branch
-      - '!testpypi' # excludes testpypi branch
+      - "**"
+      - "!master" # excludes master branch
+      - "!testpypi" # excludes testpypi branch
     tags-ignore:
-      - '*.*'
+      - "*.*"
   pull_request: {}
 jobs:
   build:
     name: Test (${{ matrix.python-version }}, ${{ matrix.os }})
     strategy:
       fail-fast: false
       matrix:
-        os: [ 'macos-latest', 'windows-latest' ]
+        os: ["macos-latest", "windows-latest"]
         python-version: ["3.12", "3.11", "3.10", "3.9", "3.8"]
         include:
-        - os: ubuntu-latest
-          python-version: "3.8"
-          codecov: true
-        - os: ubuntu-latest
-          python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.10"
-        - os: ubuntu-latest
-          python-version: "3.11"
-        - os: ubuntu-latest
-          python-version: "3.12"
+          - os: ubuntu-latest
+            python-version: "3.8"
+            codecov: true
+          - os: ubuntu-latest
+            python-version: "3.9"
+          - os: ubuntu-latest
+            python-version: "3.10"
+          - os: ubuntu-latest
+            python-version: "3.11"
+          - os: ubuntu-latest
+            python-version: "3.12"
     defaults:
       run:
         shell: bash
@@ -50,7 +50,7 @@ jobs:
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-           virtualenvs.prefer-active-python: true
+          virtualenvs.prefer-active-python: true
 
       - name: 🔩 list Poetry settings
         run: poetry config --list
@@ -61,9 +61,36 @@ jobs:
       - name: 🔎 poetry run python run_test.py
         run: poetry run python run_test.py
 
+      # Enforce pre-commit hooks ===========================
+      - name: Get changed files
+        if: (matrix.codecov)
+        id: changed-files
+        uses: tj-actions/changed-files@v45
+        with:
+          since_last_remote_commit: true
+
+      - uses: actions/cache@v4
+        if: (matrix.codecov)
+        id: cache-precommit
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-precommit-hooks-v2-${{ hashFiles('**/.pre-commit-config.yaml') }}
+
+      - name: Installing pre-commit hooks (cached)
+        if: (matrix.codecov) && (steps.cache-precommit.outputs.cache-hit != 'true')
+        run: poetry run pre-commit install --install-hooks
+
+      - name: Run style checking via pre-commit
+        if: (matrix.codecov && steps.changed-files.outputs.all_changed_files)
+        run: |
+          echo "Changed files:"
+          echo "${{ steps.changed-files.outputs.all_changed_files }}" | tr ' ' '\n'
+          poetry run pre-commit run --files ${{ steps.changed-files.outputs.all_changed_files }}
+
+      # ======================================================
       - name: 🔼 Upload coverage to Codecov
         if: (matrix.codecov)
-        uses: codecov/codecov-action@v1.0.13
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -36,6 +36,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+.venv/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -65,6 +66,8 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/markdown_notebooks
+docs/modules/
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -2,20 +2,57 @@ repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
   hooks:
+  # Prevent committing to the master branch
   - id: no-commit-to-branch
     args: [--branch, master]
+  # Format yaml files
   - id: check-yaml
+  # Fix end-of-file issues
   - id: end-of-file-fixer
+  # Fix trailing whitespace
   - id: trailing-whitespace
+  # Prevent debug statements
   - id: debug-statements
   - id: fix-encoding-pragma
   - id: mixed-line-ending
+# Code formatting
 - repo: https://github.com/ambv/black
   rev: 24.2.0
   hooks:
   - id: black
+# Further linting (e.g. module imported but not used)
 - repo: https://github.com/PyCQA/flake8
   rev: 7.0.0
   hooks:
   - id: flake8
-exclude: scripts/|docs/|tests/
+# Verify that requirements.txt is up to date with poetry dependencies every commit
+- repo: https://github.com/python-poetry/poetry
+  rev: 1.8.3
+  hooks:
+    - id: poetry-export
+      args: [
+        "-f",
+        "requirements.txt",
+        "--output",
+        "requirements.txt",
+        "--with",
+        "dev",
+        "--with",
+        "test",
+        "--with",
+        "docs",
+        "-E",
+        "clipboard download express gel",
+      ]
+      files: 'requirements.txt'
+# Remove metadata from jupyter notebooks. This will always be triggered when you commit a change in a notebook.
+# Simply do `git add` and commit again.
+- repo: local
+  hooks:
+    - id: nbstripout
+      name: nbstripout with keep-output
+      entry: |
+        python -m nbstripout --keep-output $@
+      language: system
+      files: \.ipynb$
+      exclude: tests/

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.flake8",
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,15 @@
+{
+    "files.exclude": {
+        "**/.git": true,
+        "**/.svn": true,
+        "**/.hg": true,
+        "**/CVS": true,
+        "**/.DS_Store": true,
+        "**/*.pyc": true,
+        "**/__pycache__": true
+    },
+    // Set flake8 path
+    "flake8.path": [".venv/bin/flake8"],
+    "black-formatter.path": [".venv/bin/black"],
+    "python.defaultInterpreterPath": ".venv/bin/python",
+}