[Documentation]: Adding advanced tutorial and improvements to documentation

.github/workflows/docs-gh-pages.yml

@@ -1,40 +1,100 @@
-name: Build and Deploy Documentation
+name: Docs — Build & Preview
 
 on:
   push:
-    branches:
-      - main
+    branches: [ main ]            # regular prod deploy
+    paths:
+      - 'mkdocs.yml'
+      - 'docs/**'
+  pull_request:                    # preview only when docs are touched
+    branches: [ '**' ]
+    paths:
+      - 'mkdocs.yml'
+      - 'docs/**'
 
 jobs:
-  build-and-deploy-docs:
+  build:
     runs-on: ubuntu-latest
+    outputs:
+      short_sha: ${{ steps.sha.outputs.short }}
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0  # Fetch all history for .git-restore-mtime to work correctly
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
+        with: { fetch-depth: 0 }
 
-      - name: Install uv via GitHub Action
-        uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v6
 
-      - name: Install mesa-frames + docs dependencies
+      - name: Install mesa-frames + docs deps
         run: |
           uv pip install --system .
           uv pip install --group docs --system
 
-      - name: Build MkDocs site (general documentation)
-        run: mkdocs build --config-file mkdocs.yml --site-dir ./site
+      - name: Convert jupytext .py notebooks to .ipynb
+        run: |
+          set -euxo pipefail
+          # Convert any jupytext .py files to .ipynb without executing them.
+          # Enable nullglob so the pattern expands to empty when there are no matches
+          # and globstar so we recurse into subdirectories (e.g., user-guide/).
+          shopt -s nullglob globstar || true
+          files=(docs/general/**/*.py)
+          if [ ${#files[@]} -eq 0 ]; then
+            echo "No jupytext .py files found under docs/general"
+          else
+            for src in "${files[@]}"; do
+              [ -e "$src" ] || continue
+              dest="${src%.py}.ipynb"
+              echo "Converting $src -> $dest"
+              # jupytext will write the .ipynb alongside the source file
+              uv run jupytext --to notebook "$src"
+            done
+          fi
+
+      - name: Build MkDocs site
+        run: uv run mkdocs build --config-file mkdocs.yml --site-dir ./site
+
+      - name: Build Sphinx docs (API)
+        run: uv run sphinx-build -b html docs/api site/api
+
+      - name: Short SHA
+        id: sha
+        run: echo "short=$(git rev-parse --short HEAD)" >> "$GITHUB_OUTPUT"
+
+      - name: Upload site artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: site
+          path: site
 
-      - name: Build Sphinx docs (API documentation)
-        run: sphinx-build -b html docs/api site/api
+  deploy-main:
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with: { name: site, path: site }
+      - name: Deploy to GitHub Pages (main)
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
+          publish_dir: ./site
+          force_orphan: true
 
-      - name: Deploy to GitHub Pages
+  deploy-preview:
+    needs: build
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with: { name: site, path: site }
+      - name: Deploy preview under subfolder
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
           publish_dir: ./site
-          force_orphan: true
+          destination_dir: preview/${{ github.head_ref || github.ref_name }}/${{ needs.build.outputs.short_sha }}
+          keep_files: true        # keep previous previews
+          # DO NOT set force_orphan here
+      - name: Print preview URL
+        run: |
+          echo "Preview: https://${{ github.repository_owner }}.github.io/$(basename ${{ github.repository }})/preview/${{ github.head_ref || github.ref_name }}/${{ needs.build.outputs.short_sha }}/"

.github/workflows/publish.yml

@@ -17,43 +17,78 @@ jobs:
       with:
         fetch-depth: 0
         token: ${{ secrets.VERSION_PUSH_TOKEN }}
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v3
     - name: Set release version
       run: |
         # Get the tag from the GitHub release
         TAG=${GITHUB_REF#refs/tags/}
         # Remove 'v' prefix if present
         VERSION=${TAG#v}
-        hatch version $VERSION
+        uvx hatch version $VERSION
     - name: Build package
-      run: hatch build
+      run: uvx hatch build
     - name: Run tests
-      run: hatch run test:pytest
+      run: uvx hatch run test:pytest
     - name: Publish package to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
     - name: Verify PyPI Release
       run: |
         # Verify PyPI release
         PACKAGE_NAME="mesa_frames"
-        CURRENT_VERSION=$(hatch version)
-        pip install $PACKAGE_NAME==$CURRENT_VERSION
+        CURRENT_VERSION=$(uvx hatch version)
+        uv pip install --system $PACKAGE_NAME==$CURRENT_VERSION
         python -c "import mesa_frames; print(mesa_frames.__version__)"
     - name: Update GitHub Release
       uses: softprops/action-gh-release@v1
       if: startsWith(github.ref, 'refs/tags/')
       with:
         files: |
           dist/*
+    - name: Generate changelog from release notes
+      id: notes
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const fs = require('fs');
+          const tag = (context.payload.release && context.payload.release.tag_name)
+            ? context.payload.release.tag_name
+            : (process.env.GITHUB_REF || '').replace('refs/tags/', '');
+
+          const body = (context.payload.release && context.payload.release.body) ? context.payload.release.body : '';
+          if (!body || body.trim().length === 0) {
+            core.setFailed('Release body is empty. Ensure the GitHub Release is created with auto-generated notes configured by .github/release.yml or supply a body.');
+          }
+
+          fs.writeFileSync('RELEASE_BODY.md', body, 'utf8');
+          core.setOutput('tag', tag);
+    - name: Prepend notes to CHANGELOG.md
+      env:
+        TAG: ${{ steps.notes.outputs.tag }}
+      run: |
+        VERSION_NO_V=${TAG#v}
+        DATE_UTC=$(date -u +%Y-%m-%d)
+        echo "## Version ${VERSION_NO_V} — ${DATE_UTC}" > RELEASE_HEADER.md
+        echo "" >> RELEASE_HEADER.md
+        if [ -f CHANGELOG.md ]; then
+          cat RELEASE_HEADER.md RELEASE_BODY.md CHANGELOG.md > CHANGELOG.new
+        else
+          cat RELEASE_HEADER.md RELEASE_BODY.md > CHANGELOG.new
+        fi
+        mv CHANGELOG.new CHANGELOG.md
+    - name: Commit and push CHANGELOG update
+      env:
+        TAG: ${{ steps.notes.outputs.tag }}
+      run: |
+        git config user.name github-actions
+        git config user.email [email protected]
+        git add CHANGELOG.md
+        # Avoid CI cycles
+        git commit -m "Changelog: add notes for ${TAG} [skip ci]" || echo "No changelog changes to commit"
+        git push origin main || true
     - name: Create or recreate version branch
       run: |
-        CURRENT_VERSION=$(hatch version)
+        CURRENT_VERSION=$(uvx hatch version)
         BRANCH_NAME="v$CURRENT_VERSION"
 
         git config user.name github-actions
@@ -72,15 +107,15 @@ jobs:
     - name: Update to Next Version
       run: |
         # Bump to next development version
-        hatch version patch
-        hatch version dev
+        uvx hatch version patch
+        uvx hatch version dev
 
         # Get the new version
-        NEW_VERSION=$(hatch version)
+        NEW_VERSION=$(uvx hatch version)
 
         # Commit and push the version bump
         git config user.name github-actions
         git config user.email [email protected]
-        git add mesa_frames/__init__.py
+        git add mesa_frames/__init__.py CHANGELOG.md
         git commit -m "Bump version to $NEW_VERSION [skip ci]"
-        git push origin main
+        git push origin main

.gitignore

@@ -154,3 +154,12 @@ cython_debug/
 *.code-workspace
 llm_rules.md
 .python-version
+docs/site
+docs/api/_build
+docs/general/tutorials/data_csv
+docs/general/tutorials/data_parquet
+docs/general/tutorials/*.ipynb
+docs/api/reference/**/mesa_frames.*.rst
+examples/**/results
+benchmarks/**/results
+benchmarks/**/plots

CHANGELOG.md

@@ -0,0 +1,40 @@
+## Version 0.1.0-alpha — 2024-08-28
+
+## What's Changed
+
+* Refactoring mesa.Agent, mesa.AgentSet, mesa.Model -> AgentSetDF, AgentsDF, ModelDF by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/8>
+* setup: Migrate from setup.py to pyproject.toml by @rht in <https://github.com/adamamer20/mesa-frames/pull/13>
+* ci: Add pre-commit configuration by @rht in <https://github.com/adamamer20/mesa-frames/pull/14>
+* Merge requirements.txt into pyproject.toml by @rht in <https://github.com/adamamer20/mesa-frames/pull/15>
+* ci: Add GA for tests by @rht in <https://github.com/adamamer20/mesa-frames/pull/17>
+* Changes to AgentSetDF and AgentsDF before time.py -> CopyMixin by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/16>
+* benchmark: Split Polars agent into native and concise by @rht in <https://github.com/adamamer20/mesa-frames/pull/23>
+* benchmark: Split pandas agent into native and concise by @rht in <https://github.com/adamamer20/mesa-frames/pull/24>
+* speed up mesa readme_plot script by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/26>
+* Adding DataFrameMixin for improved reusability/encapsulation by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/27>
+* Abstract SpaceDF by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/29>
+* Adding Abstract DiscreteSpaceDF by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/30>
+* Adding abstract GridDF by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/32>
+* Additional methods and fixes to DataFrameMixin by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/43>
+* Concrete GridPandas by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/44>
+* [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in <https://github.com/adamamer20/mesa-frames/pull/55>
+* Fixes and Tests for PolarsMixin by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/56>
+* Adding Comparison and Indexing methods to DataFrameMixin by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/58>
+* Concrete GridPolars by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/60>
+* Sugarscape Instantaneous Growback (Pandas-with-loop implementation) by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/63>
+* Adding pydoclint and properly format docstring by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/69>
+* Docs with material-from-mkdocs by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/70>
+* Enforce correct numpy docstring formatting with ruff.pydocstyle by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/74>
+* API Documentation with Sphinx by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/75>
+* Move images from docs to docs/general to make it available for mkdocs by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/79>
+* Adding user guide by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/81>
+* Adding SugarScape IG (polars with loops) by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/71>
+* Automatic publishing on PyPI on new release by @adamamer20 in <https://github.com/adamamer20/mesa-frames/pull/77>
+
+## New Contributors
+
+* @adamamer20 made their first contribution in <https://github.com/adamamer20/mesa-frames/pull/8>
+* @rht made their first contribution in <https://github.com/adamamer20/mesa-frames/pull/13>
+* @pre-commit-ci made their first contribution in <https://github.com/adamamer20/mesa-frames/pull/55>
+
+**Full Changelog**: <https://github.com/adamamer20/mesa-frames/commits/v0.1.0-alpha>