v.2.0.2 to main

.github/workflows/build_and_test.yml

@@ -4,15 +4,45 @@ on:
   push:
     branches:
       - '**'
+    paths-ignore:
+      - 'python/docs/**'
+      - 'doc_resources/**'
+      - 'Doxyfile'
+      - '**/*.md'
+      - '**/*.html'
+      - '.github/workflows/build_docs.yml'
   pull_request:
+    paths-ignore:
+      - 'python/docs/**'
+      - 'doc_resources/**'
+      - 'Doxyfile'
+      - '**/*.md'
+      - '**/*.html'
+      - '.github/workflows/build_docs.yml'
   workflow_call:
+    inputs:
+      minimal:
+        description: 'Build only the ubuntu-latest / python-3.11 wheel; skip C++ tests, Windows, macOS, and wheel tests.'
+        required: false
+        type: boolean
+        default: false
+      ref:
+        description: 'Branch, tag, or SHA to check out before building (defaults to the calling workflow''s ref).'
+        required: false
+        type: string
+        default: ''
   workflow_dispatch:
     inputs:
       full_matrix:
         description: 'Run full OS and Python matrix'
         required: false
         type: boolean
         default: false
+      minimal:
+        description: 'Build only the ubuntu-latest / python-3.11 wheel; skip C++ tests, Windows, macOS, and wheel tests.'
+        required: false
+        type: boolean
+        default: false
 
 concurrency:
   group: build-${{ github.ref }}
@@ -34,16 +64,20 @@ jobs:
           # Mac available to the maintainer). Intel macOS support is paused
           # pending a reproducer or an upstream fix. Re-add "macos-15-intel"
           # below when ready to revisit.
-          if [[ "${{ github.ref }}" == "refs/heads/main" || "${{ github.ref }}" == "refs/heads/develop" || "${{ github.ref }}" == refs/tags/* || "${{ inputs.full_matrix }}" == "true" || "${{ github.event.pull_request.base.ref }}" == "develop" || "${{ github.event.pull_request.base.ref }}" == "main" ]]; then
+          if [[ "${{ inputs.minimal }}" == "true" ]]; then
+            echo 'os=["ubuntu-latest"]' >> $GITHUB_OUTPUT
+            echo 'python_versions=["3.11"]' >> $GITHUB_OUTPUT
+          elif [[ "${{ github.ref }}" == "refs/heads/main" || "${{ github.ref }}" == "refs/heads/develop" || "${{ github.ref }}" == refs/tags/* || "${{ inputs.full_matrix }}" == "true" || "${{ github.event.pull_request.base.ref }}" == "develop" || "${{ github.event.pull_request.base.ref }}" == "main" ]]; then
             echo 'os=["ubuntu-latest","macos-14"]' >> $GITHUB_OUTPUT
-            echo 'python_versions=["3.9","3.10","3.11","3.12","3.13"]' >> $GITHUB_OUTPUT
+            echo 'python_versions=["3.9","3.10","3.11","3.12","3.13","3.14"]' >> $GITHUB_OUTPUT
           else
             echo 'os=["ubuntu-latest","macos-14"]' >> $GITHUB_OUTPUT
             echo 'python_versions=["3.11"]' >> $GITHUB_OUTPUT
           fi
 
   test_cpp_unix:
     name: C++ tests on ${{ matrix.os }}
+    if: ${{ inputs.minimal != true }}
     needs: [set_matrix]
     runs-on: ${{ matrix.os }}
     strategy:
@@ -107,6 +141,7 @@ jobs:
 
   test_cpp_windows:
     name: C++ tests on Windows
+    if: ${{ inputs.minimal != true }}
     runs-on: windows-latest
     env:
       CONDA_PKGS_DIRS: ${{ github.workspace }}\conda_pkgs
@@ -157,7 +192,7 @@ jobs:
         run: ctest --output-on-failure --parallel
 
   build_macos_ubuntu_wheels:
-    name: ${{ matrix.os }} Python-${{ matrix.python-version }} wheels 
+    name: ${{ matrix.os }} Python-${{ matrix.python-version }} wheels
     needs: [set_matrix]
     runs-on: ${{ matrix.os }}
     strategy:
@@ -168,6 +203,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
+        with:
+          ref: ${{ inputs.ref || github.ref }}
       - name: Cache cibuildwheel + pip + Homebrew
         uses: actions/cache@v5
         with:
@@ -176,7 +213,8 @@ jobs:
             ~/.cache/cibuildwheel
             ~/Library/Caches/Homebrew
             /tmp/boost_1_90_0.tar.bz2
-            /tmp/eigenpy-3.11.0.tar.gz
+            /tmp/eigen-3.4.0.tar.gz
+            /tmp/eigenpy-3.12.0.tar.gz
           key: ${{ runner.os }}-cibw-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'python/pyproject.toml', 'CMakeLists.txt', 'core/CMakeLists.txt', '.github/workflows/build_and_test.yml') }}
           restore-keys: |
             ${{ runner.os }}-cibw-${{ matrix.python-version }}-
@@ -193,7 +231,7 @@ jobs:
         run: |
           SW_VERS=$(sw_vers -productVersion | cut -d. -f1)
           echo "MACOSX_DEPLOYMENT_TARGET=${SW_VERS}.0" >> $GITHUB_ENV
-      - uses: pypa/cibuildwheel@v2.23
+      - uses: pypa/cibuildwheel@v3.4.1
         env:
           # Build cp39 through cp313 for both Linux (manylinux) and macOS.
           # Boost.Python and eigenpy are rebuilt per target Python in BEFORE_BUILD
@@ -207,9 +245,13 @@ jobs:
           # against the manylinux2014 system python3 produces a libboost_python39 that
           # all five wheels would then bundle, breaking import on cp310/311/312/313.
           CIBW_BEFORE_ALL_LINUX: >
-            yum install -y wget gmp-devel mpfr-devel libmpc-devel eigen3-devel libtool &&
+            yum install -y wget gmp-devel mpfr-devel libmpc-devel libtool &&
             cd /tmp &&
-            { [ -f eigenpy-3.11.0.tar.gz ] || wget -q https://github.com/stack-of-tasks/eigenpy/releases/download/v3.11.0/eigenpy-3.11.0.tar.gz ; }
+            { [ -f eigen-3.4.0.tar.gz ] || wget -q https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz ; } &&
+            rm -rf eigen-3.4.0 && tar xzf eigen-3.4.0.tar.gz &&
+            cmake -S eigen-3.4.0 -B eigen-3.4.0/bld -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release &&
+            cmake --install eigen-3.4.0/bld &&
+            { [ -f eigenpy-3.12.0.tar.gz ] || wget -q https://github.com/stack-of-tasks/eigenpy/releases/download/v3.12.0/eigenpy-3.12.0.tar.gz ; }
           # On macOS, Homebrew's boost-python3 / eigenpy bottles track the current
           # Homebrew default Python (now 3.14), so a cp313 wheel that bundles them
           # imports a libboost_python314.dylib into a 3.13 interpreter and segfaults.
@@ -218,8 +260,8 @@ jobs:
           CIBW_BEFORE_ALL_MACOS: >
             brew install gmp mpfr libmpc eigen@3 &&
             cd /tmp &&
-            { [ -f eigenpy-3.11.0.tar.gz ] || curl -fsSL -o eigenpy-3.11.0.tar.gz https://github.com/stack-of-tasks/eigenpy/releases/download/v3.11.0/eigenpy-3.11.0.tar.gz ; }
-          
+            { [ -f eigenpy-3.12.0.tar.gz ] || curl -fsSL -o eigenpy-3.12.0.tar.gz https://github.com/stack-of-tasks/eigenpy/releases/download/v3.12.0/eigenpy-3.12.0.tar.gz ; }
+
           # Build Boost and eigenpy fresh against the active per-Python interpreter
           # so each wheel bundles a matching libboost_python3X.
           CIBW_BEFORE_BUILD_LINUX: >
@@ -236,8 +278,8 @@ jobs:
             printf 'using python : %s : %s : %s : %s ;\n' "$PY_VER" "$(which python)" "$PY_INC" "$PY_LIB" > user-config.jam &&
             ./b2 install -j$(nproc) --user-config=user-config.jam python=$PY_VER &&
             cd /tmp &&
-            rm -rf eigenpy-3.11.0 && tar zxf eigenpy-3.11.0.tar.gz &&
-            cd eigenpy-3.11.0 && mkdir -p bld && cd bld &&
+            rm -rf eigenpy-3.12.0 && tar zxf eigenpy-3.12.0.tar.gz &&
+            cd eigenpy-3.12.0 && mkdir -p bld && cd bld &&
             cmake .. -DCMAKE_PREFIX_PATH=/tmp/deps-py -DCMAKE_INSTALL_PREFIX=/tmp/deps-py -DCMAKE_BUILD_TYPE=Release -DCMAKE_INTERPROCEDURAL_OPTIMIZATION=ON -DPython3_EXECUTABLE=$(which python) -DPython3_NumPy_INCLUDE_DIR=$(python -c "import numpy; print(numpy.get_include())") -DBUILD_TESTING=OFF -DCMAKE_INSTALL_DO_STRIP=ON &&
             make -j2 install &&
             find /tmp/deps-py -name '*.so*' -type f | while read f; do
@@ -260,8 +302,8 @@ jobs:
             printf 'using python : %s : %s : %s : %s ;\n' "$PY_VER" "$(which python)" "$PY_INC" "$PY_LIB" > user-config.jam &&
             ./b2 install -j$(sysctl -n hw.ncpu) --user-config=user-config.jam python=$PY_VER hardcode-dll-paths=true dll-path=/tmp/deps-py/lib &&
             cd /tmp &&
-            rm -rf eigenpy-3.11.0 && tar zxf eigenpy-3.11.0.tar.gz &&
-            cd eigenpy-3.11.0 && mkdir -p bld && cd bld &&
+            rm -rf eigenpy-3.12.0 && tar zxf eigenpy-3.12.0.tar.gz &&
+            cd eigenpy-3.12.0 && mkdir -p bld && cd bld &&
             cmake .. -DCMAKE_PREFIX_PATH="/tmp/deps-py;/opt/homebrew" -DCMAKE_INSTALL_PREFIX=/tmp/deps-py -DPython3_EXECUTABLE=$(which python) -DPython3_NumPy_INCLUDE_DIR=$(python -c "import numpy; print(numpy.get_include())") -DBUILD_TESTING=OFF &&
             make -j2 install
           CIBW_BEFORE_BUILD: "pip install scikit-build-core numpy"
@@ -275,14 +317,15 @@ jobs:
           if-no-files-found: error
 
   build_windows_wheels:
-    name: Windows Python-${{ matrix.python-version }} wheels 
+    name: Windows Python-${{ matrix.python-version }} wheels
+    if: ${{ inputs.minimal != true }}
     runs-on: windows-latest
     env:
       CONDA_PKGS_DIRS: ${{ github.workspace }}\conda_pkgs
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
       - uses: actions/checkout@v5
         with:
@@ -338,6 +381,7 @@ jobs:
 
   test_wheels_linux_macos:
     name: Test wheels on ${{ matrix.os }} / py${{ matrix.python-version }}
+    if: ${{ inputs.minimal != true }}
     needs: [set_matrix, build_macos_ubuntu_wheels]
     runs-on: ${{ matrix.os }}
     strategy:
@@ -371,12 +415,13 @@ jobs:
 
   test_wheels_windows:
     name: Test wheel on windows-${{ matrix.python-version }}
+    if: ${{ inputs.minimal != true }}
     needs: [build_windows_wheels]
     runs-on: windows-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
       - uses: actions/checkout@v5
@@ -403,4 +448,4 @@ jobs:
           $py = "C:\Miniconda\envs\b2-windows\python.exe"
           & $py -m pip install --no-index --find-links dist/ bertini2
           & $py -m pip install pytest
-          & $py -m pytest python/test/ -v
+          & $py -m pytest python/test/ -v

.github/workflows/build_docs.yml

@@ -0,0 +1,159 @@
+name: Build and deploy documentation 📝
+
+on:
+  workflow_call:
+    # When called from publish.yml, the caller's build_and_test job has
+    # already produced the wheel artifact this workflow needs. The internal
+    # build_and_test job below is skipped in that case.
+    inputs:
+      deploy:
+        description: 'Deploy to GitHub Pages after building'
+        required: false
+        type: boolean
+        default: true
+  workflow_dispatch:
+    inputs:
+      deploy:
+        description: 'Deploy to GitHub Pages after building'
+        required: false
+        type: boolean
+        default: true
+      ref:
+        description: 'Branch, tag, or SHA to build docs for (defaults to the dispatched ref).'
+        required: false
+        type: string
+        default: ''
+
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_and_test:
+    name: Build wheel (for docs)
+    # Only run when triggered manually. workflow_call invocations assume the
+    # caller already ran build_and_test in the same workflow run, so the
+    # wheel artifact is already available.
+    if: github.event_name == 'workflow_dispatch'
+    uses: ./.github/workflows/build_and_test.yml
+    with:
+      # Docs only need the ubuntu-latest / python-3.11 wheel; skip the full
+      # OS/Python matrix and the wheel/C++ test jobs.
+      minimal: true
+      ref: ${{ inputs.ref }}
+
+  build_docs:
+    name: Build docs
+    needs: [build_and_test]
+    # `build_and_test` is skipped when invoked via workflow_call; treat that
+    # as success so build_docs runs in both modes.
+    if: |
+      always() &&
+      (needs.build_and_test.result == 'success' || needs.build_and_test.result == 'skipped')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+          # gitpython (used by python/docs/source/conf.py to derive version)
+          # needs the full history; the default depth=1 leaves it unable to
+          # resolve HEAD's commit object on some refs.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Compute build metadata
+        id: meta
+        run: |
+          SHA=$(git rev-parse HEAD)
+          SHORT=$(git rev-parse --short HEAD)
+          DATE=$(date -u +'%Y-%m-%d %H:%M UTC')
+          echo "sha=$SHA"          >> "$GITHUB_OUTPUT"
+          echo "short=$SHORT"      >> "$GITHUB_OUTPUT"
+          echo "date=$DATE"        >> "$GITHUB_OUTPUT"
+          echo "Build metadata: $SHORT ($SHA) at $DATE"
+
+      - name: Install system dependencies (Doxygen)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y doxygen graphviz
+
+      - name: Fetch doxygen-awesome-css
+        run: |
+          curl -sSL https://github.com/jothepro/doxygen-awesome-css/archive/refs/tags/v2.3.4.tar.gz | tar -xz
+          mv doxygen-awesome-css-2.3.4 doxygen-awesome-css
+
+      - name: Build C++ docs (Doxygen)
+        env:
+          PROJECT_NUMBER: "${{ steps.meta.outputs.short }} (${{ steps.meta.outputs.date }})"
+        run: |
+          mkdir -p build/docs/cpp site
+          # Append PROJECT_NUMBER override via stdin; Doxygen reads stdin
+          # config when invoked with `-` and merges with the file.
+          (cat Doxyfile; echo "PROJECT_NUMBER = $PROJECT_NUMBER") | doxygen -
+          mv build/docs/cpp site/cpp
+
+      - name: Install Python deps for Sphinx
+        # The bertini2 wheel bundles the eigenpy C++ libraries it links
+        # against; no Python `eigenpy` install is required to import bertini
+        # for sphinx autodoc.
+        run: |
+          python -m pip install --upgrade pip
+          pip install \
+            sphinx sphinx-rtd-theme sphinxcontrib-bibtex gitpython \
+            scikit-build-core build numpy
+
+      - name: Download built wheel
+        uses: actions/download-artifact@v5
+        with:
+          name: wheels-ubuntu-latest-3.11
+          path: dist/
+
+      - name: Install bertini from built wheel
+        run: pip install --no-index --find-links dist/ bertini2
+
+      - name: Build Python docs (Sphinx)
+        working-directory: python/docs
+        env:
+          BERTINI_GIT_SHA: ${{ steps.meta.outputs.sha }}
+          BERTINI_BUILD_DATE: ${{ steps.meta.outputs.date }}
+        run: |
+          sphinx-build -b html -W --keep-going source ../../site/python
+
+      - name: Add landing page
+        env:
+          COMMIT_SHA: ${{ steps.meta.outputs.sha }}
+          COMMIT_SHORT: ${{ steps.meta.outputs.short }}
+          BUILD_DATE: ${{ steps.meta.outputs.date }}
+        run: |
+          sed \
+            -e "s|__COMMIT_SHA__|${COMMIT_SHA}|g" \
+            -e "s|__COMMIT_SHORT__|${COMMIT_SHORT}|g" \
+            -e "s|__BUILD_DATE__|${BUILD_DATE}|g" \
+            doc_resources/landing/index.html > site/index.html
+          cp doc_resources/landing/style.css site/style.css
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy_docs:
+    name: Deploy to GitHub Pages
+    needs:
+      - build_docs
+    if: needs.build_docs.result == 'success' && inputs.deploy
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/github-gitlab-sync.yml

@@ -3,7 +3,7 @@ on:
   push
 jobs:
   sync:
-    if: github.repository == 'bertiniteam/b2'
+    if: github.repository == 'bertiniteam/b2' #only on official 
     runs-on: ubuntu-latest
     steps:
     - name: Sync to GitLab
@@ -19,4 +19,4 @@ jobs:
         gitlab_pat: ${{ secrets.GITLAB_PAT }}
         # Whether to force push to GitLab. Defaults to false.
 
-        #force_push: # optional, default is false
+        force_push: true # optional, default is false