FY24 documentation improvements (part 1)

.github/workflows/build_docs.yml

@@ -6,6 +6,11 @@ on:
     branches: [main]
   pull_request:
     branches: [main]
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed # This is important for the ghpage preview to clean up after itself
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -24,26 +29,39 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.8"
+      - run: sudo apt install graphviz
       - run: pip install -r requirements.txt
+      - name: Install PyTorch
+        run: pip install torch==2.2.2
       - run: |
           cmake \
             -DCMAKE_BUILD_TYPE=Release \
-            -DCMAKE_UNITY_BUILD=OFF \
-            -DNEML2_UNIT=ON \
-            -DNEML2_REGRESSION=OFF \
-            -DNEML2_VERIFICATION=OFF \
-            -DNEML2_BENCHMARK=OFF \
-            -DNEML2_PROFILING=OFF \
-            -DNEML2_PYBIND=OFF \
+            -DCMAKE_UNITY_BUILD=ON \
+            -DNEML2_TESTS=OFF \
+            -DNEML2_RUNNER=OFF \
+            -DNEML2_PYBIND=ON \
             -DNEML2_DOC=ON \
             .
-      - run: make doc-syntax -j 2
-      - run: make doc-html
-      - run: cat doc/doxygen.log
+      - run: cmake --build . --target html -j 2 --
+      - run: cat doc/doxygen.html.log
+      - run: cat doc/doxygen.python.log
+      - name: Preview GitHub Pages
+        if: ${{ github.event_name == 'pull_request' }}
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: doc/build/html
       - name: Deploy to GitHub Pages
         if: ${{ github.event_name == 'push' }}
         uses: JamesIves/[email protected]
         with:
           branch: gh-pages
           folder: doc/build/html
-          single-commit: true
+          clean-exclude: pr-preview/
+          force: false
+      - name: Scold users about missing docs
+        if: ${{ github.event_name == 'pull_request'}}
+        uses: thollander/actions-comment-pull-request@v2
+        with:
+            filePath: doc/syntax_error.log
+            comment_tag: doc_scold
+            GITHUB_TOKEN: ${{ secrets.PR_ACTION }}

.github/workflows/python.yml

@@ -30,7 +30,7 @@ jobs:
       - uses: psf/black@stable
         with:
           options: "--check -v"
-          src: "python/neml2 tests/python"
+          src: "python/neml2 python/tests"
   build-test:
     name: Build and test Python bindings
     needs: black
@@ -53,32 +53,19 @@ jobs:
         run: pip install -r requirements.txt
       - name: Install PyTorch
         run: pip install torch==2.2.2
-      - run: |
-          cmake \
-            -DCMAKE_BUILD_TYPE=Debug \
-            -DCMAKE_UNITY_BUILD=ON \
-            -DNEML2_UNIT=OFF \
-            -DNEML2_REGRESSION=OFF \
-            -DNEML2_VERIFICATION=OFF \
-            -DNEML2_BENCHMARK=OFF \
-            -DNEML2_PROFILING=OFF \
-            -DNEML2_PYBIND=ON \
-            -DNEML2_DOC=OFF \
-            -B build \
-            .
-      - run: cd build && make -j 2
-      - run: PYTHONPATH=build/python pytest --junitxml=build/python/pytest.xml tests
+      - run: pip install -v .
+      - run: pytest --junitxml=pytest.xml python/tests
       - name: Publish Test Results
         uses: EnricoMi/publish-unit-test-result-action@v2
         if: matrix.os == 'ubuntu-latest'
         with:
-          files: build/python/pytest.xml
+          files: pytest.xml
           check_name: Python Binding Test Results (${{ matrix.os }})
       - name: Publish Test Results
         uses: EnricoMi/publish-unit-test-result-action/composite@v2
         if: matrix.os == 'macos-12'
         with:
-          files: build/python/pytest.xml
+          files: pytest.xml
           check_name: Python Binding Test Results (${{ matrix.os }})
   sdist:
     name: Build source distribution
@@ -93,45 +80,8 @@ jobs:
         with:
           name: package-sdist
           path: dist/*.tar.gz
-  wheels:
-    needs: build-test
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-12]
-    runs-on: ${{ matrix.os }}
-    steps:
-      - name: Backup docker
-        if: matrix.os == 'ubuntu-latest'
-        run: sudo mv /var/lib/docker ${GITHUB_WORKSPACE}/docker
-      - name: Maximize build space
-        if: matrix.os == 'ubuntu-latest'
-        uses: easimon/maximize-build-space@master
-        with:
-          remove-dotnet: "true"
-          remove-android: "true"
-          remove-haskell: "true"
-          remove-codeql: "true"
-          build-mount-path: "/var/lib/docker/"
-      - name: Remount docker
-        if: matrix.os == 'ubuntu-latest'
-        run: sudo sh -c "mv ${GITHUB_WORKSPACE}/docker/* /var/lib/docker"
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-      - uses: jwlawson/actions-setup-cmake@v2
-        with:
-          cmake-version: "3.23"
-      - name: Build wheels
-        uses: pypa/[email protected]
-      - name: Upload wheels
-        if: github.event_name == 'release' && github.event.action == 'published'
-        uses: actions/upload-artifact@v4
-        with:
-          name: package-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl
   PyPI:
-    needs: [sdist, wheels]
+    needs: sdist
     environment: pypi
     permissions:
       id-token: write
@@ -140,7 +90,7 @@ jobs:
     steps:
       - uses: actions/download-artifact@v4
         with:
-          pattern: package-*
+          pattern: package-sdist
           path: dist
           merge-multiple: true
       - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -68,20 +68,17 @@ jobs:
           cmake \
             -DCMAKE_BUILD_TYPE=${{ matrix.btype }} \
             -DCMAKE_UNITY_BUILD=${{ matrix.unity }} \
-            -DNEML2_UNIT=ON \
-            -DNEML2_REGRESSION=ON \
-            -DNEML2_VERIFICATION=ON \
-            -DNEML2_BENCHMARK=OFF \
-            -DNEML2_PROFILING=OFF \
+            -DNEML2_TESTS=ON \
+            -DNEML2_RUNNER=OFF \
             -DNEML2_PYBIND=OFF \
             -DNEML2_DOC=OFF \
             .
       - run: make -j 2
-      - run: cd tests && ./unit_tests -r junit > unit_tests.xml
+      - run: cd tests && ./unit/unit_tests -r junit > unit_tests.xml
         continue-on-error: true
-      - run: cd tests && ./regression_tests -r junit > regression_tests.xml
+      - run: cd tests && ./regression/regression_tests -r junit > regression_tests.xml
         continue-on-error: true
-      - run: cd tests && ./verification_tests -r junit > verification_tests.xml
+      - run: cd tests && ./verification/verification_tests -r junit > verification_tests.xml
         continue-on-error: true
       - name: Publish Test Results
         uses: EnricoMi/publish-unit-test-result-action@v2
@@ -117,11 +114,9 @@ jobs:
           cmake \
             -DCMAKE_BUILD_TYPE=${{ matrix.btype }} \
             -DCMAKE_UNITY_BUILD=${{ matrix.unity }} \
-            -DNEML2_UNIT=ON \
-            -DNEML2_REGRESSION=ON \
-            -DNEML2_VERIFICATION=ON \
-            -DNEML2_BENCHMARK=ON \
-            -DNEML2_PROFILING=ON \
+            -DNEML2_TESTS=ON \
+            -DNEML2_RUNNER=ON \
+            -DNEML2_RUNNER_AS_PROFILER=ON \
             -DNEML2_PYBIND=OFF \
             -DNEML2_DOC=OFF \
             .
@@ -147,11 +142,9 @@ jobs:
           cmake \
             -DCMAKE_BUILD_TYPE=Coverage \
             -DCMAKE_UNITY_BUILD=OFF \
-            -DNEML2_UNIT=ON \
-            -DNEML2_REGRESSION=ON \
-            -DNEML2_VERIFICATION=ON \
-            -DNEML2_BENCHMARK=OFF \
-            -DNEML2_PROFILING=OFF \
+            -DNEML2_TESTS=ON \
+            -DNEML2_RUNNER=OFF \
+            -DNEML2_PYBIND=OFF \
             -DNEML2_DOC=OFF \
             .
       - run: make -j 2
@@ -182,23 +175,23 @@ jobs:
           echo -e "\
             #include \"neml2/base/Registry.h\"\n\
             int main() {\n\
-              neml2::Registry::print(std::cout);\n\
               return 0;\n\
             }\
             " > main.cxx
       - run: cat main.cxx
       - name: Create a CMakeLists.txt file for testing purposes
         run: |
           echo -e "\
-            cmake_minimum_required(VERSION 3.5)
+            cmake_minimum_required(VERSION 3.23)
             project(FOO)\n\
             add_subdirectory(neml2)\n\
             add_executable(foo main.cxx)\n\
+            add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)\n\
             target_link_libraries(foo neml2)\n\
             " > CMakeLists.txt
       - run: cat CMakeLists.txt
       - name: Configure with CMake
-        run: cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF -DNEML2_DOC=OFF -B build .
+        run: cmake -DNEML2_TESTS=OFF -B build .
       - name: Compile
         run: cd build && make -j 2
       - run: cd build && ./foo

.gitignore

@@ -38,3 +38,4 @@ neml2.egg-info
 src/neml2/base/config.h
 install
 conftest.py
+.env

.gitmodules

@@ -1,13 +0,0 @@
-[submodule "extern/Catch2"]
-	path = extern/Catch2
-    url = https://github.com/catchorg/Catch2.git
-    ignore = dirty
-[submodule "extern/doxygen-awesome-css"]
-	path = extern/doxygen-awesome-css
-	url = https://github.com/jothepro/doxygen-awesome-css.git
-[submodule "extern/hit/hit"]
-	path = extern/hit/hit
-	url = https://github.com/idaholab/hit.git
-[submodule "extern/gperftools"]
-	path = extern/gperftools
-	url = https://github.com/gperftools/gperftools.git