Merge pull request #213 from precice/develop

Release ASTE version v3.3.0

.github/pull_request_template.md

@@ -5,6 +5,7 @@
 * [ ] I used the [`pre-commit` hook](https://precice.org/dev-docs-dev-tooling.html#setting-up-pre-commit) and used `pre-commit run --all` to apply all available hooks.
 * [ ] I added a test to cover the proposed changes in our test suite.
 * [ ] I updated the documentation in `docs/README.md`.
+* [ ] I added a changelog entry in `./changelog-entries/` (create if necessary).
 * [ ] I updated potential breaking changes in the tutorial [`precice/tutorials/aste-turbine`](https://github.com/precice/tutorials/tree/develop/aste-turbine).
 
 <!-- add more questions/tasks if necessary -->

.github/workflows/aste_ci.yml

@@ -13,63 +13,93 @@ concurrency:
   cancel-in-progress: ${{github.event_name == 'pull_request'}}
 
 jobs:
+  vtk:
+    name: Build VTK from source
+    runs-on: ubuntu-latest
+    container:
+      image: precice/precice:nightly
+      options: --shm-size=2gb
+    env:
+      CMAKE_BUILD_PARALLEL_LEVEL: 4
+    steps:
+      - name: Check VTK cache
+        id: cache-vtk
+        uses: actions/cache@v4
+        with:
+          key: ${{ runner.os }}-aste-vtk
+          path: |
+            /usr/local/include/vtk-*/
+            /usr/local/lib/libvtk*
+            /usr/local/lib/cmake/vtk-*/
+            /usr/local/bin/vtk*
+            /usr/local/bin/pvtkpython
+            /usr/local/lib/python*/site-packages/vtk.py
+            /usr/local/lib/python*/site-packages/vtkmodules/*
+            /etc/profile.d/99-vtk.sh
+      - name: Build VTK
+        if: steps.cache-vtk.outputs.cache-hit != 'true'
+        run: |
+          git clone https://gitlab.kitware.com/vtk/vtk.git && cd vtk
+          git checkout v9.3.0
+          mkdir build && cd build
+          cmake -DVTK_WRAP_PYTHON="ON" -DVTK_USE_MPI="ON" -DCMAKE_BUILD_TYPE=Release ..
+          cmake --build . && cmake --install .
+          echo 'export PYTHONPATH="${PYTHONPATH}:/usr/local/lib/python3.10/site-packages/"' > /etc/profile.d/99-vtk.sh
+
   build:
+    needs: vtk
+    name: ${{ format('{0} {1}', matrix.CXX, matrix.TYPE) }}
     runs-on: ubuntu-latest
-    container: precice/precice:nightly
-    timeout-minutes: 80
+    container:
+      image: precice/precice:nightly
+      options: --shm-size=2gb
+    defaults:
+      run:
+        shell: "bash --login -eo pipefail {0}"
+    strategy:
+      fail-fast: false
+      matrix:
+        CXX: ["clang++", "g++"]
+        TYPE: ["Debug", "Release"]
     env:
+      CXX: ${{ matrix.CXX }}
       CXX_FLAGS: "-Werror -Wall -Wextra -Wno-unused-parameter"
       CTEST_OUTPUT_ON_FAILURE: "Yes"
+      CMAKE_BUILD_PARALLEL_LEVEL: 4
     steps:
+      - name: Restore VTK from cache
+        uses: actions/cache@v4
+        with:
+          fail-on-cache-miss: true
+          key: ${{ runner.os }}-aste-vtk
+          path: |
+            /usr/local/include/vtk-*/
+            /usr/local/lib/libvtk*
+            /usr/local/lib/cmake/vtk-*/
+            /usr/local/bin/vtk*
+            /usr/local/bin/pvtkpython
+            /usr/local/lib/python*/site-packages/vtk.py
+            /usr/local/lib/python*/site-packages/vtkmodules/*
+            /etc/profile.d/99-vtk.sh
       - name: setup system
         run: |
           apt-get -y update && apt-get -y upgrade
-          apt-get install -y python3-pip pkg-config time
-          pip3 install --upgrade pip
-      - name: install VTK
-        run: |
-          git clone https://gitlab.kitware.com/vtk/vtk.git && cd vtk
-          git checkout v9.3.0
-          mkdir build && cd build
-          cmake -DVTK_WRAP_PYTHON="ON" -DVTK_USE_MPI="ON" -DCMAKE_BUILD_TYPE=Release ..
-          cmake --build . -j 2 && cmake --install .
-          echo "PYTHONPATH=/usr/local/lib/python3.10/site-packages/:${PYTHONPATH}" >> $GITHUB_ENV
-          cd
+          apt-get install -qq -y python3-pip python3-jinja2 python3-scipy python3-sympy libmetis-dev time clang
       - uses: actions/checkout@v4
       - name: install example dependencies
         run: |
           python3 -m pip install -r requirements.txt
-      - name: prepare directories
-        run: |
-          mkdir build_gcc build_clang
-      - name: build aste gcc
-        working-directory: build_gcc
-        env:
-          CC: gcc
-          CXX: g++
-        run: |
-          cmake ..
-          cmake --build .
-      - name: Adjust user rights
-        run: chown -R precice .
-      - name: run test gcc
-        working-directory: build_gcc
-        run: |
-          su -c "ctest" precice
-      - name: install clang
+      - name: prepare build directory
         run: |
-          apt-get -y install clang
-      - name: build aste clang
-        working-directory: build_clang
-        env:
-          CC: clang
-          CXX: clang++
+          mkdir build
+      - name: build aste
+        working-directory: build
         run: |
-          cmake ..
+          cmake -DCMAKE_BUILD_TYPE=${{ matrix.TYPE }} ..
           cmake --build .
       - name: Adjust user rights
         run: chown -R precice .
-      - name: run test clang
-        working-directory: build_clang
+      - name: run test
+        working-directory: build
         run: |
           su -c "ctest" precice

.github/workflows/aste_ci_mac.yml

@@ -0,0 +1,73 @@
+name: ASTE macOS CI
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+    branches: [master, develop]
+  schedule:
+    - cron: '0 8 * * 2'  # run once in a week (here Tue at 8am)
+
+concurrency:
+  group: ${ {github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build-macos:
+    runs-on: macos-latest
+    timeout-minutes: 20
+    env:
+      CXX_FLAGS: "-Werror -Wall -Wextra -Wno-unused-parameter"
+      CTEST_OUTPUT_ON_FAILURE: "Yes"
+    steps:
+      - name: Setup system
+        run: |
+          brew update
+          brew install cmake eigen boost openmpi pkg-config ninja gnu-time vtk
+      - name: Install preCICE
+        run: |
+          git clone https://github.com/precice/precice.git
+          cd precice
+          mkdir build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=/usr/local \
+                -DCMAKE_BUILD_TYPE=RelWithDebInfo \
+                -DPRECICE_FEATURE_MPI_COMMUNICATION=ON \
+                -DPRECICE_FEATURE_PETSC_MAPPING=OFF \
+                -DPRECICE_FEATURE_PYTHON_ACTIONS=OFF \
+                -DBUILD_TESTING=OFF \
+                -G Ninja ..
+          ninja
+          sudo ninja install
+          cd ../..
+      - uses: actions/checkout@v4
+      - name: Setup python
+        uses: actions/setup-python@v5
+        with:
+         python-version: '3.12'
+         check-latest: true
+
+      - name: Set up environment and install dependencies
+        run: |
+          python3 -m venv --system-site-packages venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install numpy polars vtk
+          echo "VIRTUAL_ENV=$(pwd)/venv" >> $GITHUB_ENV
+          echo "$VIRTUAL_ENV/bin" >> $GITHUB_PATH
+
+      - name: Prepare build directory
+        run: mkdir build
+      - name: Build project with clang
+        working-directory: build
+        env:
+          CC: clang
+          CXX: clang++
+        run: |
+          cmake ..
+          cmake --build .
+      - name: Run tests
+        working-directory: build
+        run: |
+          source ${{ env.VIRTUAL_ENV }}/bin/activate
+          ctest

.pre-commit-config.yaml

@@ -41,6 +41,6 @@ repos:
     rev: v0.39.0
     hooks:
       - id: markdownlint
-        exclude: changelog-entries
+        exclude: 'changelog-entries|^CHANGELOG\.md$'
       - id: markdownlint-fix
-        exclude: changelog-entries
+        exclude: 'changelog-entries|^CHANGELOG\.md$'

CHANGELOG.md

@@ -0,0 +1,129 @@
+# ASTE Change Log
+
+All notable changes to this project will be documented in this file.
+
+## [v3.3.0] - 2024-11-07
+
+### Added
+
+- Added a code of conduct from Covenant (see `CODE_OF_CONDUCT.md`). [#205](https://github.com/precice/aste/pull/205)
+- Added contributing guidelines (see `docs/CONTRIBUTING.md`). [#205](https://github.com/precice/aste/pull/205)
+- Added documentation to the mapping tester. [#209](https://github.com/precice/aste/pull/209)
+- Added scoping support to gathering events. [#207](https://github.com/precice/aste/pull/207)
+- Added macOS continuous integration support for ASTE. [#202](https://github.com/precice/aste/pull/202)
+- Added a cached VTK build in ASTE CI for faster build times. [#211](https://github.com/precice/aste/pull/211)
+
+### Changed
+
+- Changed CMake to always find Boost using its CMake Config. [#194](https://github.com/precice/aste/pull/194)
+- Highlighted ASTE's dependency on preCICE more clearly in the documentation. [#206](https://github.com/precice/aste/pull/206)
+- Made `run-all` script for examples more robust. [#201](https://github.com/precice/aste/pull/201)
+
+### Fixed
+
+- Fixed linker errors when FindBoost uses the CMake Config. [#194](https://github.com/precice/aste/pull/194)
+- Fixed SEGFAULT in `precice-aste-run` if no mesh is found for the given name. [#196](https://github.com/precice/aste/pull/196)
+
+## [v3.2.0] - 2024-07-31
+
+### Fixed
+
+- Fixed CMake installation for VTK 9 and higher. [#184](https://github.com/precice/aste/pull/184)
+
+### Changed
+
+- Updated documentation for current VTK issues. [#185](https://github.com/precice/aste/pull/185)
+- Updated CI to use manual installation of VTK. [#187](https://github.com/precice/aste/pull/187)
+- Cleaned up Python requirements. [#193](https://github.com/precice/aste/pull/193)
+
+## [v3.1.0] - 2024-03-22
+
+### Added
+
+- Introduced a Halton Mesh Generator for improved mesh sampling. [#155](https://github.com/precice/aste/pull/155)
+- Added a unit grid generator. [#154](https://github.com/precice/aste/pull/154)
+- Added connectivity to the Halton Mesh Generator using Delaunay Triangulation. [#157](https://github.com/precice/aste/pull/157)
+- Set up Dependabot for dependency updates. [#164](https://github.com/precice/aste/pull/164)
+- Added pre-commit hooks for website linting. [#183](https://github.com/precice/aste/pull/183)
+
+### Changed
+
+- Updated codebase from C++14 to C++17 standard. [#138](https://github.com/precice/aste/pull/138)
+- Replaced `boost::filesystem` with `std::filesystem`. [#160](https://github.com/precice/aste/pull/160)
+- Updated ASTE for compatibility with preCICE version 3. [#161](https://github.com/precice/aste/pull/161)
+- Merged `initialize` and `initializeData` functions. [#158](https://github.com/precice/aste/pull/158)
+- Renamed test executable from `test` to `precice-aste-test`. [#175](https://github.com/precice/aste/pull/175)
+- Updated preCICE packages in continuous integration. [#167](https://github.com/precice/aste/pull/167)
+
+### Fixed
+
+- Improved handling of ASTE and preCICE logging. [#136](https://github.com/precice/aste/pull/136)
+- Fixed wrong variable in Franke3D function. [#173](https://github.com/precice/aste/pull/173)
+- Fixed vertex resolution in partitioner and joiner. [#180](https://github.com/precice/aste/pull/180)
+- Changed scripts to use `env time` to bypass built-in `time`. [#178](https://github.com/precice/aste/pull/178)
+
+### Released
+
+- Released ASTE version compatible with preCICE v3. [#182](https://github.com/precice/aste/pull/182)
+
+## [v3.0.0] - 2022-09-28
+
+### Added
+
+- Fully ported ASTE to the VTK library, eliminating custom data structures.
+- Unified user interface for the main C++ core (`precice-aste-run`) and Python tools.
+- Introduced replay-mode to emulate participants in coupled simulations.
+- Added support for `nearest-neighbor-gradient` and `linear-cell` interpolation mappings.
+- Supported processing of tetrahedral meshes and gradient data.
+- Created dedicated ASTE documentation and tutorial resources.
+
+### Changed
+
+- Improved logging for the C++ executable and Python tools.
+- Renamed executables for consistency.
+- Updated VTK version requirements and improved component detection.
+- Switched to pre-commit hooks for code formatting.
+- Refactored codebase for better performance and maintainability.
+
+### Fixed
+
+- Resolved compiler warnings and code style issues.
+- Fixed MPI linking issues for test executables.
+- Corrected logger names and typos in documentation.
+- Fixed issues with `vtk_calculator` removing `diffdata` in diff mode.
+
+### Removed
+
+- Removed obsolete scripts and deprecated functions.
+
+## [v2.0.0] - 2020-02-10
+
+### Added
+
+- Support for preCICE v2, including migration to the single-step setup.
+
+### Changed
+
+- Updated configuration files to be compatible with preCICE v2.
+
+## [v1.1.0] - 2019-11-20
+
+### Added
+
+- Connectivity information to mesh creation and partition tools.
+- Filter for cell types in mesh handling.
+
+### Changed
+
+- Sped up edge generation using `boost::flat_map` for better performance.
+- Modernized CMake configurations for improved build process.
+- Migrated `preciceMap`, `aste`, and `visualize_partition` tools to the new system.
+
+### Fixed
+
+- Issues with connectivity output ensuring correct data representation.
+- Build issues in CMake configuration.
+
+### Removed
+
+- Dependency on the `prettyprint` library to reduce external dependencies.