musica 0.6.1.dev0__tar.gz → 0.7.0__tar.gz

musica-0.7.0/.clang-format

@@ -0,0 +1,43 @@
+---
+BasedOnStyle: Google
+AlignAfterOpenBracket: 'AlwaysBreak'
+AllowAllConstructorInitializersOnNextLine: 'false'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+AlignConsecutiveMacros: 'true'
+AllowShortCaseLabelsOnASingleLine: 'true'
+AllowShortFunctionsOnASingleLine: 'None'
+AllowShortIfStatementsOnASingleLine: 'Never'
+AllowShortLoopsOnASingleLine: 'false'
+BreakBeforeBraces: Allman
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+Cpp11BracedListStyle: 'false'
+ColumnLimit: 125 
+IndentWidth: 2
+IndentPPDirectives: BeforeHash
+NamespaceIndentation: All
+PackConstructorInitializers: 'Never'
+SpaceAfterTemplateKeyword: 'false'
+SpaceBeforeCtorInitializerColon: 'true'
+SpaceBeforeInheritanceColon: 'true'
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: 'true'
+SpaceInEmptyBlock: true
+Standard: 'Latest'
+IncludeBlocks: Regroup
+IncludeCategories:
+  # MUSICA project headers
+  - Regex:           '<(musica)\/'
+    Priority:        2
+  # MICM, TUV-X headers
+  - Regex:           '<(micm|tuvx)[[:alnum:].(-|_)*]+>'
+    Priority:        3
+  # External libraries headers
+  - Regex:           '<[[:alnum:].(-|_)*]+\/'
+    Priority:        4
+  # System headers
+  - Regex:           '<[[:alnum:].(-|_)*]+>'
+    Priority:        5
+  # Main, local, private headers
+  - Regex:           '".*'
+    Priority:        1

musica-0.7.0/.clang-tidy

@@ -0,0 +1,21 @@
+---
+
+Checks: >
+  -*,
+  readability-identifier-naming,
+
+WarningsAsErrors: '*'
+
+CheckOptions:
+  - key:             readability-identifier-naming.FunctionCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.ClassCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.MemberCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.MemberSuffix
+    value:           _
+  - key:             readability-identifier-naming.ClassConstantCase
+    value:           UPPER_CASE
+  - key:             readability-identifier-naming.GlobalConstantCase
+    value:           UPPER_CASE

musica-0.7.0/.dockerignore

@@ -0,0 +1,19 @@
+# ignore all
+*
+
+# add things to copy
+!.git/
+!.gitmodules
+!CMakeLists.txt
+!valgrind.supp
+!cmake/
+!configs
+!docs/
+!fortran/
+!include/
+!lib/
+!src/
+!python/
+!pyproject.toml
+!LICENSE
+!README.md

musica-0.7.0/.github/workflows/clang_format.yml

@@ -0,0 +1,54 @@
+name: Clang-Format
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  format:
+    name: Run Clang-Format
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install Clang-Format
+        run: sudo apt-get update && sudo apt-get install clang-format && clang-format --version
+
+      - name: Check out code, run clang format, push changes
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Run clang-format
+        run: |
+          find include -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-format -i --style=file --verbose {} +
+          find src -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-format -i --style=file --verbose {} +
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-formatting branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:main-formatting
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using Clang-Format"
+          title: "Auto-format code changes"
+          body: "This is an automated pull request to apply code formatting using Clang-Format."
+          branch: main-formatting

musica-0.7.0/.github/workflows/clang_tidy.yml

@@ -0,0 +1,59 @@
+name: Clang-Tidy
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  format:
+    name: Run clang-tidy
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install clang-tidy
+        run: sudo apt-get update && sudo apt-get install clang-tidy && clang-tidy --version
+
+      - name: Check out code, run clang-tidy, push changes
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Run clang-tidy
+        # Currently disabled
+        if: false
+        run: |
+          find include -type f \( -name '*.hpp' -or -name '*.h' \) -exec clang-tidy --config-file="./.clang-tidy" --fix-errors {} +
+          find src -type f \( -name '*.cpp' -or -name '*.c' \) ! -path 'src/test/*' -exec clang-tidy --config-file="./.clang-tidy" --fix-errors {} +
+          find python -type f \( -name '*.cpp' -or -name '*.c' \) -exec clang-tidy --config-file="./.clang-tidy" --fix-errors {} +
+
+        continue-on-error: true
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
+          git commit -am "Auto-format code using clang-tidy" || echo "No changes to commit"
+
+      - name: Push changes to clang-tidy-format branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:clang-tidy-format
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using clang-tidy"
+          title: "Auto-format code changes"
+          body: "This is an automated pull request to apply code formatting using clang-tidy."
+          branch: clang-tidy-format

musica-0.7.0/.github/workflows/docker.yml

@@ -0,0 +1,59 @@
+name: Docker
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.memcheck
+          - Dockerfile.fortran-gcc
+          - Dockerfile.openmp
+          - Dockerfile.mpi
+          - Dockerfile.mpi_openmp
+          - Dockerfile.python
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
+
+      - name: Build Docker image
+        run: docker build -t musica -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t musica bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info

musica-0.7.0/.github/workflows/fetch_content_integration.yml

@@ -0,0 +1,44 @@
+name: FetchContentIntegration
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    env:
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile.fortran-intel
+          - Dockerfile.fortran-gcc.integration
+          - Dockerfile.fortran-nvhpc
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Print branch name
+        run: echo "Branch name is $BRANCH_NAME"
+
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
+
+      - name: Build Docker image
+        run: docker build -t musica --build-arg MUSICA_GIT_TAG=${BRANCH_NAME} -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'

musica-0.7.0/.github/workflows/gh_pages.yml

@@ -0,0 +1,134 @@
+# Build and deploy documentation to GitHub Pages
+name: GitHub Pages
+
+on: [ push, pull_request ]
+
+env:
+  DEFAULT_BRANCH: "release"
+
+jobs:
+  build-and-deploy:
+    name: Build and deploy to gh-pages
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        gcc-version: [13]
+    env:
+      CXX: g++-${{ matrix.gcc-version }}
+      CC: gcc-${{ matrix.gcc-version }}
+      FC: gfortran-${{ matrix.gcc-version }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          lfs: true
+
+      - name: Debugging information
+        run: |
+          echo "github.ref:" ${{github.ref}}
+          echo "github.event_name:" ${{github.event_name}}
+          echo "github.head_ref:" ${{github.head_ref}}
+          echo "github.base_ref:" ${{github.base_ref}}
+          set -x
+          git rev-parse --abbrev-ref HEAD
+          git branch
+          git branch -a
+          git remote -v
+          python -V
+          pip list --not-required
+          pip list
+
+      # Clone and set up the old gh-pages branch
+      - name: Clone old gh-pages
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          git fetch
+          ( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
+          rm -rf _gh-pages/.git/
+          mkdir -p _gh-pages/branch/
+
+      # If a push and default branch, copy build to _gh-pages/ as the "main"
+      # deployment.
+      - name: Build and copy documentation (default branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          mkdir -p _build/html/versions
+
+          # create two copies of the documentation
+          # 1. the frozen version, represented as vX.X in the version switcher
+          docker build -t musica -f docker/Dockerfile.docs .
+          id=$(docker create musica)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          version=$(sed -nr "s/^release = f'v(.+)\{suffix\}'.*$/\1/p" docs/source/conf.py)
+          mv tmpdocs _build/html/versions/${version}
+
+          # 2. stable, represented as vX.X (stable) in the version switcher
+          # edit conf.py to produce a version string that looks like vX.X (stable)
+          docker build -t musica -f docker/Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          id=$(docker create musica)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          mv tmpdocs _build/html/versions/stable
+          # Delete everything under _gh-pages/ that is from the
+          # primary branch deployment.  Excludes the other branches
+          # _gh-pages/branch-* paths, and not including
+          # _gh-pages itself.
+          find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' ! -path '_gh-pages/versions*' -delete
+          rsync -a _build/html/versions/stable/* _gh-pages/
+          mkdir -p _gh-pages/versions
+          rsync -a _build/html/versions/* _gh-pages/versions
+          # mv docs/switcher.json _gh-pages
+
+      # If a push and not on default branch, then copy the build to
+      # _gh-pages/branch/$brname (transforming '/' into '--')
+      - name: Build and copy documentation (branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          !contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          docker build -t musica -f docker/Dockerfile.docs .
+          id=$(docker create musica)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          brname="${{github.ref}}"
+          brname="${brname##refs/heads/}"
+          brdir=${brname//\//--}   # replace '/' with '--'
+          rm -rf   _gh-pages/branch/${brdir}
+          rsync -a tmpdocs/ _gh-pages/branch/${brdir}
+
+      # Go through each branch in _gh-pages/branch/, if it's not a
+      # ref, then delete it.
+      - name: Delete old feature branches
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          for brdir in `ls _gh-pages/branch/` ; do
+              brname=${brdir//--/\/}   # replace '--' with '/'
+              if ! git show-ref remotes/origin/$brname ; then
+                  echo "Removing $brdir"
+                  rm -r _gh-pages/branch/$brdir/
+              fi
+          done
+
+      # Add the .nojekyll file
+      - name: nojekyll
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          touch _gh-pages/.nojekyll
+
+      # Deploy
+      # https://github.com/peaceiris/actions-gh-pages
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _gh-pages/
+          force_orphan: true

musica-0.7.0/.github/workflows/mac.yml

@@ -0,0 +1,96 @@
+name: Mac
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  c_cxx:
+    runs-on: macos-latest
+    continue-on-error: true 
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11, fc: gfortran-11}
+          - { cpp: g++-12, c: gcc-12, fc: gfortran-12}
+          - { cpp: g++-13, c: gcc-13, fc: gfortran-13}
+          - { cpp: clang++, c: clang, fc: gfortran-12}
+        build_type: [Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+      FC: ${{ matrix.compiler.fc }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: brew install netcdf netcdf-fortran
+
+      - uses: actions/setup-python@v5
+      - run: pip install numpy --user
+
+      - name: Run Cmake 
+        if: matrix.compiler.cpp != 'g++-13'
+        run: |
+            PYTHON_PATH=$(which python)
+            cmake -S . -B build \
+                -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
+                -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
+                -D Python3_EXECUTABLE=$PYTHON_PATH 
+
+      - name: Run Cmake 
+        if: matrix.compiler.cpp == 'g++-13'
+        run: |
+            PYTHON_PATH=$(which python)
+            # for some reason gcc 13 was having issues finding the correct osx sdk
+            # it seems it was a known issue: https://github.com/actions/runner-images/issues/9997
+            # for some reason, passing in an empty string for the osx sysroot fixed the issue
+            cmake -S . -B build \
+                -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
+                -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
+                -D Python3_EXECUTABLE=$PYTHON_PATH \
+                -D CMAKE_OSX_SYSROOT=""
+
+      - name: Build
+        run: cmake --build build --verbose --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+
+  fortran:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+        build_type: [Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: brew install netcdf netcdf-fortran
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+
+      - name: Build
+        run: cmake --build build --verbose --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -E "tuvx_c_api|tuvx_fortran_api" -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

musica-0.7.0/.github/workflows/pep8.yml

@@ -0,0 +1,45 @@
+name: Pep8
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  autopep8:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive .
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-autopep8 branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:main-autopep8
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using autopep8"
+          title: "Auto-format code by autopep8"
+          body: "This is an auto-generated PR with fixes by autopep8."
+          branch: main-autopep8

musica-0.7.0/.github/workflows/pip.yml

@@ -0,0 +1,37 @@
+name: Pip
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-13, ubuntu-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        # python versions: https://devguide.python.org/versions/
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Add requirements
+      run: python -m pip install --upgrade wheel setuptools
+
+    - name: Build and install
+      run: pip install --verbose .[test]
+
+    - name: Test
+      run: python -m unittest discover -s python/test