Merge pull request #10 from ygeunkim/feature/python

Add a python version
ygeunkim · Sep 14, 2024 · a451039 · a451039
2 parents 21b8a57 + 2a8599d
commit a451039
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,4 @@
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^revdep$
+^python$
diff --git a/.github/workflows/py-conda-check.yaml b/.github/workflows/py-conda-check.yaml
@@ -0,0 +1,72 @@
+on:
+  push:
+    branches: ['feature/python', 'feature/py-*'] # change to [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*'] after finish
+#   pull_request:
+#     branches: [main, master, 'hotfix/*', 'release/*', develop]
+
+name: py-conda-check
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    defaults:
+      run:
+        working-directory: python
+
+    name: ${{ matrix.os }} (${{ matrix.python-version }})
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set LLVM on macOS
+        if: runner.os == 'macOS'
+        run: |
+          brew update
+          brew install llvm libomp
+          LLVM_LOC=$(brew --prefix llvm)
+          OMP_LOC=$(brew --prefix libomp)
+          echo "LLVM_LOC=$LLVM_LOC" >> $GITHUB_ENV
+          echo "OMP_LOC=$OMP_LOC" >> $GITHUB_ENV
+          echo "CC=$LLVM_LOC/bin/clang" >> $GITHUB_ENV
+          echo "CXX=$LLVM_LOC/bin/clang++" >> $GITHUB_ENV
+          echo "CPPFLAGS=-I$LLVM_LOC/include -I$OMP_LOC/include" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$LLVM_LOC/lib -L$OMP_LOC/lib" >> $GITHUB_ENV
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          activate-environment: bvhar-env
+          environment-file: python/requirements/environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: Verify conda
+        run: |
+          conda info
+          conda list
+          conda env list
+
+      - name: Install
+        run: conda run -n bvhar-env pip install -e . -v
+
+      - name: Verify installation
+        run: |
+          conda run -n bvhar-env pip list
+          conda run -n bvhar-env conda list
+      
+      - name: OpenMP check
+        run: conda run -n bvhar-env python -c "from bvhar.utils import checkomp; checkomp.check_omp()"
+
+      - name: Test
+        run: conda run -n bvhar-env pytest
diff --git a/.github/workflows/py-github-check.yaml b/.github/workflows/py-github-check.yaml
@@ -0,0 +1,123 @@
+on:
+  push:
+    branches: ['feature/python', 'feature/py-*'] # change to [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*'] after finish
+  #   pull_request:
+  #     branches: [main, master, 'hotfix/*', 'release/*', develop]
+
+name: py-github-check
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    name: ${{ matrix.os }} (${{ matrix.python-version }})
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Verify git
+        run: git --version
+
+      - name: Set system dependencies on Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libboost-all-dev libeigen3-dev
+          echo $(sudo apt list --installed)
+          echo "EIGEN_INCLUDE_DIR=/usr/include/eigen3" >> $GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=/usr/include/boost" >> $GITHUB_ENV
+      
+      - name: Set system dependencies on macOS
+        if: runner.os == 'macOS'
+        run: |
+          brew update
+          brew install llvm libomp boost eigen
+          EIGEN_LOC=$(brew --prefix eigen)
+          BOOST_LOC=$(brew --prefix boost)
+          LLVM_LOC=$(brew --prefix llvm)
+          OMP_LOC=$(brew --prefix libomp)
+          echo "EIGEN_INCLUDE_DIR=$EIGEN_LOC/include/eigen3" >> $GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=$BOOST_LOC/include" >> $GITHUB_ENV
+          echo "LLVM_LOC=$LLVM_LOC" >> $GITHUB_ENV
+          echo "OMP_LOC=$OMP_LOC" >> $GITHUB_ENV
+          echo "CC=$LLVM_LOC/bin/clang" >> $GITHUB_ENV
+          echo "CXX=$LLVM_LOC/bin/clang++" >> $GITHUB_ENV
+          echo "CPPFLAGS=-I$LLVM_LOC/include -I$OMP_LOC/include" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$LLVM_LOC/lib -L$OMP_LOC/lib" >> $GITHUB_ENV
+      
+      - name: Set system dependencies on Windows
+        if: runner.os == 'Windows'
+        run: |
+          choco install eigen -y --no-progress
+          choco install boost-msvc-14.3 -y --no-progress
+          $eigenPath = (
+            Get-ChildItem -Path "C:\ProgramData\chocolatey\lib\eigen" -Recurse -Filter "Eigen" |
+            Select-Object -First 1
+          ).Parent.FullName
+          if ($eigenPath) {
+            echo "eigen is installed in $eigenPath"
+          } else {
+            Write-Error "Wrong eigen path"
+            exit 1
+          }
+          $boostPath = $null
+          $boostCand = @("C:\local", "C:\ProgramData\chocolatey\lib")
+          foreach ($cand in $boostCand) {
+            $isPath = (
+                Get-ChildItem -Path $cand -Directory |
+                Where-Object { $_.Name -match  "boost" } |
+                Sort-Object LastWriteTime -Descending |
+                Select-Object -First 1
+            ).FullName
+            if ($isPath) {
+                $boostPath = $isPath
+                break
+            }
+          }
+          if ($boostPath) {
+            echo "boost is installed in $boostPath"
+          } else {
+            Write-Error "Wrong boost path"
+            exit 1
+          }
+          echo "EIGEN_INCLUDE_DIR=$eigenPath" >> $Env:GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=$boostPath" >> $Env:GITHUB_ENV
+
+      - name: Verify Eigen and boost on non-Windows
+        if: runner.os != 'Windows'
+        run: |
+          ls ${{ env.EIGEN_INCLUDE_DIR }}
+          ls ${{ env.BOOST_INCLUDE_DIR }}
+          mkdir temp-dir
+      
+      - name: Verify Eigen and boost on Windows
+        if: runner.os == 'Windows'
+        run: |
+          dir ${{ env.EIGEN_INCLUDE_DIR }}
+          dir ${{ env.BOOST_INCLUDE_DIR }}
+          New-Item -ItemType Directory -Force -Path temp-dir
+
+      - name: Install package from github
+        # change branch after finishing the feature
+        run: |
+          pip install --upgrade pip
+          python -m pip install -e 'git+https://github.com/ygeunkim/bvhar.git@feature/python#egg=bvhar&subdirectory=python'
+        working-directory: temp-dir
+
+      - name: Verify installation
+        run: pip list
+        working-directory: temp-dir
+
+      - name: OpenMP check
+        run: python -c "from bvhar.utils import checkomp; checkomp.check_omp()"
+        working-directory: temp-dir
diff --git a/.github/workflows/py-pip-check.yaml b/.github/workflows/py-pip-check.yaml
@@ -0,0 +1,127 @@
+on:
+  push:
+    branches: ['feature/python', 'feature/py-*'] # change to [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*'] after finish
+  #   pull_request:
+  #     branches: [main, master, 'hotfix/*', 'release/*', develop]
+
+name: py-pip-check
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    defaults:
+      run:
+        working-directory: python
+
+    name: ${{ matrix.os }} (${{ matrix.python-version }})
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set system dependencies on Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libboost-all-dev libeigen3-dev
+          echo $(sudo apt list --installed)
+          echo "EIGEN_INCLUDE_DIR=/usr/include/eigen3" >> $GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=/usr/include/boost" >> $GITHUB_ENV
+      
+      - name: Set system dependencies on macOS
+        if: runner.os == 'macOS'
+        run: |
+          brew update
+          brew install llvm libomp boost eigen
+          EIGEN_LOC=$(brew --prefix eigen)
+          BOOST_LOC=$(brew --prefix boost)
+          LLVM_LOC=$(brew --prefix llvm)
+          OMP_LOC=$(brew --prefix libomp)
+          echo "EIGEN_INCLUDE_DIR=$EIGEN_LOC/include/eigen3" >> $GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=$BOOST_LOC/include" >> $GITHUB_ENV
+          echo "LLVM_LOC=$LLVM_LOC" >> $GITHUB_ENV
+          echo "OMP_LOC=$OMP_LOC" >> $GITHUB_ENV
+          echo "CC=$LLVM_LOC/bin/clang" >> $GITHUB_ENV
+          echo "CXX=$LLVM_LOC/bin/clang++" >> $GITHUB_ENV
+          echo "CPPFLAGS=-I$LLVM_LOC/include -I$OMP_LOC/include" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$LLVM_LOC/lib -L$OMP_LOC/lib" >> $GITHUB_ENV
+      
+      - name: Set system dependencies on Windows
+        if: runner.os == 'Windows'
+        run: |
+          choco install eigen -y --no-progress
+          choco install boost-msvc-14.3 -y --no-progress
+          $eigenPath = (
+            Get-ChildItem -Path "C:\ProgramData\chocolatey\lib\eigen" -Recurse -Filter "Eigen" |
+            Select-Object -First 1
+          ).Parent.FullName
+          if ($eigenPath) {
+            echo "eigen is installed in $eigenPath"
+          } else {
+            Write-Error "Wrong eigen path"
+            exit 1
+          }
+          $boostPath = $null
+          $boostCand = @("C:\local", "C:\ProgramData\chocolatey\lib")
+          foreach ($cand in $boostCand) {
+            $isPath = (
+                Get-ChildItem -Path $cand -Directory |
+                Where-Object { $_.Name -match  "boost" } |
+                Sort-Object LastWriteTime -Descending |
+                Select-Object -First 1
+            ).FullName
+            if ($isPath) {
+                $boostPath = $isPath
+                break
+            }
+          }
+          if ($boostPath) {
+            echo "boost is installed in $boostPath"
+          } else {
+            Write-Error "Wrong boost path"
+            exit 1
+          }
+          echo "EIGEN_INCLUDE_DIR=$eigenPath" >> $Env:GITHUB_ENV
+          echo "BOOST_INCLUDE_DIR=$boostPath" >> $Env:GITHUB_ENV
+
+      - name: Verify Eigen and boost on non-Windows
+        if: runner.os != 'Windows'
+        run: |
+          ls ${{ env.EIGEN_INCLUDE_DIR }}
+          ls ${{ env.BOOST_INCLUDE_DIR }}
+      
+      - name: Verify Eigen and boost on Windows
+        if: runner.os == 'Windows'
+        run: |
+          dir ${{ env.EIGEN_INCLUDE_DIR }}
+          dir ${{ env.BOOST_INCLUDE_DIR }}
+
+      - name: Install requirements
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements/requirements.txt
+      
+      - name: Verify pip
+        run: pip list
+
+      - name: Install
+        run: pip install -e . -v
+
+      - name: Verify installation
+        run: pip list
+
+      - name: OpenMP check
+        run: python -c "from bvhar.utils import checkomp; checkomp.check_omp()"
+
+      - name: Test
+        run: pytest
diff --git a/.github/workflows/py-test-coverage.yaml b/.github/workflows/py-test-coverage.yaml
@@ -0,0 +1,51 @@
+on:
+  push:
+    branches: ['feature/python', 'feature/py-*'] # change to [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*'] after finish
+  # pull_request:
+  #   branches: [main, master, 'hotfix/*', 'release/*', develop]
+
+name: py-test-coverage
+
+jobs:
+  py-test-coverage:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        working-directory: python
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          activate-environment: bvhar-dev
+          environment-file: python/requirements/environment-dev.yml
+          python-version: '3.11'
+          auto-activate-base: false
+
+      - name: Install dependencies
+        run: conda run -n bvhar-dev pip install -e . -v
+
+      - name: Test coverage
+        run: conda run -n bvhar-dev pytest --cov=./ --cov-report=xml | tee pytest_output.txt
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          working-directory: python
+          codecov_yml_path: ../codecov.yml
+          flags: python
+
+      - name: Show pytest output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find . -name 'pytest_output.txt' -exec cat '{}' \; || true
+        shell: bash