Update build process and PyPI release

sameeul · Nov 8, 2023 · 51e1971 · 51e1971
1 parent c187714
commit 51e1971
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diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -0,0 +1,78 @@
+name: name: Publish to PyPi
+
+on:
+  release:
+    types: [published]
+
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
+      MACOSX_DEPLOYMENT_TARGET: "10.15"
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, windows-latest]
+        cibw_archs: ["auto64"]
+        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out
+        with:
+          submodules: recursive    
+
+      - uses: ilammy/msvc-dev-cmd@v1
+        name: Add MSVS Path
+
+      - uses: ilammy/setup-nasm@v1
+        name: Add NASM
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.9'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==2.16.2 delvewheel wheel
+
+      - name: Building wheels 
+        run: |
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: ${{ matrix.cibw_build }}
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_SKIP: "*musllinux*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          CIBW_BEFORE_ALL_MACOS: brew install llvm libomp nasm &&
+                          bash ci-utils/install_prereq_linux.sh &&
+                          mkdir -p /tmp/argolid_bld &&
+                          cp -r local_install /tmp/argolid_bld
+          CIBW_BEFORE_ALL_LINUX: curl -L http://mirror.centos.org/centos/8-stream/PowerTools/x86_64/os/Packages/nasm-2.15.03-3.el8.x86_64.rpm -o nasm-2.15.03-3.el8.x86_64.rpm &&
+                                   yum -y install nasm-2.15.03-3.el8.x86_64.rpm &&
+                                   bash ci-utils/install_prereq_linux.sh &&
+                                   mkdir -p /tmp/argolid_bld &&
+                                   cp -r local_install /tmp/argolid_bld
+          CIBW_BEFORE_ALL_WINDOWS: ci-utils\install_prereq_win.bat &&
+                                   xcopy /E /I /y local_install C:\TEMP\argolid_bld\local_install 
+          CIBW_ENVIRONMENT_MACOS: REPAIR_LIBRARY_PATH="/tmp/argolid_bld/local_install/lib:/tmp/argolid_bld/local_install/lib64" ON_GITHUB="TRUE" PATH="$(brew --prefix llvm)/bin:$PATH" COMPILER="/usr/local/opt/llvm/bin/clang++" CFLAGS="-I /usr/local/include -I/usr/local/opt/llvm/include" CXXFLAGS="-I /usr/local/include -I/usr/local/opt/llvm/include" LDFLAGS="-L /usr/local/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" CXX="/usr/local/opt/llvm/bin/clang++" CC="/usr/local/opt/llvm/bin/clang" ARGOLID_DEP_DIR="/tmp/argolid_bld/local_install"
+          CIBW_ENVIRONMENT_LINUX: LD_LIBRARY_PATH="/tmp/argolid_bld/local_install/lib:/tmp/argolid_bld/local_install/lib64:$LD_LIBRARY_PATH" ON_GITHUB="TRUE" ARGOLID_DEP_DIR="/tmp/argolid_bld/local_install" 
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} && DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}
+          CIBW_ENVIRONMENT_WINDOWS: PATH="$TEMP\\argolid\\bin;$PATH" ON_GITHUB="TRUE" ARGOLID_DEP_DIR="C:\\TEMP\\argolid_bld\\local_install"
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
+          CIBW_ARCHS: ${{ matrix.cibw_archs }}
+          CIBW_TEST_REQUIRES: bfio==2.3.2 tensorstore
+          CIBW_TEST_COMMAND: python -W default -m unittest discover -s {project}/tests -v
+
+      - name: Install Dependencies
+        run: python -m pip install --upgrade twine requests
+
+      - name: Publish to PyPi
+        run: python -m twine upload dist/*.whl
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+          TWINE_REPOSITORY: pypi
diff --git a/.github/workflows/wheel_build.yml b/.github/workflows/wheel_build.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.12.1 delvewheel wheel
+          python -m pip install cibuildwheel==2.16.2 delvewheel wheel
 
       - name: Building wheels 
         run: |

diff --git a/ci-utils/install_prereq_linux.sh b/ci-utils/install_prereq_linux.sh
@@ -14,9 +14,9 @@ fi
 mkdir -p $LOCAL_INSTALL_DIR
 mkdir -p $LOCAL_INSTALL_DIR/include
 
-curl -L https://github.com/PolusAI/filepattern/archive/refs/tags/v2.0.3.zip -o v2.0.3.zip 
-unzip v2.0.3.zip
-cd filepattern-2.0.3
+curl -L https://github.com/PolusAI/filepattern/archive/refs/tags/v2.0.4.zip -o v2.0.4.zip 
+unzip v2.0.4.zip
+cd filepattern-2.0.4
 mkdir build
 cd build
 cmake -Dfilepattern_SHARED_LIB=ON -DCMAKE_PREFIX_PATH=../../$LOCAL_INSTALL_DIR -DCMAKE_INSTALL_PREFIX=../../$LOCAL_INSTALL_DIR ../src/filepattern/cpp

diff --git a/ci-utils/install_prereq_win.bat b/ci-utils/install_prereq_win.bat
@@ -1,9 +1,9 @@
 mkdir local_install
 mkdir local_install\include
 
-curl -L https://github.com/PolusAI/filepattern/archive/refs/tags/v2.0.3.zip -o v2.0.3.zip 
-tar -xvf v2.0.3.zip
-pushd filepattern-2.0.3
+curl -L https://github.com/PolusAI/filepattern/archive/refs/tags/v2.0.4.zip -o v2.0.4.zip 
+tar -xvf v2.0.4.zip
+pushd filepattern-2.0.4
 mkdir build
 pushd build
 cmake -Dfilepattern_SHARED_LIB=ON -DCMAKE_PREFIX_PATH=../../local_install -DCMAKE_INSTALL_PREFIX=../../local_install ../src/filepattern/cpp

diff --git a/src/chunked_pyramid_assembler.cpp b/src/chunked_pyramid_assembler.cpp
@@ -205,7 +205,8 @@ void OmeTiffCollToChunked::GenerateOmeXML(const std::string& image_name, const s
     // Add the namespaces and attributes to the root element
     omeNode.append_attribute("xmlns") = "http://www.openmicroscopy.org/Schemas/OME/2016-06";
     omeNode.append_attribute("xmlns:xsi") = "http://www.w3.org/2001/XMLSchema-instance";
-    omeNode.append_attribute("Creator") = "Argolid 0.0.1";
+    auto creator = std::string{"Argolid "} + std::string{VERSION_INFO};
+    omeNode.append_attribute("Creator") = creator.c_str();
     omeNode.append_attribute("UUID") = "urn:uuid:ce3367ae-0512-4e87-a045-20d87db14001";
     omeNode.append_attribute("xsi:schemaLocation") = "http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd";