Merge remote-tracking branch 'upstream/main'

.github/workflows/build.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches:
       - "main"
+  pull_request: # TODO (aliddell): remove this
+    branches:
+      - "main"
 
 jobs:
   windows-and-linux-build:
@@ -93,12 +96,12 @@ jobs:
 
       - name: Build for x64
         run: |
-          cmake --preset=default -DVCPKG_TARGET_TRIPLET=x64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-x64 -B ${{github.workspace}}/build-x64 -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -DCMAKE_OSX_ARCHITECTURES="x86_64" -DNOTEST=1
+          cmake --preset=default -DVCPKG_TARGET_TRIPLET=x64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-x64 -B ${{github.workspace}}/build-x64 -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -DCMAKE_OSX_ARCHITECTURES="x86_64" -DBUILD_TESTING=OFF
           cmake --build ${{github.workspace}}/build-x64 --config ${{matrix.build_type}}
 
       - name: Build for arm64
         run: |
-          cmake --preset=default -DVCPKG_TARGET_TRIPLET=arm64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-arm64 -B ${{github.workspace}}/build-arm64 -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -DCMAKE_OSX_ARCHITECTURES="arm64" -DNOTEST=1
+          cmake --preset=default -DVCPKG_TARGET_TRIPLET=arm64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-arm64 -B ${{github.workspace}}/build-arm64 -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -DCMAKE_OSX_ARCHITECTURES="arm64" -DBUILD_TESTING=OFF
           cmake --build ${{github.workspace}}/build-arm64 --config ${{matrix.build_type}}
 
       - name: Create a universal binary
@@ -114,4 +117,52 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           name: macos-latest ${{matrix.build_type}} binaries
-          path: ${{github.workspace}}/*.zip
+          path: ${{github.workspace}}/*.zip
+
+  build-wheel:
+    strategy:
+      matrix:
+        platform:
+          - "windows-latest"
+          - "ubuntu-latest"
+          - "macos-latest" # TODO (aliddell): universal binary?
+
+    runs-on: ${{ matrix.platform }}
+
+    permissions:
+      actions: write
+
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install vcpkg
+        run: |
+          git clone https://github.com/microsoft/vcpkg.git
+          cd vcpkg && ./bootstrap-vcpkg.sh
+          echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV
+          echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH
+          ./vcpkg integrate install
+        shell: bash
+
+      - name: Install dependencies
+        run: python -m pip install -U pip "pybind11[global]" cmake build
+
+      - name: Build
+        run: python -m build
+
+      - name: Upload wheel
+        uses: actions/upload-artifact@v3
+        with:
+          path: ${{github.workspace}}/dist/*.whl

.github/workflows/release.yml

@@ -57,7 +57,7 @@ jobs:
 
       - name: Package
         run: |
-          cmake --preset=default -DVCPKG_TARGET_TRIPLET=${{matrix.vcpkg_triplet}} -B ${{github.workspace}}/pack -DCMAKE_BUILD_TYPE=Release -DNOTEST=1
+          cmake --preset=default -DVCPKG_TARGET_TRIPLET=${{matrix.vcpkg_triplet}} -B ${{github.workspace}}/pack -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF
           cmake --build ${{github.workspace}}/pack --config Release
           cpack --config ${{github.workspace}}/pack/CPackConfig.cmake -C Release -G ZIP
 
@@ -93,12 +93,12 @@ jobs:
 
       - name: Build for x64
         run: |
-          cmake --preset=default -DVCPKG_TARGET_TRIPLET=x64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-x64 -B ${{github.workspace}}/build-x64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_ARCHITECTURES="x86_64" -DNOTEST=1
+          cmake --preset=default -DVCPKG_TARGET_TRIPLET=x64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-x64 -B ${{github.workspace}}/build-x64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_ARCHITECTURES="x86_64" -DBUILD_TESTING=OFF
           cmake --build ${{github.workspace}}/build-x64 --config Release
 
       - name: Build for arm64
         run: |
-          cmake --preset=default -DVCPKG_TARGET_TRIPLET=arm64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-arm64 -B ${{github.workspace}}/build-arm64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_ARCHITECTURES="arm64"
+          cmake --preset=default -DVCPKG_TARGET_TRIPLET=arm64-osx -DVCPKG_INSTALLED_DIR=${{github.workspace}}/vcpkg-arm64 -B ${{github.workspace}}/build-arm64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_ARCHITECTURES="arm64" -DBUILD_TESTING=OFF
           cmake --build ${{github.workspace}}/build-arm64 --config Release
 
       - name: Test  # don't release if tests are failing

.github/workflows/test_pr.yml → .github/workflows/test.yml

@@ -88,11 +88,6 @@ jobs:
           submodules: true
           ref: ${{ github.event.pull_request.head.sha }}
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-
       - name: Install minio and mcli
         run: |
           apt update && apt install -y tmux wget
@@ -137,4 +132,51 @@ jobs:
           ZARR_S3_BUCKET_NAME: ${{ env.MINIO_BUCKET }}
           ZARR_S3_ACCESS_KEY_ID: ${{ env.MINIO_ACCESS_KEY }}
           ZARR_S3_SECRET_ACCESS_KEY: ${{ env.MINIO_SECRET_KEY }}
-        run: ctest -C ${{env.BUILD_TYPE}} -L s3 --output-on-failure
+        run: ctest -C ${{env.BUILD_TYPE}} -L s3 --output-on-failure
+
+  test_python:
+    name: Test on ${{ matrix.platform }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - "ubuntu-latest"
+          - "windows-latest"
+          - "macos-latest"
+
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install vcpkg
+        run: |
+          git clone https://github.com/microsoft/vcpkg.git
+          cd vcpkg && ./bootstrap-vcpkg.sh
+          echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV
+          echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH
+          ./vcpkg integrate install
+        shell: bash
+
+      - name: Install dependencies
+        run: python -m pip install -U pip "pybind11[global]" cmake build numpy pytest
+
+      - name: Build and install Python bindings
+        run: python -m pip install .
+
+      - name: Run tests
+        run: python -m pytest -v
+

.gitignore

@@ -1,13 +1,72 @@
-.idea
-build*/
 install
-.vscode
-.cache
 CMakeSettings.json
-.vs
 TestResults
-cmake-build*
 .DS_Store
 *.zip
-_CPack_Packages/
 .PVS-Studio
+
+# IDE
+.idea
+.vscode
+.vs
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build*/
+cmake-build*/
+_CPack_Packages/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/

CMakeLists.txt

@@ -1,5 +1,6 @@
 cmake_minimum_required(VERSION 3.23)
 project(acquire-zarr)
+cmake_policy(SET CMP0057 NEW) # allows IN_LIST operator (for pybind11)
 cmake_policy(SET CMP0079 NEW) # allows use with targets in other directories
 enable_testing()
 
@@ -19,9 +20,23 @@ set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-option(NOTEST "Disable all tests" OFF)
+option(BUILD_PYTHON "Build Python bindings" OFF)
+
+if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+    include(CTest)
+endif()
 
 add_subdirectory(src)
-add_subdirectory(tests)
+if (BUILD_TESTING)
+    add_subdirectory(tests)
+else ()
+    message(STATUS "Skipping test targets")
+endif ()
+
+if (${BUILD_PYTHON})
+    add_subdirectory(python)
+else ()
+    message(STATUS "Skipping Python bindings")
+endif ()
 
 include(CPack)

MANIFEST.in

@@ -0,0 +1,10 @@
+include CMakeLists.txt
+include CMakePresets.json
+include vcpkg.json
+include vcpkg-configuration.json
+include cmake/*.cmake
+recursive-include src *
+recursive-include include *
+recursive-include python *
+include LICENSE
+include README.md

include/acquire.zarr.h

@@ -103,9 +103,9 @@ extern "C"
      * @return ZarrStatusCode_Success on success, or an error code on failure.
      */
     ZarrStatusCode ZarrStream_append(ZarrStream* stream,
-                                 const void* data,
-                                 size_t bytes_in,
-                                 size_t* bytes_out);
+                                     const void* data,
+                                     size_t bytes_in,
+                                     size_t* bytes_out);
 
 #ifdef __cplusplus
 }

pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "ninja",
+    "cmake>=3.12",
+    "pybind11[global]",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -q --color=yes"
+log_cli = true # when true, messages are printed immediately
+testpaths = [
+    "python/tests",
+]

python/CMakeLists.txt

@@ -0,0 +1,26 @@
+project(acquire-zarr-py)
+
+execute_process(COMMAND python3 -m pybind11 --cmakedir
+        RESULT_VARIABLE pybind11_NOT_FOUND
+        OUTPUT_VARIABLE pybind11_DIR
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+if (pybind11_NOT_FOUND)
+    message(FATAL_ERROR "pybind11 not found in the current environment. Please install pybind11 via pip.")
+else ()
+    LIST(APPEND CMAKE_MODULE_PATH ${pybind11_DIR})
+    cmake_path(CONVERT CMAKE_MODULE_PATH TO_CMAKE_PATH_LIST CMAKE_MODULE_PATH)
+endif ()
+
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+find_package(pybind11 REQUIRED)
+
+pybind11_add_module(acquire_zarr acquire-zarr-py.cpp)
+
+target_include_directories(acquire_zarr PRIVATE ${CMAKE_SOURCE_DIR}/include)
+target_link_libraries(acquire_zarr PRIVATE acquire-zarr)
+
+set_target_properties(acquire_zarr PROPERTIES
+        MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>"
+)