py4dgeo 0.5.0__tar.gz → 0.6.0__tar.gz

py4dgeo-0.6.0/.dockerignore

@@ -0,0 +1,181 @@
+.git
+build
+Dockerfile
+env
+
+# scikit-build editable directory
+_skbuild
+
+# VSCode Configuration
+.vscode
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

py4dgeo-0.6.0/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

py4dgeo-0.6.0/.github/workflows/ci.yml

@@ -0,0 +1,204 @@
+name: CI
+
+on:
+  # We run CI on pushes to the main branch
+  push:
+    branches:
+      - main
+  # and on all pull requests to the main branch
+  pull_request:
+    branches:
+      - main
+  # as well as upon manual triggers through the 'Actions' tab of the Github UI
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    name: Testing on ${{matrix.os}} Py${{matrix.python-version}}- OpenMP ${{matrix.openmp}}
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, windows-2022]
+        python-version: ["3.8", "3.12"]
+        openmp: ['ON', 'OFF']
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install OpenMP
+      if: runner.os == 'macOS' && matrix.openmp == 'ON'
+      run: brew install libomp
+
+    - name: make build directory
+      run: cmake -E make_directory ${{runner.workspace}}/build
+
+    - name: configure cmake
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCS=OFF -DBUILD_BENCHMARKS=ON -DPY4DGEO_WITH_OPENMP=${{matrix.openmp}}
+
+    - name: build
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake --build .
+
+    - name: Install Python package and development requirements
+      run: |
+        python -m pip install -r requirements-dev.txt
+        python -m pip install -v .
+
+    - name: Install py4dgeo test data
+      shell: bash
+      run: |
+        mkdir -p $GITHUB_WORKSPACE/tests/data
+        copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
+
+    - name: run tests
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: ctest --output-on-failure -C Debug
+
+    - name: Run Python tests
+      run: |
+        python -m pytest --nbval
+
+  coverage-test:
+    name: Coverage Testing
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: Install LCov
+      run: |
+        sudo apt-get install -y lcov
+
+    - name: Install Python package and development requirements
+      run: |
+        python -m pip install -r requirements-dev.txt
+        python -m pip install -v --editable .
+
+    - name: Install py4dgeo test data
+      shell: bash
+      run: |
+        mkdir -p $GITHUB_WORKSPACE/tests/data
+        copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
+
+    - name: make build directory
+      run: cmake -E make_directory ${{runner.workspace}}/build
+
+    - name: configure cmake
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="--coverage" -DBUILD_DOCS=OFF
+
+    - name: build
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake --build .
+
+    - name: run tests
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: ctest -C Debug
+
+    - name: collect coverage report
+      shell: bash
+      working-directory: ${{runner.workspace}}
+      run: |
+        lcov --directory ./build --capture --output-file coverage.info
+        lcov_cobertura coverage.info -o coverage2.xml
+
+    - name: Run coverage tests
+      run: |
+        python -m pytest --cov=src --cov-report=xml
+
+    - name: Upload coverage to Codecov.io
+      working-directory: ${{runner.workspace}}
+      run: |
+        curl --connect-timeout 10 --retry 5 -Os https://uploader.codecov.io/latest/linux/codecov
+        chmod +x codecov
+        ./codecov -f py4dgeo/coverage.xml -F python
+        ./codecov -f coverage2.xml -F cxx
+
+  address-sanitizer:
+    name: Address sanitizer run
+    runs-on: ubuntu-20.04
+    env:
+      ASAN_OPTIONS: "detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1"
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install Python development requirements
+      run: |
+        python -m pip install -r requirements-dev.txt
+        python -m pip install -v .
+
+    - name: Install py4dgeo test data
+      shell: bash
+      run: |
+        mkdir -p $GITHUB_WORKSPACE/tests/data
+        copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
+
+    - name: make build directory
+      run: cmake -E make_directory ${{runner.workspace}}/build
+
+    - name: configure cmake
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=address -fsanitize-address-use-after-scope -fno-omit-frame-pointer" -DCMAKE_EXE_LINKER_FLAGS="-fsanitize=address -fsanitize-address-use-after-scope -fno-omit-frame-pointer" -DBUILD_DOCS=OFF
+
+    - name: build
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: cmake --build .
+
+    - name: run c++ tests
+      shell: bash
+      working-directory: ${{runner.workspace}}/build
+      run: ctest --rerun-failed --output-on-failure -C Debug
+
+    - name: run python tests
+      shell: bash
+      working-directory: ${{runner.workspace}}/py4dgeo
+      # for LD_PRELOAD see https://github.com/google/sanitizers/issues/934#issuecomment-649516500
+      run: |
+        mv ../build/_py4dgeo.*.so src/py4dgeo/.
+        echo "leak:/usr/bin/bash" > supp.txt
+        echo "leak:_PyObject_New" >> supp.txt
+        echo "leak:_PyObject_GC" >> supp.txt
+        echo "leak:insert_to_emptydict" >> supp.txt
+        echo "leak:new_keys_object" >> supp.txt
+        echo "leak:PyDict_Copy" >> supp.txt
+        echo "leak:PyUnicode_New" >> supp.txt
+        echo "leak:pyo3::types::function::PyCFunction::internal_new_from_pointers" >> supp.txt
+        echo "leak:pyo3::types::function::PyCFunction::internal_new::" >> supp.txt
+        # hack to prevent external libs from dlclosing libraries,
+        # which otherwise results in <module not found> LSAN leaks that cannot be suppressed
+        # https://github.com/google/sanitizers/issues/89#issuecomment-406316683
+        echo "#include <stdio.h>" > dlclose.c
+        echo "int dlclose(void *handle) { return 0; }" >> dlclose.c
+        clang -shared dlclose.c -o libdlclose.so
+        LSAN_OPTIONS=suppressions="$(pwd)/supp.txt" PYTHONPATH=src LD_PRELOAD="$(gcc -print-file-name=libasan.so) /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $(pwd)/libdlclose.so" PYTHONMALLOC=malloc pytest -s

py4dgeo-0.6.0/.github/workflows/pypi.yml

@@ -0,0 +1,134 @@
+name: Build Wheels + PyPI deploy
+
+on:
+  workflow_dispatch:
+    inputs:
+      deploy_to_testpypi:
+        description: "Whether the build should be deployed to test.pypi.org"
+        required: true
+        default: "false"
+      deploy_to_pypi:
+        description: "Whether the build should be deployed to pypi.org"
+        required: true
+        default: "true"
+
+jobs:
+  build-wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-20.04
+            arch: "x86_64"
+          - os: windows-2022
+            arch: "AMD64"
+          - os: macos-11
+            arch: "x86_64"
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Build wheels (arch=${{ matrix.arch }})
+      uses: pypa/cibuildwheel@v2.16
+      env:
+        CIBW_ARCHS: "${{ matrix.arch }}"
+
+    - uses: actions/upload-artifact@v3
+      with:
+        path: ./wheelhouse/*.whl
+
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: artifact
+          path: dist/*.tar.gz
+
+  test-sdist:
+    name: Test source distribution on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: [build-sdist]
+    strategy:
+      matrix:
+        os:
+          - ubuntu-20.04
+          - windows-2022
+          - macos-11
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.9'
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Install OpenMP
+        if: runner.os == 'macOS'
+        run: brew install libomp
+
+      - name: Install from SDist
+        shell: bash
+        run:
+          python -m pip install dist/*.tar.gz
+
+      - name: Install test requirements
+        run:
+          python -m pip install -r requirements-dev.txt
+
+      - name: Run test suite
+        run:
+          python -m pytest
+
+  upload_testpypi:
+    needs: [build-sdist, test-sdist, build-wheels]
+    runs-on: ubuntu-20.04
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event.inputs.deploy_to_testpypi == 'true'
+        with:
+          repository_url: https://test.pypi.org/legacy/
+
+  upload_pypi:
+    needs: [build-sdist, build-wheels, upload_testpypi]
+    runs-on: ubuntu-20.04
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event.inputs.deploy_to_pypi == 'true'

py4dgeo-0.6.0/.gitignore

@@ -0,0 +1,179 @@
+# Ignore our test directory, it is automatically populated
+tests/data
+
+# scikit-build editable directory
+_skbuild
+
+# VSCode Configuration
+.vscode
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

py4dgeo-0.6.0/.gitmodules

@@ -0,0 +1,15 @@
+[submodule "ext/Catch2"]
+	path = ext/Catch2
+	url = https://github.com/catchorg/Catch2.git
+[submodule "ext/pybind11"]
+	path = ext/pybind11
+	url = https://github.com/pybind/pybind11.git
+[submodule "ext/eigen"]
+	path = ext/eigen
+	url = https://gitlab.com/libeigen/eigen.git
+[submodule "ext/nanoflann"]
+	path = ext/nanoflann
+	url = https://github.com/jlblancoc/nanoflann.git
+[submodule "ext/benchmark"]
+	path = ext/benchmark
+	url = https://github.com/google/benchmark