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Update to 0.2.0 (#4)
* Add build workflow * Fix build workflow * Fix build script * Fix build script * Fix build script * Add `libglu1-mesa-dev` dependency for build script * Add `libglew-dev` dependency to build script * Add `-Dpybind11_DIR=` * Set `$CONDA_PREFIX` environment variable * Fix build workflow * Remove doxygen from build script * Fix bug in setup.py * Fix build script * Disable tests * Fix bug in setup.py * Use `sudo` for `setup.py install` in build script * Fix build script * Build wheel and upload artifact * Reduce artifact size * Fix artifact * Exclude debug build from artifact * Clean up artifact * Fix workflow * Add Docker build workflow * Add `pyyaml` as build dependency to build script * Update build instructions * Fix build workflow * Fix Docker workflow * Fix workflow * Add debug code to workflow * Fix Dockerfile * Squashed commit of the following: commit 750d7f8 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:32:42 2023 +0100 Fix Dockerfile commit cc5fc3f Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:28:01 2023 +0100 Fix Dockerfile commit 0006721 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:24:11 2023 +0100 Fix Dockerfile commit fba55bb Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:15:22 2023 +0100 Fix Dockerfile commit 8891b25 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:10:23 2023 +0100 Fix Dockerfile commit d282592 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 10:03:30 2023 +0100 Fix Dockerfile commit 2a4edd0 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:59:18 2023 +0100 Fix Dockerfile commit dc78de0 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:53:39 2023 +0100 Fix Dockerfile commit 7d97369 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:46:30 2023 +0100 Add debug info to Dockerfile commit e789036 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:40:22 2023 +0100 Fix Dockerfile commit dc48cc7 Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:27:00 2023 +0100 Add debug code commit be4c97e Author: Leonid Kostrykin <[email protected]> Date: Wed Dec 13 09:22:19 2023 +0100 Fix Dockerfile * Add examples to Dockerfile * Update README.md * Fix Dockerfile * Fix Dockerfile * Fix Dockerfile * Fix Dockerfile * Fix Dockerfile * Fix Dockerfile * Update README.md * Fix `docker run` instruction * Refactor for 0.2.0 (#1) * Add environment.yml * Update CMakeLists.txt * Clean up build script * Add `libopengl-devel` dependency * Fix build * Clean up tests, fix linking * Clean up `egl.Context` binding * Drop `carna.py` * Update settings.json * Clean up `base.Spatial` and `base.Node` * Implement `SpatialView` and add memory tests * Add `Node.test__attach_child__circular` * Add `Node.test__attach_child__nonfree` * Add `Node.test__movable` * Add `Node.test__tag` * Add `Node.test__localTransform` * Add `Node.test__detach_from_parent` * Add `CARNA_EXRA_CHECKS` environment variable * Add `Camera` tests * Add `Geometry` tests (incomplete) * Add `Geometry.test__geometry_type` and `Geometry.test__features_count` * Clean up code * Add `Material` and tests * Fix typo * Add `Geometry.put_feature` and `Geometry.remove_feature` * Add `Geometry.clear_features` * Add `Geometry.has_feature` * Clean up code * Add `ContextView` * Pin `pybind11 <3` * Refactor structure * Add `Surface` (no tests yet) * Add `FrameRenderer` and tests * Clean up test/test_egl.py * Add `configure_carna_log` * Add `math` * Add `MeshFactory` * Add `OpaqueRenderingStage` * Add `CarnaRenderingTestCase` * Make build directory readonly in VSCode * Fix `Surface::end` * Fix tests * Add `helpers.FrameRendererHelper` * Add `FrameRenderer.append_stage` * Remove extra checks (not working properly across submodules) * Add convenience layer * Add `renderer` convenience function * Extend spatial convenience functions * Add RTD setup * Add sphinx build to build script * Fix doc building * Update docs * Make `carna.renderer` a class instead of a function * Update docs * Update integration test * Add `frustum` method to convenience renderer * Update docs * Update docs * Update docs * Rename `configure_carna_log` to `logging` * Add `VolumeGridHelperBase` * Add `VolumeGridHelper_IntensityVolumeUInt16` * Add `VolumeGridHelper_IntensityVolumeUInt16.intensities_role` * Add `VolumeGridHelper_IntensityVolumeUInt16_NormalMap3DInt8` * Add `VolumeGridHelper_IntensityVolumeUInt8` * Add `VolumeGridHelper_IntensityVolumeUInt8_NormalMap3DInt8` * Add `VolumeGridHelper_*.create_node` * Add `MaskRenderingStage` (test fail) * Add failing `EGLContext` test case * Fix bug in `EGLContext` d'tor (tests pass) * Add `Color` and tests * Add `MaskRenderingStage` attributes, methods, and tests * Add docs * Add `volume` convenience function * Add debug build mode * Fix bug with lazy data loading behaviour of `VolumeGridHelper` https://kostrykin.github.io/Carna/html/classCarna_1_1base_1_1ManagedTexture3D.html#a37f03f311b2d1bd87ccb12f545d70f04 * Update docs * Update docs * Add logo to docs * Add `renderer.animation` * Use `solid` shaders instead of `unshaded` for example materials * Fix `animation.render` to produce smooth animations * Fix docs * Add `MIPStage` and `MIPLayer` * Fix bug in `EGLContext` (enable resource sharing) * Add `CuttingPlanesStage` * Add script to install Carna development version * Fix install_carna_dev.bash * Employ `.carna-dev` in CMakeLists.txt * Add `ColorMapView` * Fix install_carna_dev.bash * Add `MIPStage.color_map` * Update test results * Add `color_map_helper` and fix tests * Update build instructions * Add `carna.base.AssertionFailure` * Migrate to `Carna::base::MeshRenderingMixin` * Rename `Dimensions` to `Extent` and `millimeters` to `units` * Migrate build process from Carna to LibCarna * Migrate LICENSE to MIT * Migrate code from Carna to CarnaLib * Add logo * Add example notebook * Clean up convenience layer * Add `_transform` to convenience layer * Replace `np.bool` by `bool` * Add support for h264 rendering in `imshow` * Always build docs from scratch This is to avoid errors with nbsphinx. * Add examples/cthead.ipynb * Import colormaps from matplotlib * Add `DVRStage` * Add DVR to cells.ipynb * Update example notebooks * Rename `libcarna.animation` to `libcarna.animate` * Update example notebooks * Simplify `animate` syntax * Update example notebooks * Clean up `_expand_module` * Update example notebooks * Add material scheme validation * Update example notebooks * Add `dvr.replicate` * Add `mip.replicate` * Update example notebooks * Add `transform_into_voxels_from` method for volumes * Update example notebooks * Fix HUV normalization * Add `drr` * Update example notebooks * Update docs and example notebooks * Add `normalize_hounsfield_units` function * Add more debugging checks to `EGLContext` * Rename `mesh_factory` to `meshes` * Add `camera.proj` and `camera.frustum` methods * Refactor `_transform` and `_spatial_mixin` * Update * Update example notebooks * Add `libcarna.data` * Add `libcarna.data.toy` * Add `cutting_planes` * Add `cutting_planes` and `mask_renderer` * Rename `render` to `render_stage` * Fix `base.MeshFactory` * Clean up API, docs, and examples * Migrate `cutting_planes` to use color maps instead of windowing * Add `.normalized` and `.raw` convenience methods for `volume` geometries * Add fundamental colorbars * Refactor `colormap_helper` * Add colorbar labels, update example notebooks * Update example notebooks * Add spatial annotations example * Fix bugs, add segmentation example * Update README.md and example notebooks * Add `material.line_width` * Add track visualization example * Add `mesh` and `material` arguments to `geometry` function * Adapt to newest upstream changes * Add keyword aliases * Add more aliases and update docs * Update CI to build wheel * Add testing to CI * Update requirements * Update build workflows * Fix .github/workflows/build_all.yml * Fix .github/workflows/build_all.yml * Fix .github/workflows/build_all.yml * Fix .github/workflows/build.yml * Add example notebooks to test CI, fix triggers * Update README.md * Update environment.yml * Add `workflow_dispatch` trigger * Update build.yml * Update build.yml * Update build.yml * Update build.yml * Update build.yml * Update build.yml * Update build_all.yml * Update CI * Update CI * Update CI * Update CI * Update CI * Update CI * Update CI, update environment.yml * Update CI * Fix setup.py * Remove dangling files * Add dependencies to setup.py * Update CI * Update CI * Migrate to unity build * Update CI * Update CI * Update CI * Update CI * Update CI * Update CI * Remove libcarna from setup.py dependencies (not a Python dependency) * Fix dependencies * Update CI * Add test/__init__.py * Fix Python<3.12 compatibility * Update CI * Update CI * Update CI * Update CI * Fix compatibility with Python<3.11 * Debug * Add `LibCarna::egl::EGLContext::Details::selectDisplay` * Debug * Debug * Add `LIBCARNA_PYTHON_LOGGING` environment variable * Debug * Update CI * Install `libegl` via conda instead of apt * Add `typing_extensions` as dependency in setup.py * Update CI * Update CI * Update CI * Update CI * Remove support for Python 3.9 * Debug * Debug * Debug * Debug, add `EGLContext.vendor` and `EGLContext.renderer` * Update image comparison methods * Update image comparison methods * Update image comparison methods * Add vendor-specific expected test outputs * Employ vendor-specific expected test outputs * Remove debug output * Install missing dependencies * Add summary of notebook changes * Fix CI * Install ffmpeg * Remove notebooks from CI (taking too long) * Add more keyword aliases * Refactor `_spatial_mixin` rotation/translation/scaling methods * Update README.md * Remove MANIFEST.in * Update .readthedocs.yaml * Update .readthedocs.yaml * Update .readthedocs.yaml * Update RTD integration (#2) * Add `LIBCARNA_PYTHON_NBSPHINX_EXECUTE` environment variable * Add docs building for testing to CI * Update RTD integration, remove doc building from CI * Update docs/conf.py * Update .readthedocs.yaml * Update .readthedocs.yaml * Update .readthedocs.yaml * Update README.md * Update README.md * Update README.md * Update README.md * Migrate build system to `python-build` (#3) * Migrate to `python-build` * Clean-up setup.py.in * Fix linux_build.bash * Update CMakeLists.txt * Fix linux_build.bash * Fix linux_build.bash * Update build * Update tests * Fix linux_build.bash * Update CMake files * Update CI and RTD integration * Update build.yml * Rename `LIBCARNA_PYTHON_BUILD_TEST` to `LIBCARNA_PYTHON_BUILD_TESTS` * Update README.md * Update docs
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‎.github/workflows/build.yml‎

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name: Build and Test
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on:
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workflow_call:
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inputs:
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python-version:
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required: true
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type: string
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jobs:
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build:
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name: Build
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runs-on: ubuntu-latest
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steps:
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- name: Git checkout
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uses: actions/checkout@v4
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniconda-version: latest
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auto-update-conda: true
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- name: Patch required Python version
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run: |
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sed -i "s|python .\+|python ==${{ inputs.python-version }}|g" environment.yml
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cat environment.yml
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- name: Create and validate conda environment
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shell: bash
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run: |
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conda env create -f environment.yml --prefix ./.env
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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python -V
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python -c "import sys; v = sys.version_info; assert f'{v.major}.{v.minor}' == '${{ inputs.python-version }}'"
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- name: Extract libcarna version
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id: meta
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shell: bash
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run: |
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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export libcarna_version=$(conda list --json |jq -rj '[ .[] | select( .name == "libcarna" ) ][0].version')
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echo "libcarna_version=$libcarna_version" >> "$GITHUB_OUTPUT"
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- name: Build wheel
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shell: bash
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run: ./linux_build.bash
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- name: Upload wheel
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uses: actions/upload-artifact@v4
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with:
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name: dist-${{ inputs.python-version }}
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path: build/dist/libcarna_python-*.whl
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outputs:
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libcarna_version: ${{ steps.meta.outputs.libcarna_version }}
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test:
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needs: build
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name: Test
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runs-on: ubuntu-latest
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steps:
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- name: Git checkout
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uses: actions/checkout@v4
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- name: Install dependencies
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run: |
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sudo apt-get update -y -qq
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sudo apt-get install -y -qq libegl1
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- name: Download artifact
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uses: actions/download-artifact@v4
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with:
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name: dist-${{ inputs.python-version }}
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniconda-version: latest
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auto-update-conda: true
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- name: Create and validate conda environment
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shell: bash
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run: |
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conda create --prefix ./.env -c conda-forge -c bioconda \
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python==${{ inputs.python-version }} \
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libcarna==${{ needs.build.outputs.libcarna_version }} \
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pip
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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python -V
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python -c "import sys; v = sys.version_info; assert f'{v.major}.{v.minor}' == '${{ inputs.python-version }}'"
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- name: Install wheel
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run: |
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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pip install libcarna_python-*.whl
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- name: Test installation
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run: |
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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python -c "import libcarna; assert libcarna.libcarna_version == '${{ needs.build.outputs.libcarna_version }}'"
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- name: Install dependencies for tests and examples
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run: |
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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pip install -r test/requirements.txt
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pip install -r docs/requirements.txt
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- name: Run tests
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run: |
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eval "$(conda shell.bash hook)"
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conda activate ./.env
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python -m unittest -vv
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env:
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LIBCARNA_PYTHON_LOGGING: true
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- name: Upload failed test output
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uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: test-output-${{ inputs.python-version }}
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path: |
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test/test/results/actual

‎.github/workflows/build_all.yml‎

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name: Build and Test
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on:
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workflow_dispatch:
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push:
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branches: [ 'master', 'develop' ]
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paths-ignore:
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- 'docs/**'
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- '.git*'
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- 'LICENSE'
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- 'LICENSE-*'
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- '**/*.md'
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- '.readthedocs.yaml'
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- '.vscode/**'
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- 'install_libcarna_dev.bash'
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- 'linux_build.bash'
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pull_request:
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branches-ignore: [ 'master' ]
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jobs:
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build_and_test:
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name: Build and Test ${{ matrix.python-version }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.10', '3.11', '3.12']
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uses: ./.github/workflows/build.yml
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secrets: inherit
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with:
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python-version: ${{ matrix.python-version }}

‎.gitignore‎

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/.env
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/condaenv.*
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/build
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/docs/build
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/dist
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/CarnaPy.egg-info
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/misc/conda-recipe/carnapy
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/LibCarna_Python.egg-info
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/.libcarna-dev
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/test/results/actual
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.ipynb_checkpoints
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*.swp
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*.pyc
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*.DS_Store

‎.readthedocs.yaml‎

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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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version: 2
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# Sphinx setup
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sphinx:
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fail_on_warning: true
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configuration: docs/conf.py
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# Install build dependencies
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conda:
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environment: environment.yml
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# Specify the build process
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build:
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os: ubuntu-24.04
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tools:
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python: "miniconda-latest"
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jobs:
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install:
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- bash ./linux_build.bash
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- pip install build/dist/libcarna_python-*.whl
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pre_build:
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- pip install -r docs/requirements.txt
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build:
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html:
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- LIBCARNA_PYTHON_NBSPHINX_EXECUTE=never sphinx-build -M html docs $READTHEDOCS_OUTPUT

‎.vscode/settings.json‎

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{
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"python.analysis.extraPaths": [
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"./build/make_release"
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],
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"search.exclude": {
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"docs/examples": true,
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"docs/build": true
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},
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"files.readonlyInclude": {
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"build/**": true,
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},
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"[git-commit]": {
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"editor.rulers": [50]
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},
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"editor.rulers": [
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119
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],
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"files.associations": {
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"any": "cpp",
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"array": "cpp",
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"atomic": "cpp",
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"barrier": "cpp",
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"bit": "cpp",
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"bitset": "cpp",
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"cctype": "cpp",
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"cfenv": "cpp",
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"charconv": "cpp",
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"chrono": "cpp",
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"cinttypes": "cpp",
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"clocale": "cpp",
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"cmath": "cpp",
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"codecvt": "cpp",
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"compare": "cpp",
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"complex": "cpp",
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"concepts": "cpp",
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"csetjmp": "cpp",
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"csignal": "cpp",
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"cstdarg": "cpp",
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"cstdint": "cpp",
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"cstdio": "cpp",
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"cstdlib": "cpp",
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"cstring": "cpp",
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"ctime": "cpp",
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"cuchar": "cpp",
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"cwchar": "cpp",
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"cwctype": "cpp",
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"list": "cpp",
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"iosfwd": "cpp",
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"shared_mutex": "cpp",
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"*.py.in": "python"
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}
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}

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