Fix missing charset_normalizer dependency #57
Workflow file for this run
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| name: Build | |
| on: | |
| push: | |
| tags: | |
| - 'v[0-9]+.[0-9]+.[0-9]+*' | |
| jobs: | |
| build-envs: | |
| name: Build Conda Environments | |
| strategy: | |
| matrix: | |
| os: [ | |
| windows-latest, | |
| ubuntu-latest, | |
| macos-latest | |
| ] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out Repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| miniconda-version: "latest" | |
| python-version: 3.10.11 | |
| - name: Create and Package Conda Environment (Darwin/Linux) | |
| if: runner.os == 'Linux' || runner.os == 'macOS' | |
| shell: bash -l {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| conda env create -f src/environment.yml --name build_env | |
| conda activate build_env | |
| conda-pack --ignore-missing-files -o env-${{ matrix.os }}.tar.gz | |
| - name: Create and Package Conda Environment (Windows) | |
| if: runner.os == 'Windows' | |
| shell: cmd /C call {0} | |
| run: >- | |
| conda config --set channel_priority strict | |
| && conda env create -f src/environment.yml --name build_env | |
| && conda activate build_env | |
| && conda-pack --ignore-missing-files -o env-${{ matrix.os }}.tar.gz | |
| - name: Upload environment archive | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.os }}-env | |
| path: env-${{ matrix.os }}.tar.gz | |
| create-rel: | |
| name: Create Release | |
| needs: build-envs | |
| runs-on: ubuntu-latest | |
| outputs: | |
| release_upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| steps: | |
| - name: Create a Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| with: | |
| # The name of the tag. This should come from the webhook payload, `github.GITHUB_REF` when a user pushes a new tag | |
| tag_name: ${{ github.ref }} | |
| # The name of the release. For example, `Release v1.0.1` | |
| release_name: Release ${{ github.ref }} | |
| # Text describing the contents of the tag. | |
| body: Release Autonomously Generated By CI on Pushed Tag | |
| # `true` to create a draft (unpublished) release, `false` to create a published one. Default: `false` | |
| draft: false # optional | |
| # `true` to identify the release as a prerelease. `false` to identify the release as a full release. Default: `false` | |
| prerelease: false # optional | |
| build-dist: | |
| name: Build Module Archive | |
| needs: create-rel | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Zip | |
| uses: montudor/action-zip@v1 | |
| - name: Zip Package Sources and Env | |
| run: | | |
| cd src | |
| mv ../LICENSE . | |
| mv ../NOTICE . | |
| zip -qq -r ../PresidioDeidentificationForOHNLPTK.zip . | |
| cd .. | |
| - name: Create Directory Structure for Release | |
| shell: bash | |
| run: | | |
| mkdir dist | |
| mkdir dist/python_modules | |
| mv ./PresidioDeidentificationForOHNLPTK.zip dist/python_modules/PresidioDeidentificationForOHNLPTK.zip | |
| mv ./resources dist/python_resources | |
| - name: Zip Package Dist for Final Release (Online/Compact) | |
| run: | | |
| cd dist | |
| zip -qq -r ../PresidioDeidentificationForOHNLPTK.zip . | |
| cd .. | |
| - name: Upload Release Asset (Online/Compact) | |
| id: upload-release-asset | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| with: | |
| upload_url: ${{ needs.create-rel.outputs.release_upload_url }} | |
| asset_path: ./PresidioDeidentificationForOHNLPTK.zip | |
| asset_name: PresidioDeidentificationForOHNLPTK.zip | |
| asset_content_type: application/zip | |
| build-dist-standalone: | |
| name: Build Module Archive (Standalone) | |
| needs: create-rel | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ | |
| windows, | |
| ubuntu, | |
| macos | |
| ] | |
| include: | |
| - os: windows | |
| dist_name: win32 | |
| - os: ubuntu | |
| dist_name: linux | |
| - os: macos | |
| dist_name: darwin | |
| env: | |
| OS_NAME: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Zip | |
| uses: montudor/action-zip@v1 | |
| - name: Download runner/ubuntu env file | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: ubuntu-latest-env | |
| - name: Download dist env file | |
| if: matrix.os != 'ubuntu' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: ${{ matrix.os }}-latest-env | |
| - name: Rename dist env files | |
| shell: bash | |
| run: | | |
| mkdir python_envs | |
| mkdir python_envs/${{ matrix.dist_name }} | |
| mv env-${{ matrix.os }}-latest.tar.gz python_envs/${{ matrix.dist_name }}/PresidioDeidentificationforOHNLPTK.tar.gz | |
| - name: Rename runner env file | |
| if: matrix.os != 'ubuntu' | |
| shell: bash | |
| run: | | |
| mkdir python_envs/linux | |
| mv env-ubuntu-latest.tar.gz python_envs/linux/PresidioDeidentificationforOHNLPTK.tar.gz | |
| - name: Zip Package Sources and Env | |
| run: | | |
| cd src | |
| zip -qq -r ../PresidioDeidentificationForOHNLPTK.zip . | |
| cd .. | |
| - name: Unpack Environment to Execute Build Script | |
| shell: bash -l {0} | |
| run: | | |
| mkdir build_env | |
| tar -xzf python_envs/linux/PresidioDeidentificationforOHNLPTK.tar.gz -C build_env | |
| source build_env/bin/activate | |
| conda-unpack | |
| python src/build.py | |
| - name: Create Directory Structure for Release | |
| shell: bash | |
| run: | | |
| mkdir dist | |
| mkdir dist/python_modules | |
| mv ./resources dist/python_resources | |
| mv ./python_envs dist/python_envs | |
| mv ./obi_deid_roberta_i2b2 ./dist/python_resources/obi_deid_roberta_i2b2 | |
| mv ./PresidioDeidentificationForOHNLPTK.zip dist/python_modules/PresidioDeidentificationForOHNLPTK.zip | |
| - name: Zip Package Dist for Final Release (Online/Compact) | |
| run: | | |
| cd dist | |
| zip -qq -r ../PresidioDeidentificationForOHNLPTK.zip . | |
| cd .. | |
| - name: Upload Release Asset | |
| id: upload-release-asset | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| with: | |
| upload_url: ${{ needs.create-rel.outputs.release_upload_url }} | |
| asset_path: ./PresidioDeidentificationForOHNLPTK.zip | |
| asset_name: PresidioDeidentificationForOHNLPTK-Standalone-${{ matrix.dist_name }}.zip | |
| asset_content_type: application/zip | |