New callback to save a list of iterates every set number of iterations #1305
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: build | |
| on: | |
| release: | |
| types: [published] | |
| push: | |
| branches: [master] | |
| tags: ['**'] | |
| paths-ignore: | |
| - 'CHANGELOG.md' | |
| - 'CITATION.cff' | |
| - 'LICENSE' | |
| - 'scripts/**' | |
| - 'NOTICE.txt' | |
| - 'README.md' | |
| pull_request: | |
| branches: [master] | |
| paths-ignore: | |
| - 'CHANGELOG.md' | |
| - 'CITATION.cff' | |
| - 'LICENSE' | |
| - 'scripts/**' | |
| - 'NOTICE.txt' | |
| - 'README.md' | |
| jobs: | |
| test-cuda: | |
| defaults: {run: {shell: 'bash -el {0}'}} | |
| runs-on: [self-hosted, python, cuda] | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| numpy-version: [1.25] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: {fetch-depth: 0, submodules: recursive} | |
| - id: reqs | |
| name: set requirements | |
| run: | | |
| envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}" | |
| echo "envname=$envname" >> $GITHUB_OUTPUT | |
| sed -ri -e 's/^(name: ).*/\1$envname/' -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' scripts/requirements-test.yml | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: scripts/requirements-test.yml | |
| activate-environment: ${{ steps.reqs.outputs.envname }} | |
| run-post: false | |
| - id: build | |
| name: build | |
| run: | | |
| conda activate "${{ steps.reqs.outputs.envname }}" | |
| cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" | |
| cmake --build ./build --target install | |
| - name: test | |
| run: | | |
| conda activate "${{ steps.reqs.outputs.envname }}" | |
| TESTS_FORCE_GPU=1 python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test | |
| - if: always() | |
| name: Post Run conda-incubator/setup-miniconda@v3 | |
| shell: bash | |
| run: | | |
| sed -i '/${{ steps.reqs.outputs.envname }}/d' ~/.profile | |
| source ~/.profile | |
| conda env remove -n "${{ steps.reqs.outputs.envname }}" | |
| test: | |
| defaults: {run: {shell: 'bash -el {0}'}} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - python-version: '3.10' | |
| numpy-version: 1.23 | |
| - python-version: 3.12 | |
| numpy-version: 1.26 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: {fetch-depth: 0, submodules: recursive} | |
| - name: set requirements | |
| run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: scripts/requirements-test.yml | |
| activate-environment: cil_dev | |
| - name: build | |
| run: | | |
| cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" | |
| cmake --build ./build --target install | |
| - name: test | |
| run: python -m unittest discover -v ./Wrappers/Python/test | |
| conda-matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| python-version: ${{ steps.matrix.outputs.python-version }} | |
| numpy-version: ${{ steps.matrix.outputs.numpy-version }} | |
| steps: | |
| - id: matrix | |
| run: | | |
| if ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }}; then | |
| echo "python-version=['3.10', 3.11]" >> $GITHUB_OUTPUT | |
| echo "numpy-version=[1.23, 1.24, 1.25, 1.26]" >> $GITHUB_OUTPUT | |
| else | |
| echo "python-version=['3.10']" >> $GITHUB_OUTPUT | |
| echo "numpy-version=[1.23]" >> $GITHUB_OUTPUT | |
| fi | |
| conda: | |
| defaults: {run: {shell: 'bash -el {0}'}} | |
| runs-on: ubuntu-latest | |
| needs: conda-matrix | |
| strategy: | |
| matrix: | |
| python-version: ${{ fromJson(needs.conda-matrix.outputs.python-version) }} | |
| numpy-version: ${{ fromJson(needs.conda-matrix.outputs.numpy-version) }} | |
| include: | |
| - python-version: 3.12 | |
| numpy-version: 1.26 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: conda-forge | |
| - name: conda build & test | |
| working-directory: recipe | |
| run: | | |
| conda install boa | |
| conda mambabuild . -c conda-forge -c https://tomography.stfc.ac.uk/conda --override-channels --python=${{ matrix.python-version }} --numpy=${{ matrix.numpy-version }} --output-folder . | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: cil-package-py${{ matrix.python-version }}-np${{ matrix.numpy-version }} | |
| path: recipe/linux-64/cil* | |
| - name: anaconda upload -c ccpi | |
| if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') | |
| run: | | |
| conda install anaconda-client | |
| anaconda -v -t ${{ secrets.CCPI_CONDA_TOKEN }} upload --force --label ${{ startsWith(github.ref, 'refs/tags') && 'main' || 'dev' }} recipe/linux-64/cil* | |
| - name: conda upload -c tomography.stfc.ac.uk/conda | |
| if: startsWith(github.ref, 'refs/tags') | |
| run: | | |
| echo '${{ secrets.STFC_SSH_KEY }}' > ./key | |
| chmod 600 ./key | |
| rsync -e 'ssh -o StrictHostKeyChecking=no -i ./key' -P recipe/linux-64/cil* \ | |
| '${{ secrets.STFC_SSH_HOST }}:${{ secrets.STFC_SSH_CONDA_DIR }}/linux-64/' | |
| conda-reindex: | |
| if: startsWith(github.ref, 'refs/tags') | |
| needs: conda | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: conda index tomography.stfc.ac.uk/conda | |
| run: | | |
| echo '${{ secrets.STFC_SSH_KEY }}' > ./key | |
| chmod 600 ./key | |
| ssh -o StrictHostKeyChecking=no -i ./key ${{ secrets.STFC_SSH_HOST }} \ | |
| 'conda index --bz2 --zst --run-exports --channeldata --rss -n ccpi ${{ secrets.STFC_SSH_CONDA_DIR }}' | |
| docs: | |
| defaults: {run: {shell: 'bash -el {0}', working-directory: docs}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: {python-version: 3.11} | |
| - uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.2' | |
| bundler-cache: true | |
| cache-version: 0 | |
| - name: install dependencies | |
| run: | | |
| conda install -c conda-forge -yq conda-merge | |
| conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml | |
| conda env update -n test | |
| conda list | |
| - name: build cil | |
| working-directory: . | |
| run: | | |
| cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" | |
| cmake --build ./build --target install | |
| - name: checkout docs | |
| uses: actions/checkout@v4 | |
| with: | |
| path: docs/build | |
| ref: gh-pages | |
| - id: pages | |
| uses: actions/configure-pages@v5 | |
| - name: update web pages (jekyll) | |
| run: make JEKYLLOPTS="--baseurl ${{ steps.pages.outputs.base_path }}" web-deps web | |
| env: {JEKYLL_ENV: production} | |
| - name: update docs pages (sphinx) | |
| run: | | |
| docs_dir="${{ github.ref_name }}" | |
| docs_dir="${docs_dir//\//_}" | |
| if test "$docs_dir" = master; then docs_dir=nightly; fi | |
| make BUILDSUBDIR="$docs_dir" dirhtml | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: DocumentationHTML | |
| path: docs/build | |
| - name: Push changes | |
| if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') | |
| uses: casperdcl/push-dir@v1 | |
| with: | |
| message: Update documentation | |
| branch: gh-pages | |
| dir: docs/build | |
| nojekyll: true | |
| docker: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA | |
| - uses: jlumbroso/[email protected] | |
| with: | |
| docker-images: false | |
| large-packages: false | |
| - uses: docker/setup-buildx-action@v3 | |
| - uses: docker/metadata-action@v5 | |
| id: meta | |
| with: | |
| images: ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=ref,event=branch | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| labels: | | |
| org.opencontainers.image.licenses=Apache-2.0 AND BSD-3-Clause AND GPL-3.0 | |
| - uses: docker/login-action@v3 | |
| if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: docker/build-push-action@v5 | |
| with: | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| context: . | |
| load: true | |
| tags: tomographicimaging/cil:test | |
| - name: test | |
| run: > | |
| docker run --rm -v .:/CIL tomographicimaging/cil:test /bin/bash -c | |
| 'python -m unittest discover -v /CIL/Wrappers/Python/test' | |
| - uses: docker/build-push-action@v5 | |
| with: | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| context: . | |
| push: ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| pass: | |
| needs: [test-cuda, test, conda, docs, docker] | |
| runs-on: ubuntu-latest | |
| steps: [{run: echo success}] |