diff --git a/.github/workflows/integration-ci.yml b/.github/workflows/integration-ci.yml new file mode 100644 index 00000000..cc7054cd --- /dev/null +++ b/.github/workflows/integration-ci.yml @@ -0,0 +1,70 @@ +name: Tutorials CI + +on: + push: + branches: + - main + pull_request: + branches: + - main + +env: + debug: 'true' + +jobs: + ingestion: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" + python-version: ["3.9"] + + steps: + # - uses: actions/checkout@v4 + - name: Download Conda YAML file + run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/main/pipeline_env.yaml + + - uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-version: latest + auto-activate-base: true + auto-update-conda: true + channels: conda-forge + channel-priority: strict + activate-environment: pipeline_env + environment-file: pipeline_env.yaml # consider moving to etc/pipeline_env.yaml + + # Note: the pinned versions in pipeline_env.yaml are not respected during the miniconda step above + - name: Pin version of pip dependencies + shell: bash -el {0} + run: pip install --force-reinstall -v \ + boto3==1.34.34 \ + botocore==1.34.34 \ + flax==0.8.0 \ + fonttools==4.47.2 \ + jax==0.4.23 \ + jaxlib==0.4.23 \ + numpy==1.22.4 \ + orbax-checkpoint==0.5.2 \ + pytorch-lightning==2.1.4 + + - name: Conda info + if: env.debug == 'true' + shell: bash -el {0} + run: conda info + + - name: Conda list + if: env.debug == 'true' + shell: pwsh + run: conda list + + # Note: all three files are renamed during the download to trim the "subsample_" prefix + - name: Preparing the data + run: | + mkdir -p teaseq/integration && cd teaseq/integration + curl -L -o teaseq.h5mu https://figshare.com/ndownloader/files/44471927 + + - name: File tree + if: env.debug == 'true' + run: tree