add multiprocessing #247
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: CI | |
| on: | |
| push: | |
| pull_request: | |
| # branches: | |
| # - main | |
| jobs: | |
| format: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| lint: | |
| name: Lint with flake8 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install flake8 | |
| run: pip install flake8 flake8-bugbear | |
| - name: Lint with flake8 | |
| run: flake8 src | |
| # legacy testing of t-test | |
| run-tutorial-ttest: | |
| name: Run - random_small - t-test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: pip install . | |
| - name: Prepare tutorial data | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=encode_data --cfg job | |
| move-dl data=random_small task=encode_data | |
| # - name: Identify associations - t-test | |
| # at least 4 refits needed for t-test | |
| - name: Identify associations - t-test | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__id_assoc_ttest --cfg job | |
| move-dl data=random_small task=random_small__id_assoc_ttest task.training_loop.num_epochs=30 task.num_refits=4 | |
| # categorical dataset pertubation - single and multiprocessed | |
| run-tutorial-cat-pert-single: | |
| name: Run - random_small - singleprocess | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: pip install . | |
| - name: Prepare tutorial data | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=encode_data --cfg job | |
| move-dl data=random_small task=encode_data | |
| - name: Train model and analyze latent space | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__latent --cfg job | |
| move-dl data=random_small task=random_small__latent task.training_loop.num_epochs=100 | |
| - name: Identify associations - bayes factors | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__id_assoc_bayes --cfg job | |
| move-dl data=random_small task=random_small__id_assoc_bayes task.training_loop.num_epochs=100 task.num_refits=2 | |
| - name: Identify associations - bayes factors - w/o training | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__id_assoc_bayes --cfg job | |
| move-dl data=random_small task=random_small__id_assoc_bayes task.training_loop.num_epochs=100 task.num_refits=2 | |
| run-tutorial-cat-pert-multi: | |
| name: Run - random_small - multiprocess | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: pip install . | |
| - name: Prepare tutorial data | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=encode_data --cfg job | |
| move-dl data=random_small task=encode_data | |
| - name: Train model and analyze latent space - multiprocess | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__latent --cfg job | |
| move-dl data=random_small task=random_small__latent task.training_loop.num_epochs=100 task.multiprocess=true | |
| - name: Identify associations - bayes factors - multiprocess | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__id_assoc_bayes --cfg job | |
| move-dl data=random_small task=random_small__id_assoc_bayes task.training_loop.num_epochs=100 task.num_refits=2 task.multiprocess=true | |
| - name: Identify associations - bayes factors - multiprocess w/o training | |
| run: | | |
| cd tutorial | |
| move-dl data=random_small task=random_small__id_assoc_bayes --cfg job | |
| move-dl data=random_small task=random_small__id_assoc_bayes task.training_loop.num_epochs=100 task.num_refits=2 task.multiprocess=true | |
| # continous dataset perturbation - single and multiprocessed | |
| run-tutorial-cont-pert-multi: | |
| name: Run - random_continuous - multiprocess | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: pip install . | |
| - name: Prepare tutorial data | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=encode_data --cfg job | |
| move-dl data=random_continuous task=encode_data | |
| - name: Train model and analyze latent space - multiprocess | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__latent task.multiprocess=true --cfg job | |
| move-dl data=random_continuous task=random_continuous__latent task.multiprocess=true | |
| - name: Identify associations - bayes factors - multiprocess | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.multiprocess=true --cfg job | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.num_refits=1 task.multiprocess=true | |
| - name: Identify associations - bayes factors - multiprocess w/o training | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.multiprocess=true --cfg job | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.num_refits=1 task.multiprocess=true | |
| run-tutorial-cont-pert-single: | |
| name: Run - random_continuous - singleprocess | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: pip install . | |
| - name: Prepare tutorial data | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=encode_data | |
| - name: Train model and analyze latent space | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__latent --cfg job | |
| move-dl data=random_continuous task=random_continuous__latent | |
| - name: Identify associations - bayes factors | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes --cfg job | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.num_refits=1 | |
| - name: Identify associations - bayes factors - w/o training (repeat) | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes --cfg job | |
| move-dl data=random_continuous task=random_continuous__id_assoc_bayes task.num_refits=1 | |
| # this reuses the same model trained in analyze latent space | |
| - name: Identify associations - KS | |
| run: | | |
| cd tutorial | |
| move-dl data=random_continuous task=random_continuous__id_assoc_ks --cfg job | |
| move-dl data=random_continuous task=random_continuous__id_assoc_ks task.num_refits=1 | |
| publish: | |
| name: Publish package | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags') | |
| needs: | |
| - format | |
| - lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install twine and build | |
| run: python -m pip install --upgrade twine build | |
| - name: Build | |
| run: python -m build | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |