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moving FAST_CI_MODE flag to pytest script (#1111)
### Description Moving FAST_CI_MODE flag to related pytest script file to avoid future lack of compatibility between the setup between Jenkins or GitHub CI ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [x] Refactor - [ ] Documentation update - [ ] Other (please describe): ### CI Pipeline Configuration Configure CI behavior by applying the relevant labels: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. - If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) - If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### Usage <!--- How does a user interact with the changed code --> ```python # TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [ ] I have tested these changes locally - [ ] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Streamlined CI configuration for notebook tests by moving fast-mode environment handling into the test script and removing redundant settings from the workflow. * **Tests** * Consolidated environment setup for notebook pytest runs to improve consistency and reliability in CI. No user-facing changes or impact on product behavior. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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.github/workflows/unit-tests-framework.yml

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- name: Run notebook tests
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env:
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BIONEMO_DATA_SOURCE: ngc
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# this variable should be used in the notebooks to run a subset of the model layers or a smaller model/dataset
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FAST_CI_MODE: true
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run: |
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chmod +x ./ci/scripts/run_pytest_notebooks.sh
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./ci/scripts/run_pytest_notebooks.sh

ci/scripts/run_pytest_notebooks.sh

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# Enable strict mode with better error handling
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set -euox pipefail
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pytest -v --nbval-lax -x -p no:python docs/ sub-packages/
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FAST_CI_MODE=true pytest -v --nbval-lax -x -p no:python docs/ sub-packages/

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