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Fix Update Testing Data Workflow #339

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merged 5 commits into from
Jun 3, 2024
Merged

Fix Update Testing Data Workflow #339

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56395b6
unpin awscli
pauladkisson Jun 3, 2024
794b6a7
Update CHANGELOG.md
pauladkisson Jun 3, 2024
bf2acea
Added conditional download block to tests workflow
pauladkisson Jun 3, 2024
30f97cf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 3, 2024
8431a5d
refactored pr tests to a dedicated workflow to streamline data download
pauladkisson Jun 3, 2024
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10 changes: 10 additions & 0 deletions .github/workflows/run-tests.yml
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Expand Up @@ -52,6 +52,16 @@ jobs:
path: ./ophys_testing_data
key: ophys-datasets-042023-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}

- if: steps.cache-ophys-datasets.outputs.cache-hit == false
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name: Install and configure AWS CLI
run: |
pip install awscli
aws configure set aws_access_key_id ${{ secrets.AWS_ACCESS_KEY_ID }}
aws configure set aws_secret_access_key ${{ secrets.AWS_SECRET_ACCESS_KEY }}
- if: steps.cache-ophys-datasets.outputs.cache-hit == false
name: Download data from S3
run: aws s3 cp --recursive s3://${{ secrets.S3_GIN_BUCKET }}//ophys_testing_data ./ophys_testing_data

- name: Run full pytest with coverage
run: pytest -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml
- if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'}}
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2 changes: 1 addition & 1 deletion .github/workflows/update-testing-data.yml
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Expand Up @@ -38,7 +38,7 @@ jobs:
- if: steps.cache-ophys-datasets.outputs.cache-hit == false
name: Install and configure AWS CLI
run: |
pip install awscli==1.29.56
pip install awscli
aws configure set aws_access_key_id ${{ secrets.AWS_ACCESS_KEY_ID }}
aws configure set aws_secret_access_key ${{ secrets.AWS_SECRET_ACCESS_KEY }}
- if: steps.cache-ophys-datasets.outputs.cache-hit == false
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@
* Remove unnecessary `scipy` import error handling: [#315](https://github.com/catalystneuro/roiextractors/pull/315)
* Fixed the typing returned by the `InscopixImagingExtractor.get_dtype` method: [#326](https://github.com/catalystneuro/roiextractors/pull/326)
* Detect Changelog Updates was moved to its own dedicated workflow to avoid daily testing failures: [#336](https://github.com/catalystneuro/roiextractors/pull/336)
* Fixed the Update Testing Data Workflow by unpinning the version of awscli: [#339](https://github.com/catalystneuro/roiextractors/pull/339)

### Improvements

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