angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
71 stars 25 forks source link

Maximize Available GitHub Storage Space #1025

Closed srivarra closed 1 year ago

srivarra commented 1 year ago

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What is the purpose of this PR?

Allows the Ubuntu Test Runner to not run out of storage space.

How did you implement your changes

Adds more shutil.rmfree function calls in the example dataset tests and adjusts those in the notebook tests. Adjusts the Test_Cell_Neighbors notebook to make use of the cached dataset on GHA. Added a decorator which can be used throughout the example dataset notebook tests to get info about storage space on the runner. For example:

class Test_1_Segment_Image_Data:
    """
    Tests Notebook 1 - Segment Image Data for completion.
    NOTE: When modifying the tests, make sure the test are in the
    same order as the tagged cells in the notebook.
    """
    .
    .
    .
    @notebooks_test_utils.get_storage
    def test_ex_data_download(self):
        notebooks_test_utils._ex_dataset_download(dataset=self.dataset, save_dir=self.base_dir,
                                                  cache_dir=self.cache_dir)

    .
    .
    .

Remaining issues

None.

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