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Merged
nathanthorpe merged 17 commits into from
Aug 5, 2025
Merged

CI-747 - Developer tools for SDK #164

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5afab9a
return dict of dataset info and params instead of wrapper class
nathanthorpe Jul 31, 2025
a17b46d
update cirro api client
nathanthorpe Jul 31, 2025
b0375d4
initial developer helper class
nathanthorpe Jul 31, 2025
c747360
add example notebook
nathanthorpe Jul 31, 2025
d2c5462
lint
nathanthorpe Jul 31, 2025
72f922e
update
nathanthorpe Jul 31, 2025
2ebb60a
add re-run sample ingest
nathanthorpe Jul 31, 2025
a9a0fed
fix test
nathanthorpe Jul 31, 2025
9c4cbad
init logger in from_running
nathanthorpe Jul 31, 2025
c9944c8
feedback
nathanthorpe Aug 1, 2025
acc2d35
refactor preprocess wide samplesheet, add to example notebook
nathanthorpe Aug 1, 2025
bca1c38
lint
nathanthorpe Aug 1, 2025
09d144f
add optional file filter predicate, for common cases such as filterin…
nathanthorpe Aug 1, 2025
429f848
typo
nathanthorpe Aug 1, 2025
52c4ad3
add note about developing regex and a note the fall back case
nathanthorpe Aug 1, 2025
d85d4c2
docs
nathanthorpe Aug 4, 2025
6ecb683
simpler samplesheet example, all None to be passed in pivot columns
nathanthorpe Aug 5, 2025
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fix test
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@nathanthorpe
nathanthorpe committed Jul 31, 2025
commit a9a0fed436afeb30fa1d4b51faa5e9b1e4c7ddf9
8 changes: 4 additions & 4 deletions tests/test_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,25 +11,25 @@

class TestPreprocess(unittest.TestCase):
def test_wide_samplesheet_1(self):
ds = PreprocessDataset(DATA_PATH + '/example_data_1')
ds = PreprocessDataset.from_path(DATA_PATH + '/example_data_1')
df = ds.wide_samplesheet()

expected_df = pandas.read_csv(DATA_PATH + '/example_data_1/expected_wide.csv')

self.assertEqual(
df.sort_index(axis=1).to_csv(index=None),
expected_df.sort_index(axis=1).to_csv(index=None)
expected_df.sort_index(axis=1).to_csv(index=False)
)

def test_wide_samplesheet_2(self):
ds = PreprocessDataset(DATA_PATH + '/example_data_2')
ds = PreprocessDataset.from_path(DATA_PATH + '/example_data_2')
df = ds.wide_samplesheet()

expected_df = pandas.read_csv(DATA_PATH + '/example_data_2/expected_wide.csv')

self.assertEqual(
df.sort_index(axis=1).to_csv(index=None),
expected_df.sort_index(axis=1).to_csv(index=None)
expected_df.sort_index(axis=1).to_csv(index=False)
)


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