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Python 3.12 requires a numpy version >= 1.26.
Our current numpy version is limited to <1.25
Steps/Code to Reproduce
$ make install-dev
$ pip install -U "numpy<2"
$ make fast
Expected Results
pass all tests in make fast
Actual Results
make mypy fails with deprecated np.product and np.NINF
make fast-test results in two failed tests where numpy 1.25 changed sorting order in pandas for index names with identical values. This is due to the unstable nature of 'quicksort' when sorting values.
In file starfish/test/full_pipelines/api/test_dartfish.py:
def test_dartfish_pipeline_cropped_data(tmpdir):
)
assert np.array_equal(
high_expression_genes['gene'].values,
['MBP', 'MOBP', 'ADCY8', 'TRIM66', 'SYT6'] # fails and need to be replaced with ['MBP', 'MOBP', 'ADCY8', 'SYT6', 'TRIM66']
)
In file starfish/test/full_pipelines/api/test_merfish.py:
def test_merfish_pipeline_cropped_data():
# assert that number of high-expression detected genes are correct
expected_counts = pd.Series(
[107, 59, 46, 32, 32],
index=('MALAT1', 'SRRM2', 'FASN', 'IGF2R', 'TLN1') # fails and need to be replaced with "index=('MALAT1', 'SRRM2', 'FASN', 'TLN1', 'IGF2R')"
)
assert np.array_equal(
expected_counts.values,
The text was updated successfully, but these errors were encountered:
Description
Python 3.12 requires a numpy version >= 1.26.
Our current numpy version is limited to <1.25
Steps/Code to Reproduce
Expected Results
pass all tests in
make fast
Actual Results
make mypy
fails with deprecated np.product and np.NINFmake fast-test
results in two failed tests where numpy 1.25 changed sorting order in pandas for index names with identical values. This is due to the unstable nature of 'quicksort' when sorting values.In file starfish/test/full_pipelines/api/test_dartfish.py:
def test_dartfish_pipeline_cropped_data(tmpdir):
)
assert np.array_equal(
high_expression_genes['gene'].values,
['MBP', 'MOBP', 'ADCY8', 'TRIM66', 'SYT6'] # fails and need to be replaced with ['MBP', 'MOBP', 'ADCY8', 'SYT6', 'TRIM66']
)
In file starfish/test/full_pipelines/api/test_merfish.py:
def test_merfish_pipeline_cropped_data():
# assert that number of high-expression detected genes are correct
expected_counts = pd.Series(
[107, 59, 46, 32, 32],
index=('MALAT1', 'SRRM2', 'FASN', 'IGF2R', 'TLN1') # fails and need to be replaced with "index=('MALAT1', 'SRRM2', 'FASN', 'TLN1', 'IGF2R')"
)
assert np.array_equal(
expected_counts.values,
The text was updated successfully, but these errors were encountered: