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Minimum dependency test job #2816

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merged 60 commits into from
Feb 15, 2024
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141eb6a
Start mindeps
ivirshup Jan 17, 2024
a07568e
Fix check_is_fitted import
ivirshup Jan 17, 2024
705acfe
Temporarilly bump anndata dep to access test utilities
ivirshup Jan 17, 2024
9a0dd1a
Support for numpy 1.23 where np.equal didn't work on strings
ivirshup Jan 17, 2024
e4dbcbc
Fix palette color mapping for pandas < 2.1
ivirshup Jan 17, 2024
355c904
Bump networkx
ivirshup Jan 17, 2024
a8bd01b
Exit on error for test script
ivirshup Jan 17, 2024
d36b977
Bump numba for numpy compat
ivirshup Jan 17, 2024
6b4823c
update ci
ivirshup Jan 18, 2024
efa8a39
Fix array comparison in both envs
ivirshup Jan 18, 2024
6b7a37f
Bump statsmodels version
ivirshup Jan 18, 2024
47beebe
Test returns different plot type with older dependencies
ivirshup Jan 18, 2024
1a5d701
Skip test that relies on pd.value_counts
ivirshup Jan 18, 2024
4b04a76
Try to use better naming test results in CI
ivirshup Jan 22, 2024
27fb272
Temporarily bump pandas
ivirshup Jan 22, 2024
4e61bea
Add dependency on pynndescent, bump packaging version
ivirshup Jan 22, 2024
ed71b11
skip doctest for dendrogram
ivirshup Jan 22, 2024
cb95628
install pre-commit in env
ivirshup Jan 22, 2024
f29be77
Bump networkx
ivirshup Jan 22, 2024
483129b
Merge branch 'master' into mindeps
ivirshup Jan 26, 2024
199cefc
Merge branch 'master' into mindeps
ivirshup Jan 29, 2024
098fea3
Get tests to collect with an old anndata version
ivirshup Jan 29, 2024
1cb9396
Fix most preprocessing tests (account for old anndata constructor)
ivirshup Jan 29, 2024
079ad46
Merge branch 'master' into mindeps
ivirshup Jan 29, 2024
5d7494a
Bump anndata min version to 0.7.8
ivirshup Jan 29, 2024
cadd7db
Fix pytest_itemcollected
ivirshup Jan 29, 2024
4a7784c
Bump min anndata version to 0.8
ivirshup Jan 29, 2024
f9cad08
Fix test_get.py cases
ivirshup Jan 29, 2024
3b8db82
Fix neighbor test
ivirshup Jan 29, 2024
78c7ee9
Fix dendrogram plotting cases
ivirshup Jan 29, 2024
e46911c
fix stacked violin ordering
ivirshup Jan 29, 2024
e01eb01
Bump tolerance for older versions of numba
ivirshup Jan 29, 2024
aa2dd50
Fix ordering for matrixplot
ivirshup Jan 29, 2024
e598ce7
Fix preprocessing tests
ivirshup Feb 7, 2024
debfc4b
xfail masking test for anndata 0.8
ivirshup Feb 7, 2024
0112aa5
Merge branch 'master' into mindeps
ivirshup Feb 7, 2024
70e5866
Fix order
flying-sheep Feb 8, 2024
bbdddf2
Fix min-deps.py
flying-sheep Feb 8, 2024
eef7055
Discard changes to scanpy/plotting/_utils.py
flying-sheep Feb 8, 2024
70d151d
removed TODOs from min-deps.py
ivirshup Feb 8, 2024
cb36a62
Remove dev script
ivirshup Feb 8, 2024
2bf0789
Merge branch 'master' into mindeps
ivirshup Feb 8, 2024
07f6d57
Rename test jobs to be more identifiable
ivirshup Feb 12, 2024
5090fff
Use marker for xfail
ivirshup Feb 12, 2024
907544e
Add warning for PCA order
ivirshup Feb 12, 2024
208d413
Fix usage of pytest.mark.xfail
ivirshup Feb 12, 2024
826d3dd
Remove commented out code from CI job
ivirshup Feb 12, 2024
e4ee55d
Obey signature test
ivirshup Feb 13, 2024
2b74f41
Merge branch 'master' into mindeps
ivirshup Feb 13, 2024
aa4eda0
Merge branch 'master' into mindeps
ivirshup Feb 13, 2024
0ee1ced
Merge branch 'master' into mindeps
ivirshup Feb 13, 2024
264aa9a
Don't error on warning for dask.dataframe
ivirshup Feb 13, 2024
6693773
update dask version
ivirshup Feb 15, 2024
b412bfb
fix dask version better
ivirshup Feb 15, 2024
bacb2e7
Merge branch 'master' into mindeps
ivirshup Feb 15, 2024
b6afd99
Fix view issue with anndata==0.8
ivirshup Feb 15, 2024
c7d95b6
Typo
ivirshup Feb 15, 2024
0ddc5e2
Release note
ivirshup Feb 15, 2024
b653dd6
coverage for min deps
ivirshup Feb 15, 2024
2b2ec5d
fix coverage for minimum-version install
ivirshup Feb 15, 2024
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update dask version
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ivirshup authored Feb 15, 2024
commit 66937737c76d34b3a889814630de8b7fbce51d5d
2 changes: 1 addition & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ scanorama = ["scanorama"] # Scanorama dataset integration
scrublet = ["scikit-image"] # Doublet detection with automatic thresholds
# Acceleration
rapids = ["cudf>=0.9", "cuml>=0.9", "cugraph>=0.9"] # GPU accelerated calculation of neighbors
dask = ["dask[array]>=2022.09"] # Use the Dask parallelization engine
dask = ["dask[array]>=2022.09.3"] # Use the Dask parallelization engine
dask-ml = ["dask-ml", "scanpy[dask]"] # Dask-ML for sklearn-like API

[tool.hatch.build]
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