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scverse / anndata

Annotated data.
http://anndata.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Tests fail on master for scanpy. (Hidden b/c they only run if scanpy is installed.) #357

Open sakoht opened 4 years ago

sakoht commented 4 years ago

It seems that the following tests on the master branch if scanpy is also installed when the tests run:

I added this to requirements_tests.txt:

scanpy==1.4.6

pytest results in travis:

FAILED anndata/tests/test_readwrite.py::test_scanpy_pbmc68k[h5ad-h5ad] - Impo...
FAILED anndata/tests/test_readwrite.py::test_scanpy_pbmc68k[h5ad-zarr] - Impo...
FAILED anndata/tests/test_readwrite.py::test_scanpy_pbmc68k[zarr-h5ad] - Impo...
FAILED anndata/tests/test_readwrite.py::test_scanpy_pbmc68k[zarr-zarr] - Impo...
FAILED anndata/tests/test_readwrite.py::test_scanpy_krumsiek11[h5ad] - Import...
FAILED anndata/tests/test_readwrite.py::test_scanpy_krumsiek11[zarr] - Import...

Does anyone know if there is an older version of anndata/scanpy that pass tests?

sakoht commented 4 years ago

I see that scanpy depends on anndata, so installing it as part of requirements_tests.txt puts a 2nd copy of anndata into the virtualenv.

Then the anndata tests that use scanpy result in anndata throwing an exception.

ivirshup commented 4 years ago

What exactly are you trying to do here? Is it just have the tests which depend on scanpy run on travis?

Could you link to your travis results? I'm a little confused about what you're asking for/ seeing.