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f3015cb9df
* Fix Makefile whitespace and .PHONY use
* Fix Makefile filename
* Modularize Makefile into client and server Makefiles
Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.
This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.
* Add auto-formatting to client and server modules
One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.
* Add yapf for automatic code formatting
* Add a root test target that calls sub-tests
* Apply yapf to python files
* Do not duplicate npm commands, simply pass through
* Update documentation
* Do not shadow reserved word len
* Add general test target
* Fix make call in dev-env
* Use black instead of yapf
* Run flake8 from the root directory
* Revert "Apply yapf to python files"
This reverts commit cdca128a01.
* Apply black to python code
* Resolve lint errors resulting from black format
* Add explanation of server unit tests in dev guidelines
46 lines
1.5 KiB
Python
46 lines
1.5 KiB
Python
from server.app.util.matrix_proxy import MatrixProxyView, ArrayProxyView
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"""
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AnnData/h5py are inconsistent in the API supported by various types of
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X matrices. Sometimes you get a fully ndarray, sometims a Scipy sparse
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matrix, sometimes h5py proxies with a subset of our needed interfaces.
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This glue code paves over all of that, providing the core set of methods
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that the cellxgene ScanPy driver assumes are in existance. Put another
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way, all of the non-portable assumptions are here.
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"""
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class ArrayProxyView_anndata_h5py(ArrayProxyView):
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"""
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override to handle sparse getitem semantics, which differ
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from numpy.
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"""
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def toarray(self):
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""" sadly, sparse indexing doesn't drop dimensions like numpy! """
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arr = self.m[self._index[0], self._index[1]]
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if self._vdim == 0:
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arr = arr.transpose()
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return arr.toarray()[0]
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class MatrixProxy_anndata_h5py(MatrixProxyView):
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"""
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AnnData sparse array stored in H5AD, or proxies for backed data.
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None of these handle indexing very well, so we plop a proxy on top.
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"""
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@classmethod
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def __supports__(cls):
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return (
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"anndata.h5py.h5sparse.SparseDataset",
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"anndata.h5py.h5sparse.backed_csc_matrix",
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"anndata.h5py.h5sparse.backed_csr_matrix",
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"h5py._hl.dataset.Dataset",
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)
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@classmethod
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def create_array(cls, *args, **kwargs):
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return ArrayProxyView_anndata_h5py(*args, **kwargs)
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