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anndata X indexing & version compatibility improvements (#1157)

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* revert MatrixProxy; replace with correct use of adata slicing

* work around 0.6 adata slicing bug

* fix incorrect var slice

* simplify slicing of X

* add warning about performance impact of anndata<=0.7

* lint and remove unused code

* improve comment

* lint

* correctly parse versions

* temp files should preserve file suffix if possible - anndata 0.7 compat

* update anndata dependency to 0.6.20

* resolve PR review comments
This commit is contained in:
Bruce Martin
2020-02-19 09:57:51 -07:00
committed by GitHub
parent c630be33df
commit 349c413d8b
7 changed files with 47 additions and 675 deletions
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server/requirements.txt
+16 -17
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@@ -1,17 +1,16 @@
anndata>=0.6.2
click>=6.7
fastobo>=0.6.1
Flask>=1.0.2
Flask-Caching>=1.4.0
Flask-Compress>=1.4.0
Flask-Cors>=3.0.6
Flask-RESTful>=0.3.6
flatbuffers>=1.10.0
fsspec>=0.4.4
numpy>=1.15.2
pandas>=0.24.2
scipy>=1.3.0
tables==3.5.1
# TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression
h5py==2.9.0
requests>=2.22.0
anndata>=0.6.20
click>=6.7
fastobo>=0.6.1
Flask>=1.0.2
Flask-Caching>=1.4.0
Flask-Compress>=1.4.0
Flask-Cors>=3.0.6
Flask-RESTful>=0.3.6
flatbuffers>=1.10.0
fsspec>=0.4.4
numpy>=1.15.2
packaging>=20.0
pandas>=0.24.2
scipy>=1.3.0
tables==3.5.1
requests>=2.22.0