Bruce Martin
922c375333
Rename "layout" to "embedding" in the UI ( #921 )
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* rename "layout" to "embedding" in the UI
* docs changes for layout
* fix typo in data docs
* new help text, per PR review
2019-09-16 15:34:14 -07:00
Charlotte Weaver
77de22d1ed
merge louvain and prepare extra requires ( #897 )
2019-08-29 12:49:19 -07:00
Charlotte Weaver
28c4d28308
extract prepare from main install ( #887 )
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* extract prepare from main install
* add requirements-prepare to manifest
2019-08-21 14:26:01 -07:00
Sidney Bell
34e5a91dc6
Add calculate_qc_metrics to `prepare ( #697 )
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* Calculate QC metrics
* Add QC metrics to prepare section of readme
* Add pointer to scanpy qc metrics function
* Don't explicitly pass qc flag as arg
* Add explicit toggle for run-qc/skip-qc
* Move qc metrics calculation to separate step/function
2019-04-09 08:56:07 -07:00
Sidney Bell
c9a56fa73a
Update scanpy version ( #688 )
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Update to version 1.3.7
2019-04-04 12:16:30 -07:00
Charlotte Weaver
83154577e4
Black -- formatter for python ( #508 )
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* Add black
* use black to format code
* Black version
2018-12-12 09:44:47 -08:00
Charlotte Weaver
aa29c91470
Prepare fixes ( #416 )
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* Error on overwrite=false but no output file
* Add prepare requirements to requirements.txt
* no saved output error -> warning
* Catch clustering import error
* lint fixes
* Fix missing output message
2018-11-09 13:51:30 -08:00
Charlotte Weaver
7d5c054b90
Launch validation ( #414 )
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* WIP
* Cleanup
* Validation
* typo
* Max category limit 100 -> 500
2018-11-07 13:01:13 -08:00
Jeremy Freeman
e2d864a336
integrate prepare cli ( #401 )
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* move prepare into main CLI as subcommand
* naming and formatting tweaks to better match launch subcommand
2018-11-03 10:48:05 -04:00
