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CLI refactor (#396)

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* refactor cli to improve ux and enable easy incorporation of prepare as a subcommand

* switches to use click, which removes some boilerplate and gets us some improved ux for free

* changes the entry point for the cli

* changes the name of the browser option to --open and makes the default false
This commit is contained in:
Jeremy Freeman
2018-11-02 10:52:50 -04:00
committed by GitHub
parent 6e46a65c32
commit 0c8a07ac13
11 changed files with 124 additions and 139 deletions
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server/app/scanpy_engine/scanpy_engine.py
+2 -2
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@@ -24,8 +24,8 @@ class ScanpyEngine(CXGDriver):
def __init__(self, data, args):
super().__init__(data, args)
self._alias_annotation_names(Axis.OBS, args.obs_names)
self._alias_annotation_names(Axis.VAR, args.var_names)
self._alias_annotation_names(Axis.OBS, args['obs_names'])
self._alias_annotation_names(Axis.VAR, args['var_names'])
self._validate_data_types()
self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1]