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add --obs-names and --var-names CLI params (#371)

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* add --obs-names and --var-names CLI params

* fix lint

* performance improvements in scanpy engine

* fix lint

* fix typo

* correctly handle sparse formats in diffexp

* fix diffexp and 1d slicing

* diffexp uses t-stat, not pval; clean up arg handling

* make _slice a static method

* revise scanpy tests to match new API
This commit is contained in:
Bruce Martin
2018-10-30 14:07:38 -07:00
committed by GitHub
parent 01369801fc
commit b181751493
7 changed files with 133 additions and 88 deletions
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server/test/test_api.py
+4 -4
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@@ -102,7 +102,7 @@ class EndPoints(unittest.TestCase):
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(result_data["data"]), 2638)
self.assertEqual(len(result_data["data"][0]), 6)
@@ -140,7 +140,7 @@ class EndPoints(unittest.TestCase):
result = self.session.put(url, json=obs_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(result_data["data"]), 15)
def test_filter_put_annotations_obs(self):
@@ -224,7 +224,7 @@ class EndPoints(unittest.TestCase):
result = self.session.get(url)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_cells", "name"])
self.assertEqual(result_data["names"], ["name", "n_cells"])
self.assertEqual(len(result_data["data"]), 1838)
self.assertEqual(len(result_data["data"][0]), 3)
@@ -260,7 +260,7 @@ class EndPoints(unittest.TestCase):
result = self.session.put(url, json=var_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(result_data["names"], ["n_cells", "name"])
self.assertEqual(result_data["names"], ["name", "n_cells"])
self.assertEqual(len(result_data["data"]), 2)
def test_filter_put_annotations_var(self):