patch release 0.9.2

* add __init__.py

* bump version

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.0
+current_version = 0.9.2
 
 [bumpversion:file:setup.py]
 search = version="{current_version}"

client/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.9.0",
+  "version": "0.9.2",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -5535,8 +5535,7 @@
         "ansi-regex": {
           "version": "2.1.1",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "aproba": {
           "version": "1.2.0",
@@ -5557,14 +5556,12 @@
         "balanced-match": {
           "version": "1.0.0",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "brace-expansion": {
           "version": "1.1.11",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "balanced-match": "^1.0.0",
             "concat-map": "0.0.1"
@@ -5579,20 +5576,17 @@
         "code-point-at": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "concat-map": {
           "version": "0.0.1",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "console-control-strings": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "core-util-is": {
           "version": "1.0.2",
@@ -5709,8 +5703,7 @@
         "inherits": {
           "version": "2.0.3",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "ini": {
           "version": "1.3.5",
@@ -5722,7 +5715,6 @@
           "version": "1.0.0",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "number-is-nan": "^1.0.0"
           }
@@ -5737,7 +5729,6 @@
           "version": "3.0.4",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "brace-expansion": "^1.1.7"
           }
@@ -5745,14 +5736,12 @@
         "minimist": {
           "version": "0.0.8",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "minipass": {
           "version": "2.2.4",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "safe-buffer": "^5.1.1",
             "yallist": "^3.0.0"
@@ -5771,7 +5760,6 @@
           "version": "0.5.1",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "minimist": "0.0.8"
           }
@@ -5852,8 +5840,7 @@
         "number-is-nan": {
           "version": "1.0.1",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "object-assign": {
           "version": "4.1.1",
@@ -5865,7 +5852,6 @@
           "version": "1.4.0",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "wrappy": "1"
           }
@@ -5951,8 +5937,7 @@
         "safe-buffer": {
           "version": "5.1.1",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "safer-buffer": {
           "version": "2.1.2",
@@ -5988,7 +5973,6 @@
           "version": "1.0.2",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "code-point-at": "^1.0.0",
             "is-fullwidth-code-point": "^1.0.0",
@@ -6008,7 +5992,6 @@
           "version": "3.0.1",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "ansi-regex": "^2.0.0"
           }
@@ -6052,14 +6035,12 @@
         "wrappy": {
           "version": "1.0.2",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         },
         "yallist": {
           "version": "3.0.2",
           "bundled": true,
-          "dev": true,
+          "dev": true
-          "optional": true
         }
       }
     },

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.9.0",
+  "version": "0.9.2",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",

server/app/scanpy_engine/scanpy_engine.py

@@ -304,7 +304,7 @@ class ScanpyEngine(CXGDriver):
         if sparse.issparse(X):  # use tuned getcol/hstack for performance
             indices = np.nonzero(var_mask)[0]
             cols = [X.getcol(i) for i in indices]
-            return sparse.hstack(cols)
+            return sparse.hstack(cols, format="csc")
         else:   # else, just use standard slicing, which is fine for dense arrays
             return X[:, var_mask]
 

server/cli/cli.py

@@ -5,7 +5,7 @@ from .prepare import prepare
 
 
 @click.group(name="cellxgene", context_settings=dict(max_content_width=85))
-@click.version_option(version="0.9.0", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
+@click.version_option(version="0.9.2", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
 def cli():
     pass
 

setup.py

@@ -8,7 +8,7 @@ with open("server/requirements.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="0.9.0",
+    version="0.9.2",
     packages=find_packages(),
     url="https://github.com/chanzuckerberg/cellxgene",
     license="MIT",