CLI Launch (#366)

* Scanpy engine now required

Without the --engine param we need to error if scanpy engine cannot be imported rather than waiting for all engines

* CLI options and help matches proposal

(but not all options hooked up yet)

* Flesh out top level args

* Move computation args to engine

* CLI input file (#374)

* Fix test command

(tests still won't work)

* Input is file instead of directory
- also renamed example file

* Csweaver/debug (#376)

* Respect debug flag for logging flask calls

* Add loading messages

* max categories (#377)

* Add max categories

* Rename max_categories to category_selection_limit

* ensure whole numbers

server/app/rest_api/rest.py

@@ -110,6 +110,9 @@ class ConfigAPI(Resource):
                 "displayNames": {
                     "engine": f"cellxgene Scanpy engine version {pkg_resources.get_distribution('cellxgene').version}",
                     "dataset": current_app.config["DATASET_TITLE"]
+                },
+                "parameters": {
+                    "category_selection_limit": current_app.data.category_selection_limit
                 }
             }
         }