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/util/utils.py

@@ -1,4 +1,5 @@
 import json
+from argparse import ArgumentTypeError
 
 from numpy import float32, integer
 
@@ -49,3 +50,13 @@ def get_mime_type(default="application/json", acceptable_types=["application/jso
         if not mime_type:
             raise MimeTypeError(f"Unsupported mime type(s) {header} in HTTP Accept header")
     return mime_type
+
+
+def whole_number(value):
+    try:
+        value = int(value)
+    except ValueError as e:
+        raise ArgumentTypeError(f"{value} is not type int") from e
+    if value < 0:
+        raise ArgumentTypeError(f"{value} is not >= 0")
+    return value