Experimental - manual annotations (#837)

* icons, partway

* redux for values

* onChange

* cancel

* annotations lifecycle for category names

* copy categorical

* edit category

* add Dataframe.withColsFrom

* render user annotations; default add/delete annotation category

* add label name to actions

* category name edit

* error checking improvements

* change schema field isUserAnnotation to writable

* always have an unassigned label; implement delete label

* implement add new label and edit label name

* label current cell selection

* fix select exact bug in crossfilter

* clean up categorical reducer

* fix tests

* remove debugging printf

* implement subset/reset for user annotations

* undo redo support for user annotations

* remove duplicate button from categories

* add modal

* remove obsolete duplicate annotation reducers

* remove old debugging printf

* connect modal to annotation create and dup

* initial full-stack wiring

* finish up end-to-end wiring

* fix existing unit tests

* fix pytests to match new schema API

* remove debugging printfs

* add label file rotation

* remove obsolete comment

* add fbs encode/decode tests

* add tests for writable annotations

* simplify code

* fix hashing bug with FBS encoding

* lint

* fix smoke tests

* improve error checking in Dataframe.withColsFrom

* add unit test for Dataframe.withColsFrom

* add unit test for Dataframe.columns and Dataframe.renameCol

* fix bug in FBS encode, add better error checks, refactor

* add FBS encode/decode test

* add clarifying comment

* clean up action type names; fix state inconsistency in crossfilter update

* change autosave timer to 2.5sec

* sort categorical metadata render order so it remains consistent

* add temporary autogenerated label for add-new-label operation

* fix hover-over label menu interference with cell highlighting

* remove debugging code

* add missing reducer cases & fix typo

* make dataframe memoize more general purpose

* add dev mode for annos

* fix error on select duplicate

* handle zero occupancy categories

* correctly maintain unclipped AND clipped world

* correctly handle zero length FBS matrix and label files

* ensure all writable categorical schema contains an unassigned category

* handle case where building occupancy stack for category with no members

* dialog for creating label, disable button if duplicate or empty

* visually separate writeable

* edit category

* fix edit category name

* remove debugging code

* fix edit annotation label

* visually define unassigned, change options

* Pull in requirements.txt from `master`

* label currently selected cells

* duplicate label

* lint

* fix pytest merge issues

* rename --label-file to --experimental-label-file

* remove debugging console log

* spelling error fix; fix bug found in PR review.

* lint

server/cli/launch.py

@@ -47,19 +47,28 @@ def common_args(func):
         show_default=True,
         help="Relative expression cutoff used when selecting top N differentially expressed genes",
     )
+    @click.option(
+        "--experimental-label-file",
+        default=None,
+        show_default=True,
+        multiple=False,
+        metavar="<user labels CSV file>",
+        help="CSV file containing user annotations; will be overwritten.  Created if does not exist.",
+    )
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
         return func(*args, **kwargs)
     return wrapper
 
 
-def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff):
+def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff, experimental_label_file):
     return {
         "layout": embedding,
         "max_category_items": max_category_items,
         "diffexp_lfc_cutoff": diffexp_lfc_cutoff,
         "obs_names": obs_names,
         "var_names": var_names,
+        "label_file": experimental_label_file,
     }
 
 
@@ -107,7 +116,8 @@ def launch(
         max_category_items,
         diffexp_lfc_cutoff,
         title,
-        scripts
+        scripts,
+        experimental_label_file
 ):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.
@@ -122,7 +132,8 @@ def launch(
 
     > cellxgene launch <url>"""
 
-    e_args = parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff)
+    e_args = parse_engine_args(embedding, obs_names, var_names, max_category_items,
+                               diffexp_lfc_cutoff, experimental_label_file)
     try:
         data_locator = DataLocator(data)
     except RuntimeError as re:
@@ -181,6 +192,11 @@ def launch(
     else:
         port = find_available_port(host)
 
+    if experimental_label_file:
+        lf_name, lf_ext = splitext(experimental_label_file)
+        if lf_ext and lf_ext != ".csv":
+            raise click.FileError(basename(experimental_label_file), hint="label file type must be .csv")
+
     # Setup app
     cellxgene_url = f"http://{host}:{port}"