Add user-defined category-label colors (#1402)

* Add user-defined category-label colors

Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152

As described in https://github.com/chanzuckerberg/cellxgene/issues/1307

* Respond to feedback from @bkmartinjr in nodejs

* Respond to feedback from @bkmartinjr in python

* Add tests to the server module

* Autoformat python, run linter

* Make colors_get error handling specific

* Respond to feedback from @bkmartinjr

* Respond to feedback from @bkmartinjr

* Fix whitespace

* Fix python lint errrors

* Update documentation

* Add --disable-user-colors option to launch and cxgtool.py

* Fix python formatting

* Rename '--disable-user-colors' to '--disable-custom-colors'

server/cli/launch.py

@@ -73,6 +73,13 @@ def config_args(func):
         show_default=True,
         help="Will not display categories with more distinct values than specified.",
     )
+    @click.option(
+        "--disable-custom-colors",
+        is_flag=True,
+        default=False,
+        show_default=False,
+        help="Disable user-defined category-label colors drawn from source data file.",
+    )
     @click.option(
         "--diffexp-lfc-cutoff",
         "-de",
@@ -146,7 +153,7 @@ def dataset_args(func):
         "--about",
         default=DEFAULT_CONFIG.single_dataset__about,
         metavar="<URL>",
-        help="URL providing more information about the dataset " "(hint: must be a fully specified absolute URL).",
+        help="URL providing more information about the dataset (hint: must be a fully specified absolute URL).",
     )
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
@@ -311,6 +318,7 @@ def launch(
     obs_names,
     var_names,
     max_category_items,
+    disable_custom_colors,
     diffexp_lfc_cutoff,
     title,
     scripts,
@@ -381,6 +389,7 @@ def launch(
             user_annotations__ontology__enable=experimental_annotations_ontology,
             user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
             presentation__max_categories=max_category_items,
+            presentation__custom_colors=not disable_custom_colors,
             embeddings__names=embedding,
             embeddings__enable_reembedding=experimental_enable_reembedding,
             diffexp__enable=not disable_diffexp,

server/cli/prepare.py

@@ -73,7 +73,8 @@ def prepare(
     (h5ad, loom, or a 10x directory), runs dimensionality reduction,
     computes nearest neighbors, computes an embedding, performs clustering,
     and saves the results. Includes additional options for naming annotations,
-    ensuring sparsity, and plotting results."""
+    ensuring sparsity, and plotting results.
+    """
 
     # collect slow imports here to make CLI startup more responsive
     click.echo("[cellxgene] Starting CLI...")