Prepare fixes (#416)

* Error on overwrite=false but no output file

* Add prepare requirements to requirements.txt

* no saved output error -> warning

* Catch clustering import error

* lint fixes

* Fix missing output message

server/cli/launch.py

@@ -74,7 +74,7 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
     app.config.update(
         DATASET_TITLE=title,
         CXG_API_BASE=api_base
-        )
+    )
 
     if not verbose:
         log = logging.getLogger("werkzeug")

server/cli/prepare.py

@@ -47,6 +47,10 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
         raise click.UsageError("Cannot use a recipe when forcing sparsity")
 
     output = expanduser(output)
+
+    if not output:
+        click.echo("Warning: No file will be saved, to save the results of cellxgene prepare include "
+                   "--output <filename> to save output to a new file")
     if isfile(output) and not overwrite:
         raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
 
@@ -112,7 +116,12 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
         sc.pp.neighbors(adata)
 
     def run_louvain(adata):
-        sc.tl.louvain(adata)
+        try:
+            sc.tl.louvain(adata)
+        except ModuleNotFoundError:
+            click.echo("\nWarning: louvain module is not installed, no clusters will be calculated. "
+                       "To fix this please install cellxgene with the optional feature louvain enabled: "
+                       "`pip install cellxgene[louvain]`")
 
     def run_layout(adata):
         if len(unique(adata.obs["louvain"].values)) < 10:

setup.py

@@ -26,5 +26,8 @@ setup(
     entry_points={
         "console_scripts":
             ["cellxgene = server.cli.cli:cli"]
-    }
+    },
+    extras_require=dict(
+        louvain=['python-igraph', 'louvain>=0.6'],
+    ),
 )