Merge pull request #225 from medema-group/dev

remove disk-only option and add TODO for reimplementation

big_scape/cli/cli_common_options.py

@@ -332,17 +332,17 @@ def common_cluster_query(fn):
                 "re-start the run from scratch"
             ),
         ),
-        click.option(
-            "--disk-only",
-            type=bool,
-            is_flag=True,
-            default=False,
-            help=(
-                "Do not store any results in memory, only on disk. This is almost certainly "
-                "slower than the default behavior, but will save some memory and can therefore be "
-                "useful for very large runs or runs with limited memory"
-            ),
-        ),
+        # click.option(
+        #     "--disk-only",
+        #     type=bool,
+        #     is_flag=True,
+        #     default=False,
+        #     help=(
+        #         "Do not store any results in memory, only on disk. This is almost certainly "
+        #         "slower than the default behavior, but will save some memory and can therefore be "
+        #         "useful for very large runs or runs with limited memory"
+        #     ),
+        # ),
         click.option(
             "--db-only-output",
             type=bool,

big_scape/cli/cluster_cli.py

@@ -138,6 +138,9 @@ def cluster(ctx, *args, **kwargs):
     ctx.obj["propagate"] = True  # compatibility with query wrt cc generation
     ctx.obj["mode"] = "Cluster"
 
+    # TODO: remove when reimplementing disk-only
+    ctx.obj["disk_only"] = False
+
     # set start time and run label
     set_start(ctx.obj)
 

big_scape/cli/query_cli.py

@@ -99,6 +99,9 @@ def query(ctx, *args, **kwarg):
     ctx.obj["exclude_classes"] = None
     ctx.obj["include_classes"] = None
 
+    # TODO: remove when reimplementing disk-only
+    ctx.obj["disk_only"] = False
+
     # set start time and label
     set_start(ctx.obj)