amend arg no-output to db-only-output

medema-group · Oct 23, 2024 · fa80b83 · fa80b83
1 parent 0c29ff0
commit fa80b83
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/big_scape/cli/cli_common_options.py b/big_scape/cli/cli_common_options.py
@@ -113,7 +113,7 @@ def common_all(fn):
             "runs with limited memory.",
         ),
         click.option(
-            "--no-output",
+            "--db-only-output",
             type=bool,
             is_flag=True,
             default=False,

diff --git a/big_scape/output/legacy_output.py b/big_scape/output/legacy_output.py
@@ -163,7 +163,7 @@ def legacy_prepare_output(
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         logging.info("Skipping all output generation")
         return
 
@@ -189,7 +189,7 @@ def legacy_prepare_cutoff_output(run: dict, cutoff: float, gbks: list[GBK]) -> N
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         return
 
     output_dir: Path = run["output_dir"]
@@ -215,7 +215,7 @@ def legacy_prepare_bin_output(
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         return
 
     output_dir: Path = run["output_dir"]
@@ -252,7 +252,7 @@ def legacy_generate_bin_output(
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         return
 
     families_members = generate_bs_families_members(
@@ -331,7 +331,7 @@ def write_record_annotations_file(run, cutoff, all_bgc_records) -> None:
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         return
 
     run_id = run["run_id"]
@@ -536,7 +536,7 @@ def write_full_network_file(run: dict, all_bgc_records: list[BGCRecord]) -> None
 
     click_context = click.get_current_context(silent=True)
 
-    if click_context and click_context.obj["no_output"]:
+    if click_context and click_context.obj["db_only_output"]:
         return
 
     output_dir = run["output_dir"]