Fix bugs uncovered by flake8

Clinical-Genomics · Jul 4, 2024 · bdcd209 · bdcd209
1 parent 1cbcc50
commit bdcd209
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/microSALT/cli.py b/microSALT/cli.py
@@ -43,7 +43,8 @@
     sys.exit(-1)
 
 
-def set_cli_config(config):
+@click.pass_context
+def set_cli_config(ctx, config):
     if config != "":
         if os.path.exists(config):
             try:

diff --git a/tests/test_config.py b/tests/test_config.py
@@ -70,7 +70,7 @@ def test_paths(exp_config):
   for entry in preset_config.keys():
     if entry != '_comment':
       if isinstance(preset_config[entry], str) and '/' in preset_config[entry] and entry not in ['database', 'genologics']:
-        unmade_fldr = preset_config[entry][thing]
+        unmade_fldr = preset_config[entry]
         assert (pathlib.Path(unmade_fldr).exists())
 
       #level two