Fix cmd_access.py/set_up.py

#7
draeger-lab · Jun 18, 2024 · 36e97f6 · 36e97f6
1 parent f4f2edf
commit 36e97f6
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/src/specimen/cmd_access.py b/src/specimen/cmd_access.py
@@ -41,7 +41,7 @@ def setup():
 # -----------------
 @setup.command()
 @click.option('--filename', '-f', default='config.yaml', type=str, show_default=True, help='Name (path) to the save the config file under.')
-@click.option('--type', '-t', default='htqb-basic', type=click.Choice(['htqb-basic', 'htqb-advanced','htqb-defaults','media','cmpb']), help='Type of config file to download. Either a more detailed one for advanced usage or a basic one for beginners with less options.')
+@click.option('--type', '-t', default='hqtb-basic', type=click.Choice(['hqtb-basic', 'hqtb-advanced','hqtb-defaults','media','cmpb']), help='Type of config file to download. Either a more detailed one for advanced usage or a basic one for beginners with less options.')
 def config(filename,type):
     """Download a configuration file (.yaml).
 

diff --git a/src/specimen/util/set_up.py b/src/specimen/util/set_up.py
@@ -133,7 +133,7 @@ def download_config(filename:str='my_basic_config.yaml', type:Literal['hqtb-basi
     The media config and the config for the cmpb / CarveMe + Modelpolisher based pipeline
     can be downloaded using 'media' and 'cmpb' respectively
 
-    For the htqb / high-quality template based pipeline:
+    For the hqtb / high-quality template based pipeline:
 
         Depending on the knowledge of the user, either a 'hqtb-basic' or an 'hqtb-advanced' type
         of configuration file can be downloaded (or 'hqtb-defaults' for developers).
@@ -142,7 +142,7 @@ def download_config(filename:str='my_basic_config.yaml', type:Literal['hqtb-basi
         - filename (str, optional): 
             Filename/filepath to save the downloaded config file under. 
             Defaults to 'my_basic_config.yaml'.
-        - type (Literal['htqb-basic','htqb-advanced','htqb-defaults','media','cmpb'], optional): 
+        - type (Literal['hqtb-basic','hqtb-advanced','hqtb-defaults','media','cmpb'], optional): 
             The type of file to download. 
             Can be 'hqtb-basic', 'hqtb-advanced' or 'hqtb-defaults' or 'media' or 'cmpb'. 
             Defaults to 'hqtb basic'.
@@ -155,19 +155,19 @@ def download_config(filename:str='my_basic_config.yaml', type:Literal['hqtb-basi
     match type:
         # the 'beginner' version
         case 'hqtb-basic':
-            config_file = files('specimen.data.config').joinpath('htqb_basic_config_expl.yaml')
+            config_file = files('specimen.data.config').joinpath('hqtb_basic_config_expl.yaml')
             with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
                 for line in cfg_file:
                     cfg_out.write(line)
         # for advanced users
         case 'hqtb-advanced':
-            config_file = files('specimen.data.config').joinpath('htqb_advanced_config_expl.yaml')
+            config_file = files('specimen.data.config').joinpath('hqtb_advanced_config_expl.yaml')
             with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
                 for line in cfg_file:
                     cfg_out.write(line)
         # for developer: the config with all internal defaults
         case 'hqtb-defaults':
-            config_file = files('specimen.data.config').joinpath('htqb_config_default.yaml')
+            config_file = files('specimen.data.config').joinpath('hqtb_config_default.yaml')
             with open(config_file, "r") as cfg_file, open(filename, 'w') as cfg_out:
                 for line in cfg_file:
                     cfg_out.write(line)
@@ -289,7 +289,7 @@ def dict_recursive_check(dictA:dict, key:str=None,
     # load both files
     match pipeline:
         case 'hqtb':
-            defaultc_path = files('specimen.data.config').joinpath('htqb_config_default.yaml')
+            defaultc_path = files('specimen.data.config').joinpath('hqtb_config_default.yaml')
         case 'cmpb':
             defaultc_path = files('specimen.data.config').joinpath('cmpb_config.yaml')
         case _: