1 files changed, 0 insertions, 41 deletions
diff --git a/biology/py-multiqc/files/patch-multiqc_utils_config.py b/biology/py-multiqc/files/patch-multiqc_utils_config.py
deleted file mode 100644
index 707b510672f0..000000000000
--- a/biology/py-multiqc/files/patch-multiqc_utils_config.py
+++ /dev/null
@@ -1,41 +0,0 @@
---- multiqc/utils/config.py.orig	2019-09-22 13:24:47 UTC
-+++ multiqc/utils/config.py
-@@ -42,13 +42,13 @@ MULTIQC_DIR = os.path.dirname(os.path.realpath(inspect
- # Default MultiQC config
- searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'config_defaults.yaml')
- with open(searchp_fn) as f:
--    configs = yaml.load(f)
-+    configs = yaml.load(f, Loader=yaml.FullLoader)
-     for c, v in configs.items():
-         globals()[c] = v
- # Module filename search patterns
- searchp_fn = os.path.join( MULTIQC_DIR, 'utils', 'search_patterns.yaml')
- with open(searchp_fn) as f:
--    sp = yaml.load(f)
-+    sp = yaml.load(f, Loader=yaml.FullLoader)
- 
- # Other defaults that can't be set in YAML
- data_tmp_dir = '/tmp' # will be overwritten by core script
-@@ -118,7 +118,7 @@ def mqc_load_config(yaml_config):
-     if os.path.isfile(yaml_config):
-         try:
-             with open(yaml_config) as f:
--                new_config = yaml.load(f)
-+                new_config = yaml.load(f, Loader=yaml.FullLoader)
-                 logger.debug("Loading config settings from: {}".format(yaml_config))
-                 mqc_add_config(new_config, yaml_config)
-         except (IOError, AttributeError) as e:
-@@ -132,11 +132,11 @@ def mqc_load_config(yaml_config):
- def mqc_cl_config(cl_config):
-     for clc_str in cl_config:
-         try:
--            parsed_clc = yaml.load(clc_str)
-+            parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader)
-             # something:var fails as it needs a space. Fix this (a common mistake)
-             if isinstance(parsed_clc, str) and ':' in clc_str:
-                 clc_str = ': '.join(clc_str.split(':'))
--                parsed_clc = yaml.load(clc_str)
-+                parsed_clc = yaml.load(clc_str, Loader=yaml.FullLoader)
-             assert(isinstance(parsed_clc, dict))
-         except yaml.scanner.ScannerError as e:
-             logger.error("Could not parse command line config: {}\n{}".format(clc_str, e))