PR#24761: fix EVcouplings v0.2.1 comptability with ruamel.yaml 0.18

Author: lexming

easyconfigs/e/EVcouplings/EVcouplings-0.2.1-foss-2024a.eb

@@ -39,15 +39,25 @@ exts_list = [
     ('evcouplings', version, {
         'source_urls': [GITHUB_SOURCE],
         'sources': ['v%(version)s.tar.gz'],
-        'checksums': ['7ff44cdbc14b7319ceef5fa50801edf78aea4892bec04475517763a6d46bd058'],
+        'patches': ['EVcouplings-0.2.1_update-ruamel-api.patch'],
+        'checksums': [
+            {'v0.2.1.tar.gz': '7ff44cdbc14b7319ceef5fa50801edf78aea4892bec04475517763a6d46bd058'},
+            {'EVcouplings-0.2.1_update-ruamel-api.patch':
+             '7e21635a7dba75fba7e0b2b5f4a63a00a3634e207f630506d7895ecceb76cf2b'},
+         ],
         # relax version requirement on ruamel.yaml
         'preinstallopts': "sed -i 's/ruamel.yaml<0.18/ruamel.yaml/' pyproject.toml &&",
     }),
 ]
 
-modextrapaths = {
-    'EVCOUPLINGS_RUNCFG_APP': 'bin/evcouplings_runcfg',
-    'EVCOUPLINGS_SUMMARIZE_APP': 'bin/evcouplings_summarize',
+modextravars = {
+    'EVCOUPLINGS_RUNCFG_APP': '%(installdir)s/bin/evcouplings_runcfg',
+    'EVCOUPLINGS_SUMMARIZE_APP': '%(installdir)s/bin/evcouplings_summarize',
+}
+
+sanity_check_paths = {
+    'files': ['bin/evcouplings', 'bin/evcouplings_runcfg', 'bin/evcouplings_summarize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
 }
 
 sanity_check_commands = [

easyconfigs/e/EVcouplings/EVcouplings-0.2.1_update-ruamel-api.patch

@@ -0,0 +1,89 @@
+update to new API in ruamel.yaml version 0.18
+see https://github.com/debbiemarkslab/EVcouplings/pull/333
+author: Alex Domingo (Vrije Universiteit Brussel)
+diff --git a/evcouplings/utils/config.py b/evcouplings/utils/config.py
+index fe8fb67..163f31f 100644
+--- a/evcouplings/utils/config.py
++++ b/evcouplings/utils/config.py
+@@ -10,7 +10,8 @@ Authors:
+   Thomas A. Hopf
+ """
+ 
+-import ruamel.yaml as yaml
++from ruamel.yaml import YAML
++from ruamel.yaml.error import MarkedYAMLError
+ 
+ 
+ class MissingParameterError(Exception):
+@@ -25,7 +26,7 @@ class InvalidParameterError(Exception):
+     """
+ 
+ 
+-def parse_config(config_str, preserve_order=False):
++def parse_config(config_str):
+     """
+     Parse a configuration string
+ 
+@@ -33,29 +34,25 @@ def parse_config(config_str, preserve_order=False):
+     ----------
+     config_str : str
+         Configuration to be parsed
+-    preserve_order : bool, optional (default: True)
+-        Preserve formatting of input configuration
+-        string
+ 
+     Returns
+     -------
+     dict
+         Configuration dictionary
+     """
++    # uses round-trip loader by default, preserving order
++    yaml = YAML(typ='safe', pure=True)
+     try:
+-        if preserve_order:
+-            return yaml.load(config_str, Loader=yaml.RoundTripLoader)
+-        else:
+-            return yaml.safe_load(config_str)
+-    except yaml.parser.ParserError as e:
++        return yaml.load(config_str)
++    except MarkedYAMLError as e:
+         raise InvalidParameterError(
+             "Could not parse input configuration. "
+             "Formatting mistake in config file? "
+-            "See ParserError above for details."
++            "See MarkedYAMLError above for details."
+         ) from e
+ 
+ 
+-def read_config_file(filename, preserve_order=False):
++def read_config_file(filename):
+     """
+     Read and parse a configuration file.
+ 
+@@ -70,7 +67,7 @@ def read_config_file(filename, preserve_order=False):
+         Configuration dictionary
+     """
+     with open(filename) as f:
+-        return parse_config(f, preserve_order)
++        return parse_config(f)
+ 
+ 
+ def write_config_file(out_filename, config):
+@@ -84,14 +81,11 @@ def write_config_file(out_filename, config):
+     config : dict
+         Config data that will be written to file
+     """
+-    if isinstance(config, yaml.comments.CommentedBase):
+-        dumper = yaml.RoundTripDumper
+-    else:
+-        dumper = yaml.Dumper
+-
++    yaml = YAML(typ='safe', pure=True)
++    yaml.default_flow_style = False
+     with open(out_filename, "w") as f:
+         f.write(
+-            yaml.dump(config, Dumper=dumper, default_flow_style=False)
++            yaml.dump(config)
+         )
+ 
+