Expand ruamel.yaml aliases

Author: marcelzwiers

bidscoin/bcoin.py

@@ -14,6 +14,7 @@
 import urllib.request
 import time
 import argparse
+import copy
 from duecredit.cmdline import cmd_summary
 from functools import lru_cache
 from importlib.metadata import entry_points
@@ -29,6 +30,7 @@
 from bidscoin import templatefolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configfile, config, DEBUG
 
 yaml = YAML()
+yaml.composer.return_alias = lambda s: copy.deepcopy(s)                         # Expand aliases (https://stackoverflow.com/questions/66977002/yaml-anchor-for-sequence/66983530#66983530)
 
 LOGGER = logging.getLogger(__name__)
 

pyproject.toml

@@ -22,7 +22,7 @@ dependencies     = ['pandas',
                     'numpy',
                     'pydicom >= 2',
                     'PyQt6',
-                    'ruamel-yaml >= 0.15.35',
+                    'ruamel-yaml > 0.17.2',
                     'tomli >= 1.1.0 ; python_version < "3.11"',
                     'coloredlogs',
                     'tqdm >= 4.60.0',

tests/test_heuristics.py

@@ -1,8 +1,10 @@
 import jsonschema
 import json
+import copy
 from bidscoin import bcoin, bidscoinroot
 from ruamel.yaml import YAML
 yaml = YAML()
+yaml.composer.return_alias = lambda s: copy.deepcopy(s)                         # Expand aliases (https://stackoverflow.com/questions/66977002/yaml-anchor-for-sequence/66983530#66983530)
 
 bcoin.setup_logging()