Ditch ruamel-yaml (keeps messing up due to the comment anchors) in fa…

…vor of pyyaml

bidscoin/bcoin.py

@@ -20,17 +20,13 @@
 from importlib.util import spec_from_file_location, module_from_spec
 from pathlib import Path
 from typing import Union
-from ruamel.yaml import YAML
 from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import templatefolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configdir, configfile, config, DEBUG
 
-yaml = YAML()
-yaml.representer.ignore_aliases = lambda *data: True                         # Expand aliases (https://stackoverflow.com/questions/58091449/disabling-alias-for-yaml-file-in-python)
-
 LOGGER = logging.getLogger(__name__)
 
 
@@ -266,7 +262,7 @@ def list_plugins(show: bool=False) -> tuple[list[Path], list[Path]]:
 
 def install_plugins(filenames: list[str]=()) -> None:
     """
-    Installs template bidsmaps and plugins and adds the plugin Options and data format section to the default template bidsmap
+    Installs template bidsmaps and plugins
 
     :param filenames:   Fullpath filenames of the and template bidsmaps plugins that need to be installed
     :return:            Nothing
@@ -276,13 +272,15 @@ def install_plugins(filenames: list[str]=()) -> None:
 
     files = [Path(file) for file in filenames if file.endswith('.yaml') or file.endswith('.py')]
 
-    # Load the default template bidsmap
-    with open(bidsmap_template, 'r') as stream:
-        template = yaml.load(stream)
-
     # Install the template bidsmaps and plugins in their targetfolder
     for file in files:
 
+        # Check if we can import the plugin
+        module = import_plugin(file.resolve())
+        if not module:
+            LOGGER.error(f"Plugin failure, please re-install a valid version of '{file.name}'")
+            continue
+
         # Copy the file to their target folder
         targetfolder = templatefolder if file.suffix == '.yaml' else pluginfolder
         LOGGER.info(f"Installing: '{file}'")
@@ -295,30 +293,12 @@ def install_plugins(filenames: list[str]=()) -> None:
             LOGGER.success(f"The '{file.name}' template bidsmap was successfully installed")
             continue
 
-        # Check if we can import the plugin
-        module = import_plugin(file)
-        if not module:
-            LOGGER.error(f"Plugin failure, please re-install a valid version of '{file.name}'")
-            continue
-
-        # Add the Options and data format section of the plugin to the default template bidsmap
-        if hasattr(module, 'OPTIONS') or hasattr(module, 'BIDSMAP'):
-            if hasattr(module, 'OPTIONS'):
-                LOGGER.info(f"Adding default {file.name} bidsmap options to the {bidsmap_template.stem} template")
-                template['Options']['plugins'][file.stem] = module.OPTIONS
-            if hasattr(module, 'BIDSMAP'):
-                for key, value in module.BIDSMAP.items():
-                    LOGGER.info(f"Adding default {key} bidsmappings to the {bidsmap_template.stem} template")
-                    template[key] = value
-            with open(bidsmap_template, 'w') as stream:
-                yaml.dump(template, stream)
-
         LOGGER.success(f"The '{file.name}' plugin was successfully installed")
 
 
 def uninstall_plugins(filenames: list[str]=(), wipe: bool=False) -> None:
     """
-    Uninstalls template bidsmaps and plugins and removes the plugin Options and data format section from the default template bidsmap
+    Uninstalls template bidsmaps and plugins
 
     :param filenames:   Fullpath filenames of the and template bidsmaps plugins that need to be uninstalled
     :param wipe:        Removes the plugin bidsmapping section if True
@@ -329,19 +309,9 @@ def uninstall_plugins(filenames: list[str]=(), wipe: bool=False) -> None:
 
     files = [Path(file) for file in filenames if file.endswith('.yaml') or file.endswith('.py')]
 
-    # Load the default template bidsmap
-    with open(bidsmap_template, 'r') as stream:
-        template = yaml.load(stream)
-
     # Uninstall the plugins
     for file in files:
 
-        # First check if we can import the plugin
-        if file.suffix == '.py':
-            module = import_plugin(pluginfolder/file.name)
-        else:
-            module = None
-
         # Remove the file from the target folder
         LOGGER.info(f"Uninstalling: '{file}'")
         sourcefolder = templatefolder if file.suffix == '.yaml' else pluginfolder
@@ -354,22 +324,6 @@ def uninstall_plugins(filenames: list[str]=(), wipe: bool=False) -> None:
             LOGGER.success(f"The '{file.name}' template bidsmap was successfully uninstalled")
             continue
 
-        # Remove the Options and data format section from the default template bidsmap
-        if not module:
-            LOGGER.warning(f"Cannot remove any {file.stem} bidsmap options from the {bidsmap_template.stem} template")
-            continue
-        if removed := hasattr(module, 'OPTIONS'):
-            LOGGER.info(f"Removing default {file.stem} bidsmap options from the {bidsmap_template.stem} template")
-            template['Options']['plugins'].pop(file.stem, None)
-        if wipe and hasattr(module, 'BIDSMAP'):
-            removed = True
-            for key, value in module.BIDSMAP.items():
-                LOGGER.info(f"Removing default {key} bidsmappings from the {bidsmap_template.stem} template")
-                template.pop(key, None)
-        if removed:
-            with open(bidsmap_template, 'w') as stream:
-                yaml.dump(template, stream)
-
         LOGGER.success(f"The '{file.stem}' plugin was successfully uninstalled")
 
 

bidscoin/bids.py

@@ -13,6 +13,7 @@
 import pandas as pd
 import ast
 import datetime
+import yaml
 import jsonschema
 import bidsschematools.schema as bst
 import dateutil.parser
@@ -25,9 +26,6 @@
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import bcoin, schemafolder, templatefolder, is_hidden, __version__
 from bidscoin.plugins import EventsParser
-from ruamel.yaml import YAML
-yaml = YAML()
-yaml.representer.ignore_aliases = lambda *data: True    # Expand aliases (https://stackoverflow.com/questions/58091449/disabling-alias-for-yaml-file-in-python)
 
 # Define custom data types (replace with proper classes or TypeAlias of Python >= 3.10)
 Plugin     = NewType('Plugin',     dict[str, Any])
@@ -53,6 +51,11 @@
 """The possible extensions of BIDS data files"""
 
 
+class NoAliasDumper(yaml.SafeDumper):
+    def ignore_aliases(self, data):
+        return True
+
+
 class DataSource:
     """Reads properties, attributes and BIDS-related features to sourcefiles of a supported dataformat (e.g. DICOM or PAR)"""
 
@@ -920,7 +923,7 @@ def __init__(self, yamlfile: Path, folder: Path=templatefolder, plugins: Iterabl
         if any(checks):
             LOGGER.info(f"Reading: {yamlfile}")
         with yamlfile.open('r') as stream:
-            bidsmap_data = yaml.load(stream)
+            bidsmap_data = yaml.safe_load(stream)
         self._data = bidsmap_data
         """The raw YAML data"""
 
@@ -1082,7 +1085,7 @@ def save(self, filename: Path=None):
         filename.parent.mkdir(parents=True, exist_ok=True)
         LOGGER.info(f"Saving bidsmap in: {filename}")
         with filename.open('w') as stream:
-            yaml.dump(self._data, stream)
+            yaml.dump(self._data, stream, NoAliasDumper, sort_keys=False)
 
     def validate(self, level: int=1) -> bool:
         """

bidscoin/bidseditor.py

@@ -933,11 +933,11 @@ def save_options(self):
         if yamlfile:
             LOGGER.info(f"Saving bidsmap options in: {yamlfile}")
             with open(yamlfile, 'r') as stream:
-                bidsmap = bids.yaml.load(stream)
+                bidsmap = bids.yaml.safe_load(stream)
             bidsmap.options = self.output_bidsmap.options
             bidsmap.plugins = self.output_bidsmap.plugins
             with open(yamlfile, 'w') as stream:
-                bids.yaml.dump(bidsmap, stream)
+                bids.yaml.safe_dump(bidsmap, stream, sort_keys=False)
 
     def sample_doubleclicked(self, item):
         """When source file is double-clicked in the samples_table, show the inspect- or edit-window"""
@@ -1346,7 +1346,7 @@ def import_menu(self, pos):
                         if Path(metafile).suffix == '.json':
                             metadata = json.load(meta_fid)
                         elif Path(metafile).suffix in ('.yaml', '.yml'):
-                            metadata = bids.yaml.load(meta_fid)
+                            metadata = bids.yaml.safe_load(meta_fid)
                         else:
                             dialect = csv.Sniffer().sniff(meta_fid.read())
                             meta_fid.seek(0)

docs/_static/dictionary-custom.txt

@@ -96,6 +96,7 @@ RDP
 README
 Radboud
 Refactored
+RunItem
 SBREF
 SDAT
 SPM
@@ -280,9 +281,9 @@ rawmapper
 rebranded
 refactoring
 regex
+ruamel
 runindex
 runitem
-RunItem
 runtime
 sbatch
 screenshot

pyproject.toml

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

tests/test_bidsmapper.py

@@ -1,19 +1,18 @@
 import pytest
 import re
-import ruamel.yaml
 from bidscoin import bcoin, bidsmapper, bidsmap_template
 
 bcoin.setup_logging()
 
 
-@pytest.mark.parametrize('subprefix', ['Doe'])
-@pytest.mark.parametrize('sesprefix', ['0'])
+@pytest.mark.parametrize('subprefix', ['Doe', 'Doe^', '*'])
+@pytest.mark.parametrize('sesprefix', ['0', '*'])
 @pytest.mark.parametrize('store', [False, True])
 def test_bidsmapper(raw_dicomdir, bids_dicomdir, bidsmap_dicomdir, subprefix, sesprefix, store):
     resubprefix = '' if subprefix=='*' else re.escape(subprefix).replace(r'\-','-')
     resesprefix = '' if sesprefix=='*' else re.escape(sesprefix).replace(r'\-','-')
     bidsmap     = bidsmapper.bidsmapper(raw_dicomdir, bids_dicomdir, bidsmap_dicomdir, bidsmap_template, [], subprefix, sesprefix, unzip='', store=store, automated=True, force=True)
-    assert isinstance(bidsmap.dataformats[0]._data, ruamel.yaml.CommentedMap)
+    assert isinstance(bidsmap.dataformats[0]._data, dict)
     assert bidsmap.options['subprefix'] == subprefix
     assert bidsmap.options['sesprefix'] == sesprefix
     assert bidsmap.dataformat('DICOM').subject                           == f"<<filepath:/{raw_dicomdir.name}/{resubprefix}(.*?)/>>"

tests/test_heuristics.py

@@ -1,9 +1,7 @@
 import jsonschema
 import json
+import yaml
 from bidscoin import bcoin, bidscoinroot
-from ruamel.yaml import YAML
-yaml = YAML()
-yaml.representer.ignore_aliases = lambda *data: True                         # Expand aliases (https://stackoverflow.com/questions/58091449/disabling-alias-for-yaml-file-in-python)
 
 bcoin.setup_logging()
 
@@ -15,5 +13,5 @@ def test_jsonschema_validate_bidsmaps():
         schema = json.load(stream)
     for template in (bidscoinroot/'heuristics').glob('*.yaml'):
         with template.open('r') as stream:
-            bidsmap = yaml.load(stream)
+            bidsmap = yaml.safe_load(stream)
         jsonschema.validate(bidsmap, schema)