Merge pull request #100 from FZJ-INM1-BDA/chore_bugfixes

bugfixes - misc

Author: dickscheid

.github/workflows/siibra-testing.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.8', '3.7' ]
+        python-version: [ '3.8', '3.7', '3.6' ]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

requirements.txt

@@ -1,4 +1,4 @@
-numpy>=1.20
+numpy
 requests
 nibabel
 anytree

siibra/core/concept.py

@@ -137,9 +137,7 @@ def _populate_datasets(self):
             type_id = Dataset.extract_type_id(spec)
             Specialist = Dataset.REGISTRY.get(type_id, None)
             if Specialist is None:
-                raise RuntimeError(
-                    f"No class available for building datasets with type {spec.get('@type',None)}. Candidates were {','.join(Dataset.REGISTRY.keys())}. Specification was: {spec}."
-                )
+                logger.warn(f"No class available for building datasets with type {spec.get('@type',None)}. Candidates were {','.join(Dataset.REGISTRY.keys())}. Specification was: {spec}.")
             else:
                 obj = Specialist._from_json(spec)
                 logger.debug(

siibra/core/region.py

@@ -44,6 +44,7 @@
     "Both",
 ]
 
+REGEX_TYPE=type(re.compile('test'))
 
 class Region(anytree.NodeMixin, AtlasConcept):
     """
@@ -274,9 +275,6 @@ def splitstr(s):
             return self.index.label == regionspec
         elif isinstance(regionspec, ParcellationIndex):
             return self.index == regionspec
-        elif isinstance(regionspec, re.Pattern):
-            # match regular expression
-            return any(regionspec.search(s) is not None for s in [self.name, self.key])
         elif isinstance(regionspec, str):
             # string is given, perform some lazy string matching
             q = regionspec.lower().strip()
@@ -292,6 +290,10 @@ def splitstr(s):
                         for w in splitstr(__class__._clear_name(regionspec))
                     ]
                 )
+        # Python 3.6 does not support re.Pattern
+        elif isinstance(regionspec, REGEX_TYPE):
+            # match regular expression
+            return any(regionspec.search(s) is not None for s in [self.name, self.key])
         else:
             raise TypeError(
                 f"Cannot interpret region specification of type '{type(regionspec)}'"

siibra/features/ieeg.py

@@ -215,7 +215,7 @@ def __init__(self,**kwargs):
             logger.debug(f"Retrieving from {fname}")
 
             obj = parse_ptsfile(loader.data.decode())
-            subject_id = fname.split("_")[0]
+            subject_id = fname.replace('ieeg_contact_points/', '').split("_")[0]
             session = dset.new_session(subject_id)
             for electrode_id, contact_points in obj.items():
                 electrode = session.new_electrode(electrode_id)

siibra/features/receptors.py

@@ -367,6 +367,8 @@ def __init__(self, region, kg_result):
         self.modality = kg_result["modality"]
 
         urls = kg_result["files"]
+        
+        self.files=urls
 
         def urls_matching(regex):
             return filter(lambda u: re.match(regex, u), urls)