Merge branch 'main' into citation-file-handling

# Conflicts:
#	bids2openminds/converter.py
#	pyproject.toml
#	test/test_person.py

Author: Raphael-Gazzotti

.github/workflows/codespell.yml

@@ -1,3 +1,4 @@
+# Codespell configuration is within pyproject.toml
 ---
 name: Codespell
 
@@ -18,7 +19,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
-        with:
-          skip: light_openMINDS-bids2openminds-logo.svg, dark_openMINDS-bids2openminds-logo.svg

.github/workflows/test.yml

@@ -34,8 +34,15 @@ jobs:
 
     - name: Install package with test dependencies
       run: |
-        pip install .[test]
+        pip install -e .[test]
 
     - name: Test installed package
       run: |
-        pytest -v
+        pytest -v --cov=bids2openminds --cov-report=lcov
+
+    - name: Upload coverage to Coveralls
+      if: matrix.os == 'ubuntu-latest'
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        path-to-lcov: coverage.lcov

CHANGES.rst

@@ -0,0 +1,31 @@
+Changelog
+=========
+
+0.2.0 (2026-05-07)
+------------------
+
+- Update to openMINDS v4
+- Add content-type metadata to file objects
+- Improved conversion report: now lists detected behavioral protocols and tasks
+
+0.1.1 (2025-06-05)
+------------------
+
+- Pin to openMINDS v3 for stability
+- Fix compatibility with updated BIDS example datasets
+- Add Read the Docs documentation
+- Add project logo
+
+0.1.0 (2024-06-21)
+------------------
+
+Initial release. Features include:
+
+- Convert BIDS datasets to openMINDS metadata collections (JSON-LD)
+- CLI interface (``bids2openminds`` command)
+- Support for subjects, authors/persons, file repositories, behavioral protocols, and dataset versions
+- NIfTI version detection and content-type mapping
+- Subject age validation and anomaly checking
+- Conversion summary report
+- Test suite using BIDS example datasets
+- Cross-platform CI (Linux, Windows, macOS)

README.md

@@ -9,7 +9,7 @@
 # bids2openminds
 A tool to generate openMINDS metadata from BIDS datasets
 
-In active development, please try the first alpha release and send us feedback by creating an issue.  
+In active development, please send us feedback by creating an issue.
 
 ## Installation
 
@@ -23,7 +23,7 @@ pip install bids2openminds
 Usage: bids2openminds [OPTIONS] INPUT_PATH
 
 Options:
-  -o, --output-path PATH          The output path or filename for OpenMINDS
+  -o, --output-path PATH          The output path or filename for openMINDS
                                   file/files.
   --single-file                   Save the entire collection into a single
                                   file (default).

bids2openminds/converter.py

@@ -1,13 +1,63 @@
 import warnings
-from bids import BIDSLayout, BIDSValidator
-from openminds import Collection
 import os
 import yaml
+import pandas as pd
+from ancpbids import BIDSLayout
+from ancpbids.query import Artifact
+from ancpbids.model_base import DatatypeFolder
+from openminds import Collection
 import click
 from . import main
 from . import utility
 from . import report
 
+_ENTITY_RENAMES = {"sub": "subject", "ses": "session"}
+
+# Root-level BIDS files that ancpBIDS does not expose as Artifacts
+_ROOT_BIDS_FILES = [
+    ("dataset_description.json", "description", ".json"),
+    ("participants.tsv", "participants", ".tsv"),
+    ("participants.json", "participants", ".json"),
+    ("CHANGES", None, None),
+    ("README", None, None),
+    ("README.md", None, None),
+]
+
+
+def layout_to_df(layout):
+    dataset = layout.get_dataset()
+    rows = []
+
+    for obj in layout.get(return_type='object', scope='raw'):
+        if not isinstance(obj, Artifact):
+            continue
+        parent = obj.get_parent()
+        datatype = parent.name if isinstance(parent, DatatypeFolder) else None
+        row = {
+            "path": obj.get_absolute_path(),
+            "suffix": obj.suffix,
+            "datatype": datatype,
+            "extension": obj.extension,
+        }
+        for entity in obj.entities:
+            key = _ENTITY_RENAMES.get(entity.key, entity.key)
+            row[key] = entity.value
+        rows.append(row)
+
+    base_dir = os.path.abspath(dataset.base_dir_)
+    for fname, suffix, extension in _ROOT_BIDS_FILES:
+        path = os.path.join(base_dir, fname)
+        if not os.path.exists(path):
+            continue
+        row = {"path": path, "datatype": None}
+        if suffix is not None:
+            row["suffix"] = suffix
+        if extension is not None:
+            row["extension"] = extension
+        rows.append(row)
+
+    return pd.DataFrame(rows)
+
 
 def convert(input_path,  save_output=False, output_path=None, multiple_files=False, include_empty_properties=False, quiet=False):
     if not (os.path.isdir(input_path)):
@@ -24,7 +74,7 @@ def convert(input_path,  save_output=False, output_path=None, multiple_files=Fal
     collection = Collection()
     bids_layout = BIDSLayout(input_path)
 
-    layout_df = bids_layout.to_df()
+    layout_df = layout_to_df(bids_layout)
 
     subjects_id = bids_layout.get_subjects()
 
@@ -74,7 +124,7 @@ def convert(input_path,  save_output=False, output_path=None, multiple_files=Fal
 
 @click.command()
 @click.argument("input-path", type=click.Path(file_okay=False, exists=True))
-@click.option("-o", "--output-path", default=None, type=click.Path(file_okay=True, writable=True), help="The output path or filename for OpenMINDS file/files.")
+@click.option("-o", "--output-path", default=None, type=click.Path(file_okay=True, writable=True), help="The output path or filename for openMINDS file/files.")
 @click.option("--single-file", "multiple_files", flag_value=False, default=False, help="Save the entire collection into a single file (default).")
 @click.option("--multiple-files", "multiple_files", flag_value=True, help="Each node is saved into a separate file within the specified directory. 'output-path' if specified, must be a directory.")
 @click.option("-e", "--include-empty-properties", is_flag=True, default=False, help="Whether to include empty properties in the final file.")

bids2openminds/main.py

@@ -6,8 +6,8 @@
 import pandas as pd
 from nameparser import HumanName
 
-import openminds.v3.core as omcore
-import openminds.v3.controlled_terms as controlled_terms
+import openminds.v4.core as omcore
+import openminds.v4.controlled_terms as controlled_terms
 from openminds import IRI
 
 from .utility import table_filter, pd_table_value, file_hash, file_storage_size, detect_nifti_version
@@ -122,6 +122,7 @@ def create_behavioral_protocol(layout, collection):
 
 
 def techniques_openminds(suffix):
+    # TODO "MRIPulseSequence" and "MRIWeighting" should be added as soon as openMINDS v4 becomes available.
     possible_types = ["Technique", "AnalysisTechnique", "StimulationApproach",
                       "StimulationTechnique"]
 

bids2openminds/report.py

@@ -7,6 +7,7 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
     file_bundle_number = 0
     files_number = 0
     behavioral_protocols_numbers = 0
+    content_type_list = ""
 
     for item in collection:
         if item.type_.endswith("Subject"):
@@ -26,6 +27,10 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
 
             behavioral_protocols_numbers += 1
 
+        if item.type_.endswith("ContentType"):
+
+            content_type_list += f"{item.name}\n"
+
     experimental_approaches_list = ""
     if dataset_version.experimental_approaches is not None:
         for approache in dataset_version.experimental_approaches:
@@ -39,6 +44,20 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
         else:
             data_types_list = f"{dataset_version.data_types.name}\n"
 
+    techniques_list = ""
+    if dataset_version.techniques is not None:
+        for technique in dataset_version.techniques:
+            techniques_list += f"{technique.name}\n"
+    else:
+        techniques_list = "No techniques were detected. Please follow the BIDS recommendations for suffixes, as bids2openminds detects techniques based on suffixes."
+
+    behavioral_protocols_list = ""
+    if dataset_version.behavioral_protocols is not None:
+        for behavioral_protocol in dataset_version.behavioral_protocols:
+            behavioral_protocols_list += f"{behavioral_protocol.name}\n"
+    else:
+        behavioral_protocols_list = "No behavioral protocols were detected. Please follow the BIDS recommendations for task labels, as bids2openminds detects behavioral protocols based on task labels."
+
     author_list = ""
     i = 1
     if dataset_version.authors is not None:
@@ -65,14 +84,6 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
 Dataset title : {dataset.full_name}
 
 
-Experimental approaches detected:
------------------------------------------- 
-{experimental_approaches_list}
-
-Detected data types:
-------------------------------------------
-{data_types_list}
-
 The following elements were converted:  
 ------------------------------------------   
 + number of authors : {len(dataset_version.authors or [])}
@@ -84,6 +95,27 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
 + number of behavioral protocols: {behavioral_protocols_numbers}
 
 
+Experimental approaches detected:
+------------------------------------------ 
+{experimental_approaches_list}
+
+Detected data types:
+------------------------------------------
+{data_types_list}
+
+Detected content types:
+------------------------------------------
+{content_type_list}
+
+Detected techniques:
+------------------------------------------
+{techniques_list}
+
+Detected behavioral protocols:
+------------------------------------------
+{behavioral_protocols_list}
+
+
 
 **Important Notes**
 ------------------------------------------ 

bids2openminds/utility.py

@@ -7,9 +7,9 @@
 
 import pandas as pd
 
-import openminds.v3.controlled_terms as controlled_terms
-from openminds.v3.core import Hash, QuantitativeValue, ContentType
-from openminds.v3.controlled_terms import UnitOfMeasurement
+import openminds.v4.controlled_terms as controlled_terms
+from openminds.v4.core import Hash, QuantitativeValue, ContentType
+from openminds.v4.controlled_terms import UnitOfMeasurement
 
 
 def read_json(file_path: str) -> dict:
@@ -174,4 +174,4 @@ def detect_nifti_version(file_name, extension, file_size):
             elif sizeof_hdr == nii2_sizeof_hdr:
                 return ContentType.by_name("application/vnd.nifti.2")
 
-    return None
+    return ContentType.by_name("application/vnd.nifti.1")

codemeta.json

@@ -33,11 +33,11 @@
     "codeRepository": "https://github.com/openMetadataInitiative/bids2openminds",
     "contIntegration": "https://github.com/openMetadataInitiative/bids2openminds/actions",
     "dateCreated": "2024-02-02",
-    "dateModified": "2025-06-05",
+    "dateModified": "2026-05-07",
     "datePublished": "2024-06-21",
     "description": "A tool to generate openMINDS metadata from BIDS datasets",
     "developmentStatus": "active",
-    "downloadUrl": "https://files.pythonhosted.org/packages/28/7b/eeedbb1d40eb92dd87d9cd566f2301d31f2cf69a2a96c8f37f150af8a83c/bids2openminds-0.1.1.tar.gz",
+    "downloadUrl": "https://files.pythonhosted.org/packages/bd/54/a5edea82cf22de4d956b4992cd837f4db7220fd44533eb59e36c7b4bc867/bids2openminds-0.2.0.tar.gz",
     "funder": {
         "@type": "Organization",
         "name": "European Commission"
@@ -61,5 +61,5 @@
         "https://pypi.org/project/click/",
         "https://pypi.org/project/nameparser/"
     ],
-    "version": "0.1.1"
+    "version": "0.2.0"
 }

docs/source/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../../CHANGES.rst