Merge branch 'main' into ancpBIDS

* main:
  Update codemeta.json for 0.2.0 release
  Release 0.2.0

Author: apdavison

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

@@ -122,7 +122,7 @@ 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.")

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

docs/source/conf.py

@@ -9,7 +9,7 @@
 project = 'bids2openminds'
 copyright = '2024, open Metadata Initiative'
 author = 'Peyman Najafi'
-release = '0.01'
+release = '0.2.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/index.rst

@@ -9,11 +9,12 @@ bids2openminds documentation
 A tool to generate `openMINDS metadata <https://openminds-documentation.readthedocs.io/en/latest/>`_ from `BIDS datasets <https://bids.neuroimaging.io/>`_
 
 .. note::
-   This project is under active development, please try the first alpha release and send us feedback by creating an issue.
+   This project is under active development, please send us feedback by creating an issue.
 
 
-We are curentlly supporting linux, windows and mac os.
+We are currently supporting Linux, Windows and Mac OS.
 
 .. toctree::
    installation
    usage
+   changelog

docs/source/usage.rst

@@ -1,14 +1,14 @@
 Usage
 =====
 
-You can use bids2openminds as both a command line tool and a python library.
+You can use bids2openminds as both a command line tool and a Python library.
 
 Usage as Python library
 =======================
 
 Overview
 ########
-The ``convert`` function processes a Brain Imaging Data Structure (BIDS) directory, converts its contents into OpenMINDS format, and optionally saves the output. It handles BIDS layout, extracts relevant information, and creates a dataset description based on BIDS data using OpenMINDS templates.
+The ``convert`` function processes a Brain Imaging Data Structure (BIDS) directory, converts its contents into openMINDS format, and optionally saves the output. It handles BIDS layout, extracts relevant information, and creates a dataset description based on BIDS data using openMINDS templates.
 
 
 Function Signature
@@ -18,15 +18,15 @@ Function Signature
 Parameters
 ##########
 - ``input_path`` (str): Path to the BIDS directory. This is required and must be a valid directory.
-- ``save_output`` (bool, default=False): If True, the converted OpenMINDS data will be saved to the specified output_path.
-- ``output_path`` (str, default=None): The path where the OpenMINDS data should be saved. If not specified, defaults to [``input_path``]/openminds.jsonld (single file mode) or [``input_path``]/openminds/ (multiple files mode).
-- ``multiple_files`` (bool, default=False): If True, the OpenMINDS data will be saved into multiple files within the specified output_path.
+- ``save_output`` (bool, default=False): If True, the converted openMINDS data will be saved to the specified output_path.
+- ``output_path`` (str, default=None): The path where the openMINDS data should be saved. If not specified, defaults to [``input_path``]/openminds.jsonld (single file mode) or [``input_path``]/openminds/ (multiple files mode).
+- ``multiple_files`` (bool, default=False): If True, the openMINDS data will be saved into multiple files within the specified output_path.
 - ``include_empty_properties`` (bool, default=False): If True, includes all the openMINDS properties with empty values in the final output. Otherwise includes only properties that have a non `None` value.
 - ``quiet`` (bool, default=False): If True, suppresses warnings and the final report output. Only prints success messages.
 
 Returns
 #######
-- ``collection`` (openminds.Collection): The OpenMINDS collection object representing the converted dataset. For more information on OpenMINDS collection please refer to `openMINDS readthedocs <https://openminds-documentation.readthedocs.io/en/latest/shared/getting_started/openMINDS_collections.html>`_.
+- ``collection`` (openminds.Collection): The openMINDS collection object representing the converted dataset. For more information on openMINDS collection please refer to `openMINDS readthedocs <https://openminds-documentation.readthedocs.io/en/latest/shared/getting_started/openMINDS_collections.html>`_.
 
 Example Usage
 #############
@@ -52,10 +52,9 @@ This function is also accessible via a command-line interface using the `click`
         input-path   Path to the BIDS directory.
 
     Options:
-        -o, --output-path PATH      The output path or filename for OpenMINDS file/files.
+        -o, --output-path PATH      The output path or filename for openMINDS file/files.
         --single-file               Save the entire collection into a single file (default).
         --multiple-files            Save each node into a separate file within the specified directory.
         -e, --include-empty-properties
                                     Include empty properties in the final file.
         -q, --quiet                 Suppress warnings and reports.
-

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bids2openminds"
-version = "0.1.1"
+version = "0.2.0"
 dependencies = [
   "ancpbids",
   "openminds >= 0.2.3",
@@ -16,7 +16,8 @@ authors = [
 ]
 description = "Generates openMINDS metadata from a BIDS dataset"
 readme = "README.md"
-license = {file = "LICENSE"}
+license = "MIT"
+license-files = ["LICENSE"]
 classifiers = [
   "Development Status :: 3 - Alpha",
   "Programming Language :: Python"