Merge branch 'main' into Content-Type

Author: Peyman-N

.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

bids2openminds/main.py

@@ -95,6 +95,7 @@ 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

@@ -44,6 +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:
@@ -70,6 +84,17 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
 Dataset title : {dataset.full_name}
 
 
+The following elements were converted:  
+------------------------------------------   
++ number of authors : {len(dataset_version.authors or [])}
++ number of converted subjects: {subject_number}  
++ number of states per subject: {text_subject_state_numbers}
++ number of files: {files_number} 
++ number of file bundles: {file_bundle_number}
++ number of techniques: {len(dataset_version.techniques or [])}
++ number of behavioral protocols: {behavioral_protocols_numbers}
+
+
 Experimental approaches detected:
 ------------------------------------------ 
 {experimental_approaches_list}
@@ -82,16 +107,13 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp
 ------------------------------------------
 {content_type_list}
 
+Detected techniques:
+------------------------------------------
+{techniques_list}
 
-The following elements were converted:  
-------------------------------------------   
-+ number of authors : {len(dataset_version.authors or [])}
-+ number of converted subjects: {subject_number}  
-+ number of states per subject: {text_subject_state_numbers}
-+ number of files: {files_number} 
-+ number of file bundles: {file_bundle_number}
-+ number of techniques: {len(dataset_version.techniques or [])}
-+ number of behavioral protocols: {behavioral_protocols_numbers}
+Detected behavioral protocols:
+------------------------------------------
+{behavioral_protocols_list}
 
 
 

pyproject.toml

@@ -47,3 +47,10 @@ line-length = 119
 
 [tool.setuptools]
 packages = ["bids2openminds"]
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.svg'
+check-hidden = true
+# ignore-regex = ''
+# ignore-words-list = ''