Update the BIDS-like saving to align with template directory

.github/workflows/bids_changelog.yml

@@ -0,0 +1,38 @@
+name: Update BIDS-like data template dir CHANGES.md
+
+on:
+  push:
+    paths:
+      - 'src/b2aiprep/data'
+  workflow_dispatch: # This allows manual triggering of the workflow
+
+jobs:
+  update-changelog:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Step 1: Check out the repository
+      - uses: actions/checkout@v3
+
+      # Step 2: Set up Node.js environment (required for auto-changelog)
+      - name: Set up Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: '16'
+
+      # Step 3: Install auto-changelog or any other changelog tool
+      - name: Install auto-changelog
+        run: npm install -g auto-changelog
+
+      # Step 4: Generate the changelog
+      - name: Generate changelog
+        run: auto-changelog -p
+
+      # Step 5: Commit and push the updated CHANGES.md file
+      - name: Commit and push changes
+        run: |
+          git config user.name "GitHub Actions"
+          git config user.email "[email protected]"
+          git add src/b2aiprep/data/b2ai-data-bids-like-template/CHANGES.md
+          git commit -m "Update b2ai-data-bids-like-template/CHANGES.md"
+          git push origin HEAD:main

.gitignore

@@ -146,5 +146,5 @@ cython_debug/
 # guide data
 guide/data/
 
-.DS_Store
+*.DS_Store
 cache-wf/

.pre-commit-config.yaml

@@ -5,29 +5,30 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.8.0
     hooks:
     -   id: black
--   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.6.2  # Replace with the latest version available
     hooks:
-    - id: flake8
-      exclude: ^(src/b2aiprep/_version\.py|versioneer\.py)$
+    -   id: ruff
+        args: ["--fix"]
+        exclude: ^(src/b2aiprep/_version\.py|versioneer\.py)$
 -   repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
     -   id: isort
         exclude: ^(src/b2aiprep/_version\.py|versioneer\.py)$
         args: ["--profile", "black"]
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
     -   id: codespell
         args: ["--skip=*.json"]

data/b2ai-data-bids-like-synthetic-1000-rows/sub-01401050-e9dd-486e-b0d4-0001ee7f861d/sub-01401050-e9dd-486e-b0d4-0001ee7f861d_airwaystenosis.json

@@ -0,0 +1,105 @@
+{
+  "resourceType": "QuestionnaireResponse",
+  "id": "01401050-e9dd-486e-b0d4-0001ee7f861d-airwaystenosis",
+  "questionnaire": "https://kind-lab.github.io/vbai-fhir/Questionnaire-drespairwaystenosisschema",
+  "status": "completed",
+  "item": [
+    {
+      "linkId": "record_id",
+      "answer": [
+        {
+          "valueString": "01401050-e9dd-486e-b0d4-0001ee7f861d"
+        }
+      ]
+    },
+    {
+      "linkId": "diagnosis_as_pft"
+    },
+    {
+      "linkId": "diagnosis_as_gsd"
+    },
+    {
+      "linkId": "diagnosis_as_gsd_yes___bronchoscopy"
+    },
+    {
+      "linkId": "diagnosis_as_gsd_yes___ct"
+    },
+    {
+      "linkId": "diagnosis_as_ds"
+    },
+    {
+      "linkId": "diagnosis_as_ds_bvfi_gs"
+    },
+    {
+      "linkId": "diagnosis_as_etiology"
+    },
+    {
+      "linkId": "diagnosis_as_etiology_auto_immune"
+    },
+    {
+      "linkId": "diagnosis_as_ds_mcg"
+    },
+    {
+      "linkId": "diagnosis_as_ds_bc"
+    },
+    {
+      "linkId": "diagnosis_as_ds_agw"
+    },
+    {
+      "linkId": "diagnosis_as_ds_ac"
+    },
+    {
+      "linkId": "diagnosis_as_ds_ac_grade_4"
+    },
+    {
+      "linkId": "diagnosis_as_ds_ods"
+    },
+    {
+      "linkId": "diagnosis_as_ds_eps"
+    },
+    {
+      "linkId": "diagnosis_as_treatment___no_treatment"
+    },
+    {
+      "linkId": "diagnosis_as_treatment___surgery"
+    },
+    {
+      "linkId": "diagnosis_as_treatment___in_office_treatment"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___endoscopic_intervention",
+      "answer": [
+        {
+          "valueBoolean": false
+        }
+      ]
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___endoscopic_excision"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___laryngotracheal_reconstruction"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___laryngotracheoplasty"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___tracheostomy"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_surgery___other"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_in_office___steroid_injections_sole"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_in_office___steroid_injections_adjunct"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_in_office___dilation"
+    },
+    {
+      "linkId": "diagnosis_as_treatment_in_office___laser"
+    }
+  ]
+}

data/b2ai-data-bids-like-synthetic-1000-rows/sub-01401050-e9dd-486e-b0d4-0001ee7f861d/sub-01401050-e9dd-486e-b0d4-0001ee7f861d_als.json

@@ -0,0 +1,128 @@
+{
+  "resourceType": "QuestionnaireResponse",
+  "id": "01401050-e9dd-486e-b0d4-0001ee7f861d-als",
+  "questionnaire": "https://kind-lab.github.io/vbai-fhir/Questionnaire-dneuroamyotrophiclateralsclerosisalsschema",
+  "status": "completed",
+  "item": [
+    {
+      "linkId": "record_id",
+      "answer": [
+        {
+          "valueString": "01401050-e9dd-486e-b0d4-0001ee7f861d"
+        }
+      ]
+    },
+    {
+      "linkId": "diagnosis_als_gsd_category_1"
+    },
+    {
+      "linkId": "diagnosis_als_gsd_category_2"
+    },
+    {
+      "linkId": "diagnosis_als_gsd_category_3"
+    },
+    {
+      "linkId": "diagnosis_als_gsd_calculation"
+    },
+    {
+      "linkId": "diagnosis_als_disease_subtype"
+    },
+    {
+      "linkId": "diagnosis_als_disease_subtype_familial"
+    },
+    {
+      "linkId": "diagnosis_als_etiology___genetic_factors"
+    },
+    {
+      "linkId": "diagnosis_als_etiology___environmental_factors"
+    },
+    {
+      "linkId": "diagnosis_als_etiology_genetic_factors___c9orf72"
+    },
+    {
+      "linkId": "diagnosis_als_etiology_genetic_factors___sod1"
+    },
+    {
+      "linkId": "diagnosis_als_etiology_genetic_factors___other"
+    },
+    {
+      "linkId": "diagnosis_als_cp___upper_motor_neuron"
+    },
+    {
+      "linkId": "diagnosis_als_cp___lower_motor_neuron"
+    },
+    {
+      "linkId": "diagnosis_als_cp___bulbar_symptoms"
+    },
+    {
+      "linkId": "diagnosis_als_cp___respiratory_involvement"
+    },
+    {
+      "linkId": "diagnosis_als_dp"
+    },
+    {
+      "linkId": "diagnosis_als_na_alsfrs_r_score"
+    },
+    {
+      "linkId": "diagnosis_als_na_fvc_percentage"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes___medications"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes___supportive_care"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___riluzole"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___edaravone"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___sodium"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___tofersen"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___symptomatic_treatment"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_medications___other"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___physical_therapy",
+      "answer": [
+        {
+          "valueBoolean": false
+        }
+      ]
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___occupational_therapy"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___speech_therapy"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___respiratory_support"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___nutrition_support",
+      "answer": [
+        {
+          "valueBoolean": false
+        }
+      ]
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___psychotherapy"
+    },
+    {
+      "linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___other"
+    }
+  ]
+}