Merge pull request #13 from NeuroHackademy2024/organize-learning-materials

Organize learning materials

Author: aptinis

.github/workflows/lint.yaml

@@ -9,6 +9,10 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
+        with:
+          # super-linter needs the full git history to get the
+          # list of files that changed across commits
+          fetch-depth: 0
 
       - name: Set up Python 3.10
         uses: actions/setup-python@v5
@@ -37,9 +41,9 @@ jobs:
           poetry run black . --check --diff
 
       - name: Run GitHub super-linter
-        uses: github/super-linter/slim@v6
+        uses: super-linter/super-linter/slim@v6
         env:
-          DEFAULT_BRANCH: master
+          DEFAULT_BRANCH: main
           # To report GitHub Actions status checks
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VALIDATE_ALL_CODEBASE: true

bids_fx.py renamed to learning_materials/bids_fx.py

@@ -1,25 +1,21 @@
 # Project: BIDSInspec
-## Objective: Create a function that can query the BIDS directory
+# Objective: Create a function that can query the BIDS directory
 # Modified: August 8, 2024 @ 9:08 PM by N.O.
-
 # Implementation via pybids
-## Complete pybids tutorial
-
+# Complete pybids tutorial
 # Install pybids via conda
-## pip install pybids
-
+# pip install pybids
 # Loading BIDS datasets
+import os
+
 from bids import BIDSLayout
 from bids.tests import get_test_data_path
-import os
 
 # Here we're using an example BIDS dataset that's bundled with the pybids tests
-data_path = os.path.join(get_test_data_path(), '7t_trt')
+data_path = os.path.join(get_test_data_path(), "7t_trt")
 
 # Initialize the layout
 layout = BIDSLayout(data_path)
 
 # Print some basic information about the layout
 layout
-
-

bids_pybids_tutorial.py renamed to learning_materials/bids_pybids_tutorial.py

@@ -1,20 +1,19 @@
 # Project: BIDSInspec
-## Objective: Complete the pybids tutorial
+# Objective: Complete the pybids tutorial
 # Modified: August 8, 2024 @ 9:08 PM by N.O.
-
 # Implementation via pybids
-## Must first complete pybids tutorial to understand the package
-
+# Must first complete pybids tutorial to understand the package
 # Install bids
 # pip install bids
 # Install pybids
-## pip install pybids
-
+# pip install pybids
 # Import
 from os.path import join
+
 from bids import BIDSLayout
 from bids.tests import get_test_data_path
-layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
+
+layout = BIDSLayout(join(get_test_data_path(), "synthetic"))
 
 # View data
 print(layout)
@@ -26,9 +25,10 @@
 print(layout.get_tasks())
 
 # Extract metadata
-# get task timing information for a given fMRI scan # cannot run since bids-dataset does not have NIfTI files
+# get task timing information for a given fMRI scan
+# cannot run since bids-dataset does not have NIfTI files
 # f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename
-#print(layout.get_events(f))
+# print(layout.get_events(f))
 
 # get metadata from json files # cannot run since bids-dataset does not have NIfTI files
 # f = layout.get(task='nback', run=1, extension='nii.gz')[0].filename

ds114/dataset_description.json renamed to learning_materials/ds114/dataset_description.json

@@ -1,3 +1,5 @@
+#!/usr/bin/env bash
+
 # Project: BIDSInspec
 ## Objective: Select BIDS directory from bids-examples.git and validate with BIDS validator
 # Modified: August 8, 2024 @ 9:08 PM by N.O.