Merge pull request #34 from yibeichan/nilearn-glm

7th tutorial - Nilearn multilevel (two-level) glm

Author: djarecka

.github/workflows/notebooks.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10']
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -28,6 +28,10 @@ jobs:
     - run: conda info
     - run: conda list
     - run: conda config --show
+    - name: Set git credentials
+      run: |
+        git config --global user.name "fake user"
+        git config --global user.email "fake@email"
     - name: Convert all md files to ipynb
       run: jupytext notebooks/*.md --to ipynb
     - name: Test notebooks with pytest

.gitignore

@@ -3,4 +3,6 @@ outputs/
 .DS_Store
 _build/
 *.ipynb
+*/*.ipynb
 .*.swp
+notebooks/*old*

environment.yml

@@ -3,10 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - git-annex
+  - datalad
   - pip
   - pip:
-    - datalad
     - pydra
     - jupyter
     - jupyter_contrib_nbextensions
@@ -17,6 +16,7 @@ dependencies:
     - nbval
     - nest_asyncio
     - psutil
+    - sh
     - pytest
     - numpy
     - pandas

jupyterbook/_config.yml

@@ -1,17 +1,20 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: Pydra Tutorial
+title: Tutorials
 author: Pydra Developers
 logo: logo.jpg
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
+only_build_toc_files: true
+
 execute:
   execute_notebooks: cache
   run_in_temp: true
   allow_errors: true
   timeout: -1
+  only_build_toc_files: true
 
 # Define the name of the latex output file for PDF builds
 latex:

jupyterbook/_toc.yml

@@ -4,14 +4,19 @@
 format: jb-book
 root: welcome
 parts:
-  - caption: Tutorials
+  - caption: Basic Concepts
+    numbered: True
     chapters:
     - file: notebooks/1_intro_pydra
     - file: notebooks/2_intro_functiontask
     - file: notebooks/3_intro_functiontask_state
     - file: notebooks/4_intro_workflow
     - file: notebooks/5_intro_shelltask
-    - file: notebooks/6_glm_from_nilearn
+  - caption: General Linear Model
+    numbered: True
+    chapters:
+    - file: notebooks/6_firstlevel_glm_nilearn
+    - file: notebooks/7_twolevel_glm_nilearn
   - caption: About Pydra
     chapters:
     - file: about/team

notebooks/1_intro_pydra.md

@@ -11,7 +11,7 @@ kernelspec:
   name: python3
 ---
 
-# 1. Pydra
+# Intro to Pydra
 
 +++
 

notebooks/2_intro_functiontask.md

@@ -11,7 +11,7 @@ kernelspec:
   name: python3
 ---
 
-# 2. FunctionTask
+# FunctionTask
 
 ```{code-cell}
 ---

notebooks/3_intro_functiontask_state.md

@@ -11,7 +11,7 @@ kernelspec:
   name: python3
 ---
 
-# 3. Tasks with States
+# Tasks with States
 
 Task might be run for a single set of input values or we can generate multiple sets, that will be called "states". If we want to run our `Task` multiple times we have to provide an input that is an iterable and specify the way we want to map values of the inputs to the specific states. In order to do it, we set so-called `splitter`.
 

notebooks/4_intro_workflow.md

@@ -11,7 +11,7 @@ kernelspec:
   name: python3
 ---
 
-# 4. Workflow
+# Workflow
 
 ```{code-cell}
 ---

notebooks/5_intro_shelltask.md

@@ -11,7 +11,7 @@ kernelspec:
   name: python3
 ---
 
-# 5. ShellCommandTask
+# ShellCommandTask
 
 ```{code-cell}
 ---