Merge pull request #367 from cpp-lln-lab/fmriprep_input

[ENH] allow fMRIprep input for GLM

Author: Remi-Gau

.dockerignore

@@ -0,0 +1,13 @@
+.vscode
+.git
+.github
+env
+demos/*/outputs/
+demos/*/inputs/
+demos/*/cfg/
+tests
+
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
+# lib

.github/workflows/miss_hit_quality.yml

@@ -28,6 +28,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
+        cd tests
+        make data
 
     - name: MISS_HIT Metrics
       run: |

.github/workflows/miss_hit_style.yml

@@ -28,8 +28,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
+        cd tests
+        make data
 
     - name: MISS_HIT Code style
       run: |
         mh_style
-

.github/workflows/run_system_tests.yml

@@ -1,15 +1,15 @@
 name: system tests
 
 # Uses the cron schedule for github actions
-# 
+#
 # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
-# 
+#
 # ┌───────────── minute (0 - 59)
 # │ ┌───────────── hour (0 - 23)
 # │ │ ┌───────────── day of the month (1 - 31)
 # │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
 # │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
-# │ │ │ │ │                                   
+# │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
 # * * * * *
@@ -20,7 +20,7 @@ on:
       - master
       - main
   pull_request:
-    branches: 
+    branches:
       - 'master'
       - 'main'
   schedule:
@@ -32,7 +32,7 @@ env:
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
 
@@ -42,7 +42,7 @@ jobs:
         sudo apt-get -y install octave liboctave-dev
         sudo apt-get -y install nodejs npm
 
-    - name: Clone cpp_spm         
+    - name: Clone cpp_spm
       uses: actions/checkout@v2
       with:
         submodules: true
@@ -55,10 +55,9 @@ jobs:
          make -C spm12/src PLATFORM=octave
          make -C spm12/src PLATFORM=octave install
          octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
-        
-    
+
+
     - name: Run system tests
       run: |
         cd manualTests/
-        octave $OCTFLAGS --eval "test_moae"                  
-
+        octave $OCTFLAGS --eval "test_moae"

.github/workflows/run_tests.yml

@@ -1,35 +1,33 @@
 name: tests and coverage
 
 # Uses the cron schedule for github actions
-# 
+#
 # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
-# 
+#
 # ┌───────────── minute (0 - 59)
 # │ ┌───────────── hour (0 - 23)
 # │ │ ┌───────────── day of the month (1 - 31)
 # │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
 # │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
-# │ │ │ │ │                                   
+# │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
 # * * * * *
 
 on:
   push:
     branches:
-      - dev
+      - master
   pull_request:
     branches: '*'
-  schedule:
-    - cron: "* * 1 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
 
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
 
@@ -38,8 +36,9 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install octave liboctave-dev
         sudo apt-get -y install nodejs npm
+        pip install datalad
 
-    - name: Clone cpp_spm         
+    - name: Clone cpp_spm
       uses: actions/checkout@v2
       with:
         submodules: true
@@ -58,12 +57,12 @@ jobs:
         git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
         make -C MOxUnit install
         git clone https://github.com/MOcov/MOcov.git --depth 1
-        make -C MOcov install    
-        
+        make -C MOcov install
+
     - name: Update octave path
       run: |
         octave $OCTFLAGS --eval "initCppSpm; savepath();"
-        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"        
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
 
     - name: Prepare data
       run: |
@@ -73,12 +72,11 @@ jobs:
         unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
         mv $inputs_folder/MoAEpilot $inputs_folder/raw
         cd tests
-        sh createDummyDataSet.sh
+        make data
         cd ..
 
     - name: Run tests
       run: |
         octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
-        bash <(curl -s https://codecov.io/bash)         
-
+        bash <(curl -s https://codecov.io/bash)

.gitignore

@@ -8,6 +8,10 @@
 *.ps
 *.png
 
+*.mat
+
+.zenodo.json
+
 # Project specific
 options_task-*date*.json
 onsets*_events.mat
@@ -20,11 +24,18 @@ venv/*
 ## visual studio code
 .vscode
 
+## from running tests in root dir
+cfg/*
+group/*
+models/*
+
+# jupyter notebooks
+.ipynb_checkpoints
+
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
 
-
 # Windows default autosave extension
 *.asv
 
@@ -56,5 +67,3 @@ codegen/
 
 # Octave session info
 octave-workspace
-
-

.gitmodules

@@ -13,3 +13,9 @@
 [submodule "lib/brain_colours"]
 	path = lib/brain_colours
 	url = https://github.com/CPernet/brain_colours.git
+[submodule "lib/rsHRF"]
+	path = lib/rsHRF
+	url = https://github.com/compneuro-da/rsHRF.git
+[submodule "lib/spm_2_bids"]
+	path = lib/spm_2_bids
+	url = https://github.com/cpp-lln-lab/spm_2_bids.git

.pre-commit-config.yaml

@@ -25,4 +25,12 @@ repos:
       entry: mh_lint
       files: ^(.*\.(m|slx))$
       language: python
-      additional_dependencies: [miss_hit]
+      additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

.readthedocs.yml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt

.zenodo.json

@@ -54,4 +54,4 @@
   ],
   "license": "GPL-3",
   "upload_type": "software"
-}
+}