[REL] Release 0.2.0

.github/workflows/check_markdown.yml

@@ -0,0 +1,32 @@
+name: Check Markdown
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - uses: actions/setup-node@v2
+      with:
+        node-version: '10'
+
+    - name: Install dependencies and check markdown
+      run: |
+        npm install `cat npm-requirements.txt`
+        npx remark *.md --frail
+        npx remark ./docs/ --frail
+        npx remark ./demos/ --frail
+        npx remark ./tests/ --frail

.github/workflows/check_md_links.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 

.github/workflows/miss_hit.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 
@@ -28,12 +27,16 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install miss_hit
+        pip3 install -r requirements.txt
 
-    - name: Miss_hit code quality
+    - name: MISS_HIT Code style
       run: |
-        mh_metric . --ci
+        mh_style --process-slx
 
-    - name: Miss_hit code style
+    - name: MISS_HIT Metrics
       run: |
-        mh_style .
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint

.github/workflows/run_system_tests.yml

@@ -0,0 +1,75 @@
+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)
+# │ │ │ │ │                                   
+# │ │ │ │ │
+# │ │ │ │ │
+# * * * * *
+
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches: 
+      - 'master'
+      - 'main'
+  schedule:
+    - cron: "* * 1 * *"
+
+env:
+  OCTFLAGS: --no-gui --no-window-system --silent
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install octave liboctave-dev
+        sudo apt-get -y install nodejs npm
+
+    - name: Clone cpp_spm         
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 2
+
+    - name: Install SPM
+      run: |
+         git clone https://github.com/spm/spm12.git --depth 1
+         make -C spm12/src PLATFORM=octave distclean
+         make -C spm12/src PLATFORM=octave
+         make -C spm12/src PLATFORM=octave install
+         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
+
+    - name: Update octave path
+      run: |
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
+
+    - name: Prepare data
+      run: |
+        output_folder='demos/MoAE/output/'
+        mkdir $output_folder
+        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
+        unzip $output_folder'MoAEpilot.zip' -d $output_folder
+
+    - name: Run system tests
+      run: |
+        cd demos/MoAE
+        octave $OCTFLAGS --eval "MoAEpilot_run"                  
+

.github/workflows/run_tests.yml

@@ -0,0 +1,83 @@
+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
+  pull_request:
+    branches: '*'
+  schedule:
+    - cron: "* * 1 * *"
+
+env:
+  OCTFLAGS: --no-gui --no-window-system --silent
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install octave liboctave-dev
+        sudo apt-get -y install nodejs npm
+
+    - name: Clone cpp_spm         
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 2
+
+    - name: Install SPM
+      run: |
+         git clone https://github.com/spm/spm12.git --depth 1
+         make -C spm12/src PLATFORM=octave distclean
+         make -C spm12/src PLATFORM=octave
+         make -C spm12/src PLATFORM=octave install
+         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
+
+    - name: Install Moxunit and MOcov
+      run: |
+        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    
+
+    - name: Update octave path
+      run: |
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
+
+    - name: Prepare data
+      run: |
+        output_folder='demos/MoAE/output/'
+        mkdir $output_folder
+        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $output_folder'MoAEpilot.zip'
+        unzip $output_folder'MoAEpilot.zip' -d $output_folder
+        cd tests
+        sh createDummyDataSet.sh
+        cd ..
+
+    - name: Run tests
+      run: |
+        octave $OCTFLAGS --eval "runTests"
+        cat test_report.log | grep 0
+        bash <(curl -s https://codecov.io/bash)         
+

.gitignore

@@ -9,23 +9,31 @@
 *.zip
 *.ps
 
-options_task-*.json
+options_task-*date*.json
 onsets*_events.mat
 
 # files in the demo folder related to running the demo analysis
-demos/MoAE/*.zip
+demos/*/*.zip
+demos/*/derivatives/*
 demos/MoAE/output/*
-demos/MoAE/derivatives/*
+demos/spm*/raw
+demos/spm*/source
 
-# test folder
+# test folder and dummy data
 tests/sub-01/*
 tests/group/*
+tests/models/*.json
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.nii*
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.tsv
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.txt
+tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.json
+tests/dummyData/derivatives/cpp_spm/sub-*/stats/*/*/*.nii*
 
 # ignore content of the build folder of the doc
 docs/build/*
 
 # ignore virtual env
-cpp_bids_spm/*
+cpp_spm/*
 
 # visual studio code stuff
 .vscode

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "lib/bids-matlab"]
 	path = lib/bids-matlab
-	url = https://github.com/cpp-lln-lab/bids-matlab.git
+	url = https://github.com/bids-standard/bids-matlab.git
 [submodule "lib/spmup"]
 	path = lib/spmup
 	url = https://github.com/CPernet/spmup.git

.readthedocs.yml

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