Merge pull request #538 from cpp-lln-lab/rc2.0.0

rc2.0.0

Author: Remi-Gau

.dockerignore

@@ -0,0 +1,16 @@
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
+.vscode
+.git
+.github
+binder
+coverage_html
+demos/*/outputs/
+demos/*/inputs/
+demos/*/cfg/
+docs
+env
+manualTests
+templates
+tests

.github/release-drafter.yml

@@ -1,5 +1,5 @@
 template: |
   ## Release Notes
-  
+
   ## CHANGES
   $CHANGES

.github/workflows/check_md_links.yml

@@ -7,12 +7,20 @@ on:
     branches:
       - main
       - dev
+    paths:
+      - '**.md'
   pull_request:
-    branches: '*'
+    branches: ['*']
+    paths:
+      - '**.md'
 
 jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: 'yes'
+        use-verbose-mode: 'yes'
+        config-file: 'mlc_config.json'

.github/workflows/miss_hit.yml

@@ -0,0 +1,45 @@
+name: miss_hit
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+    paths:
+      - '**.m'
+      - '.github/workflows/miss_hit.yml'
+  pull_request:
+    branches: ['*']
+    paths:
+      - '**.m'
+      - '.github/workflows/miss_hit.yml'
+jobs:
+
+  miss_hit:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        command: ["mh_style", "mh_metric --ci && mh_lint"]
+      fail-fast: true  # cancel all jobs if one fails
+
+    steps:
+
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+
+    - name: ${{ matrix.command }}
+      run: |
+        ${{ matrix.command }}

.github/workflows/miss_hit_quality.yml

@@ -0,0 +1,107 @@
+name: system tests with matlab
+
+# 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:
+      - main
+      - dev
+    paths:
+      - '**.m'
+      - '.github/workflows/*system*'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - '**.m'
+      - '.github/workflows/*system*'
+  schedule:
+    - cron: "0 0 1,15 * *"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+
+  system_tests_matlab:
+
+    # only trigger update on upstream repo
+    if: github.repository_owner == 'cpp-lln-lab'
+
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        script: [moae, facerep, fmriprep]
+      fail-fast: false
+
+    steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get -y -qq update
+          sudo apt-get -y install unzip wget
+
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - name: Clone cpp_spm
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 2
+
+      # Prep for later
+      # - name: Install datalad
+      #   run: |
+      #     sudo apt-get -y -qq update
+      #     sudo apt-get -y install datalad
+      # - name: Info
+      #   run: |
+      #     datalad --version
+      # - name: Get fmriprep data
+      #   run: |
+      #     cd demos/
+      #     datalad install --source https://gin.g-node.org/SPM_datasets/spm_moae_fmriprep.git \
+      #                     inputs/fmriprep
+      #     cd inputs/fmriprep && datalad get *.json \
+      #                       */*/*tsv \
+      #                       */*/*json \
+      #                       */*/*desc-preproc*.nii.gz \
+      #                       */*/*desc-brain*.nii.gz
+
+      - name: Get moae fmriprep data from OSF
+        run: |
+          mkdir -p demos/MoAE/inputs/
+          cd demos/MoAE/inputs/
+          wget https://osf.io/vufjs/download
+          unzip download
+          mv moae_fmriprep fmriprep
+
+      - name: Install SPM
+        run: |
+          git clone https://github.com/spm/spm12.git --depth 1
+
+      - name: Copy Macs toolbox to SPM inputs_folder
+        run: cp -rv lib/MACS spm12/toolbox/MACS
+
+      - name: Run ${{ matrix.script }}
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};

.github/workflows/miss_hit_style.yml

@@ -1,36 +1,46 @@
-name: system tests
+name: "system tests with octave: failure expected"
 
 # 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:
       - main
+      - dev
+    paths:
+      - '**.m'
   pull_request:
-    branches: 
+    branches:
       - 'main'
+    paths:
+      - '**.m'
   schedule:
-    - cron: "0 0 1 * *"
+    - cron: "0 0 1,15 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
 
 jobs:
-  build:
 
-    runs-on: ubuntu-20.04
+  system_tests_octave:
+
+    # only trigger update on upstream repo
+    if: github.repository_owner == 'cpp-lln-lab'
+
+    runs-on: ubuntu-latest
 
     steps:
 
@@ -40,8 +50,8 @@ jobs:
         sudo apt-get -y install octave liboctave-dev
         sudo apt-get -y install nodejs npm
 
-    - name: Clone cpp_spm         
-      uses: actions/checkout@v2
+    - name: Clone cpp_spm
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 2
@@ -53,10 +63,8 @@ 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"