Merge pull request #564 from Remi-Gau/api

[ENH] create a BIDS app API

Author: Remi-Gau

.github/workflows/miss_hit_quality.yml

@@ -9,13 +9,14 @@ on:
     branches: ['*']
 
 jobs:
+
   build:
 
     runs-on: ubuntu-latest
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1

.github/workflows/miss_hit_style.yml

@@ -1,10 +1,12 @@
 name: miss_hit_style
 
 on:
+
   push:
     branches:
       - main
       - dev
+
   pull_request:
     branches: ['*']
 
@@ -15,12 +17,12 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
 
-    - name: Set up Python 3.6
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: 3.6

.github/workflows/run_system_tests_matlab.yml

@@ -21,15 +21,18 @@ on:
       - dev
   pull_request:
     branches:
-      - 'main'
+      - main
   schedule:
     - cron: "0 0 1,15 * *"
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
+# Allows you to run this workflow manually from the Actions tab
+
+workflow_dispatch:
 
 jobs:
+
   build:
+
     runs-on: ubuntu-20.04
 
     steps:
@@ -40,7 +43,7 @@ jobs:
           release: R2020a
 
       - name: Clone cpp_spm
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: true
           fetch-depth: 2

.github/workflows/run_system_tests_octave.yml

@@ -12,23 +12,27 @@ name: "system tests with octave: failure expected"
 # │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
-# * * * * *
+# \* \* \* \* \*
 
 on:
+
   push:
     branches:
       - main
       - dev
+
   pull_request:
     branches:
       - 'main'
+
   schedule:
     - cron: "0 0 1,15 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
 
 jobs:
+
   build:
 
     runs-on: ubuntu-latest
@@ -42,7 +46,7 @@ jobs:
         sudo apt-get -y install nodejs npm
 
     - name: Clone cpp_spm
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 2

.github/workflows/run_tests_matlab.yml

@@ -1,18 +1,19 @@
 name: tests and coverage with matlab
 
 on:
+
   push:
     branches:
       - main
       - dev
+
   pull_request:
     branches: ["*"]
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
 jobs:
+
   build:
+
     runs-on: ubuntu-20.04
 
     steps:
@@ -23,7 +24,7 @@ jobs:
           release: R2020a
 
       - name: Clone cpp_spm
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: true
           fetch-depth: 2

.github/workflows/run_tests_octave.yml

@@ -1,19 +1,5 @@
 name: "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:
@@ -22,9 +8,6 @@ on:
   pull_request:
     branches: ['*']
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
 
@@ -41,7 +24,7 @@ jobs:
         sudo apt-get -y install octave liboctave-dev
 
     - name: Clone cpp_spm
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 2
@@ -52,7 +35,7 @@ jobs:
          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();"
+         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath(); exit;"
 
     - name: Install Moxunit and MOcov
       run: |
@@ -63,12 +46,11 @@ jobs:
 
     - name: Update octave path
       run: |
-        octave $OCTFLAGS --eval "initCppSpm; savepath(); exit;"
-        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath(); exit;"
+        octave $OCTFLAGS --eval "initCppSpm(dev); savepath(); exit;"
 
     - name: Prepare data
       run: |
-        octave $OCTFLAGS --eval "initCppSpm; cd demos/MoAE; download_moae_ds(true); exit;"
+        octave $OCTFLAGS --eval "cd demos/MoAE; download_moae_ds(true); exit;"
         cd tests
         make data
 

.github/workflows/tests_matlab.m

@@ -10,7 +10,7 @@
 run moxunit_set_path();
 
 cd(root_dir);
-cpp_spm('dev');
+cpp_spm('action', 'dev');
 
 cd demos/MoAE;
 download_moae_ds(true);

.gitignore

@@ -22,9 +22,6 @@ cpp_spm
 env
 venv
 
-## visual studio code
-.vscode
-
 ## from running tests in root dir
 */cfg/*
 */group/*

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "json.schemas": [
+        {
+        "fileMatch": ["model-*_smdl.json"],
+        "url": "https://raw.githubusercontent.com/bids-standard/stats-models/gh-pages/BIDSStatsModel.json"
+        }
+    ]
+}

Dockerfile

@@ -13,7 +13,6 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
     git \
     octave \
     liboctave-dev \
-    datalad &&
     apt-get clean
 
 RUN rm -rf \
@@ -22,14 +21,14 @@ RUN rm -rf \
     /var/lib/apt/lists/* \
     /var/log/apt/term*
 
-RUN mkdir /opt/spm12 &&
-    curl -SL https://github.com/spm/spm12/archive/r7487.tar.gz |
-    tar -xzC /opt/spm12 --strip-components 1 &&
-    curl -SL https://raw.githubusercontent.com/spm/spm-docker/master/octave/spm12_r7487.patch |
-    patch -p0 &&
-    make -C /opt/spm12/src PLATFORM=octave distclean &&
-    make -C /opt/spm12/src PLATFORM=octave &&
-    make -C /opt/spm12/src PLATFORM=octave install &&
+RUN mkdir /opt/spm12 && \
+    curl -SL https://github.com/spm/spm12/archive/r7487.tar.gz | \
+    tar -xzC /opt/spm12 --strip-components 1 && \
+    curl -SL https://raw.githubusercontent.com/spm/spm-docker/master/octave/spm12_r7487.patch | \
+    patch -p0 && \
+    make -C /opt/spm12/src PLATFORM=octave distclean && \
+    make -C /opt/spm12/src PLATFORM=octave && \
+    make -C /opt/spm12/src PLATFORM=octave install && \
     ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
 
 RUN octave --no-gui --eval "addpath(\"/opt/spm12\"); savepath ();"