Merge pull request #145 from cpp-lln-lab/dev

release candidate v0.1.0

Author: Remi-Gau

.all-contributorsrc

@@ -2,6 +2,7 @@
   "files": [
     "README.md"
   ],
+  "contributorsSortAlphabetically": true,
   "imageSize": 100,
   "commit": false,
   "contributors": [

.github/workflows/check_md_links.yml

@@ -0,0 +1,18 @@
+name: Check Markdown links
+
+# checking for any dead links in markdown files
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches: '*'
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/miss_hit.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: '*'
 
@@ -27,12 +28,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install install miss_hit
+        pip3 install miss_hit
 
     - name: Miss_hit code quality
       run: |
         mh_metric . --ci
 
     - name: Miss_hit code style
       run: |
-        mh_style .
+        mh_style .

.gitignore

@@ -7,8 +7,29 @@
 *.log
 *.html
 *.zip
+*.ps
 
+options_task-*.json
+onsets*_events.mat
 
 # files in the demo folder related to running the demo analysis
-demo/*.zip
-demo/output/*
+demos/MoAE/*.zip
+demos/MoAE/output/*
+demos/MoAE/derivatives/*
+
+# test folder
+tests/sub-01/*
+tests/group/*
+
+# ignore content of the build folder of the doc
+docs/build/*
+
+# ignore virtual env
+cpp_bids_spm/*
+
+# visual studio code stuff
+.vscode
+
+
+
+

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "lib/bids-matlab"]
+	path = lib/bids-matlab
+	url = https://github.com/cpp-lln-lab/bids-matlab.git
+[submodule "lib/spmup"]
+	path = lib/spmup
+	url = https://github.com/CPernet/spmup.git

.prettierrc

@@ -0,0 +1,13 @@
+{
+  "parser": "markdown",
+  "proseWrap": "always",
+  "tabWidth": 2,
+  "overrides": [
+    {
+      "files": "*.md",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

.remarkrc

@@ -0,0 +1,11 @@
+{
+  "plugins": [
+    "preset-lint-consistent",
+    "preset-lint-markdown-style-guide",
+    "preset-lint-recommended",
+    ["lint-no-duplicate-headings", false],
+    ["lint-list-item-indent", "tab-size"],
+    ["lint-maximum-line-length", true],
+    ["lint-maximum-heading-length", false]
+  ]
+}

.travis.yml

@@ -2,47 +2,104 @@
 # This will only work on your repo if you have an account on travis and you
 # have set it up to run continuous integration on this this repo
 
-# Linux distribution (bionic beaver)
 dist: bionic
 
-# Language and version
-language: python
-python:
-  - "3.6" # current default Python on Travis CI
+language: node_js
+node_js:
+  - "10"
 
 cache:
-  apt: true # only works with Pro version
+  apt: true
+  directories:
+  - node_modules
+
+# only run the CI for those branches 
+branches:
+  only:  
+    - master
+    - dev
 
 env:
   global:
     - OCTFLAGS="--no-gui --no-window-system --silent"
 
-before_install:
+# TODO maybe this could be refactored as this is not needed to check the 
+# the markdown linting
+install:
   # install octave
   - travis_retry sudo apt-get -y -qq update
   - travis_retry sudo apt-get -y install octave
   - travis_retry sudo apt-get -y install liboctave-dev
-  # install MOX unit
-  - git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
-  - cd MOxUnit
-  - make install
-  - cd ..
-  # install MOcov
-  - git clone https://github.com/MOcov/MOcov.git  --depth 1
-  - cd MOcov
-  - make install
-  - cd ..
+
   # install SPM and the relevant patches for octave
   - 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
 
-script:
-  - octave $OCTFLAGS --eval "runTests"
-  - cat test_report.log | grep 0
+  # update octave path
+  - octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
+  - octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
+  - octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
+
+jobs:
+  include:
+
+      #-------------------------------------------------------------------------
+      # first job
+      #-------------------------------------------------------------------------
+    - name: "Unit tests and coverage" 
+
+      before_script:
+
+        # install MOX unit
+        - git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+        - cd MOxUnit
+        - make install
+        - cd ..
+        
+        # install MOcov
+        - git clone https://github.com/MOcov/MOcov.git  --depth 1
+        - cd MOcov
+        - make install
+        - cd ..
+
+        # get data
+        - 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
+        
+      script:
+        - octave $OCTFLAGS --eval "runTests"
+        - cat test_report.log | grep 0
+
+      # to send the results to codecov to get our code coverage
+      after_success:
+        - bash <(curl -s https://codecov.io/bash) 
+
+      #-------------------------------------------------------------------------
+      # second job
+      #-------------------------------------------------------------------------
+    - name: "Check markdown"
+
+      before_script:
+        # install node.js dependencies
+        - npm install `cat npm-requirements.txt`
+
+      script:
+        - remark *.md --frail
+        - remark ./demos/ --frail
+        - remark ./docs/ --frail
+        - remark ./tests/ --frail
 
-after_success:
-  - bash <(curl -s https://codecov.io/bash)
+      #-------------------------------------------------------------------------
+      # third job
+      #-------------------------------------------------------------------------
+    - name: "Run demo"
 
+      if: branch = master
 
+      script:
+        - cd demos/MoAE
+        - octave $OCTFLAGS --eval "MoAEpilot_run"