Merge pull request #10 from cpp-lln-lab/update_bids_matlab

[ENH] Update bids matlab

Author: Remi-Gau

.github/workflows/miss_hit_code_quality.yml

@@ -32,12 +32,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install -r requirements.txt   
+        pip3 install -r requirements.txt
 
     - name: MISS_HIT Metrics
       run: |
         mh_metric --ci
 
     - name: MISS_HIT Bug finder
       run: |
-        mh_lint
+        mh_lint

.github/workflows/miss_hit_code_style.yml

@@ -32,8 +32,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install -r requirements.txt  
+        pip3 install -r requirements.txt
 
     - name: MISS_HIT Code style
       run: |
-        mh_style --process-slx
+        mh_style --process-slx

.github/workflows/run_tests.yml

@@ -6,15 +6,12 @@ on:
       - master
       - main
       - dev
-  pull_request:
-    branches: '*'
 
-env:
-  OCTFLAGS: --no-gui --no-window-system --silent
+  pull_request:
+    branches: ['*']
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
 
     steps:
@@ -24,37 +21,36 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install octave liboctave-dev
 
-    - name: Clone spm_2_bids         
+    - name: Clone spm_2_bids
       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
+    - name: get bids-matlab and JSONio
       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: get bids-matlab and set up paths
-      run: |
-        make install_dev
-        octave $OCTFLAGS --eval "init_env; savepath();"
-      
-    - name: Run tests
-      run: |
-        octave $OCTFLAGS --eval "run_tests"
-        cat test_report.log | grep 0
-        bash <(curl -s https://codecov.io/bash)
+        make install_dev_octave
 
-      
+    - name: MOxUnit Action
+      uses: joergbrech/[email protected]
+      with:
+        tests: tests # files or directories containing the MOxUnit test cases
+        src: src  # directories to be added to path before running the tests.
+        ext: tests/utils lib/bids-matlab lib/JSONio # External resources to add to the search put (excluded from coverage)
+        # data: # Directory for test data
+        with_coverage: true
+        cover_xml_file: coverage.xml
+
+    - name: Upload coverage
+      uses: actions/upload-artifact@v1
+      with:
+        name: coverage_file
+        path: coverage.xml
 
+    - name: Code coverage
+      uses: codecov/codecov-action@v1
+      with:
+       file:  coverage.xml # optional
+       flags: unittests # optional
+       name: codecov-umbrella # optional
+       fail_ci_if_error: true # optional (default = false)

.gitignore

@@ -6,7 +6,11 @@
 env/
 
 lib/bids-matlab
+lib/JSONio
 
+coverage_html
+coverage.xml
+test_report.log
 
 ## MATLAB / OCTAVE gitignore template
 
@@ -44,5 +48,3 @@ codegen/
 
 # Octave session info
 octave-workspace
-
-

.pre-commit-config.yaml

@@ -25,4 +25,18 @@ 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: v4.1.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files
+
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+    -   id: rst-backticks # Detect common mistake of using single backticks when writing rst
+    -   id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst

Makefile

@@ -1,6 +1,14 @@
 install_dev:
 	git clone https://github.com/bids-standard/bids-matlab.git lib/bids-matlab
 	cd lib/bids-matlab && git checkout dev
+	git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
+
+install_dev_octave:
+	git clone https://github.com/bids-standard/bids-matlab.git lib/bids-matlab
+	cd lib/bids-matlab && git checkout dev
+	git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
+	cd lib/JSONio && mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
 
 clean:
-	rm -rf lib/bids-matlab
+	rm -rf lib/bids-matlab
+	rm -rf lib/JSONio

README.md

@@ -14,6 +14,7 @@ When you have set up your repo
 [![Build Status](https://travis-ci.com/Remi-gau/template_matlab_analysis.svg?branch=master)](https://travis-ci.com/Remi-gau/template_matlab_analysis)
 
 -->
+
 # spm_2_bids
 
 Small code base to help convert the MRI spm output to a valid bids derivatives.
@@ -26,4 +27,4 @@ Most of the renaming is based on the SPM prefixes combinations.
 It is configurable to adapt to new set of prefixes.
 
 - [Dependencies](./lib/README.md)
-- [Documentation](https://spm-2-bids.readthedocs.io/en/latest/)
+- [Documentation](https://spm-2-bids.readthedocs.io/en/latest/)

binder/apt.txt

@@ -0,0 +1,5 @@
+octave
+liboctave-dev
+gnuplot
+ghostscript
+tree

binder/environment.yml

@@ -0,0 +1,2 @@
+dependencies:
+- octave_kernel

binder/postBuild

@@ -0,0 +1,11 @@
+cd ${HOME}
+
+octave --no-gui --no-window-system --silent --eval "addpath (getenv (\"HOME\")); savepath ();"
+octave --no-gui --no-window-system --silent --eval "addpath (fullfile (getenv (\"HOME\"), \"+bids\")); savepath ();"
+
+git clone git://github.com/gllmflndn/JSONio.git --depth 1
+cd JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
+
+octave --no-gui --no-window-system --silent --eval "addpath (fullfile (getenv (\"HOME\"), \"JSONio\")); savepath ();"
+
+cd ${HOME}/examples