run precommit

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

@@ -19,14 +19,14 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave liboctave-dev    
+        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        
-          
+        fetch-depth: 2
+
     - name: get bids-matlab and JSONio
       run: |
         make install_dev_octave
@@ -35,27 +35,22 @@ jobs:
       uses: joergbrech/moxunit-action@master
       with:
         tests: tests # files or directories containing the MOxUnit test cases
-        src: src lib/bids-matlab lib/JSONio # directories to be added to path before running the tests. 
+        src: src lib/bids-matlab lib/JSONio # directories to be added to path before running the tests.
         ext: tests/utils # External resources to add to the search put (excluded from coverage)
-        # data: # Directory for test data  
+        # 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         
+      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)        
-
-
-
-      
-
+       fail_ci_if_error: true # optional (default = false)

.gitignore

@@ -48,5 +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

@@ -11,4 +11,4 @@ install_dev_octave:
 
 clean:
 	rm -rf lib/bids-matlab
-	rm -rf lib/JSONio
+	rm -rf lib/JSONio

README.md

@@ -26,4 +26,4 @@ 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/postBuild

@@ -9,4 +9,3 @@ 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
-

docs/.gitignore

@@ -1 +1 @@
-build
+build

docs/requirements.txt

@@ -1,4 +1,4 @@
 Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
-sphinx_rtd_theme
+sphinx_rtd_theme