Merge pull request #180 from cpp-lln-lab/dev

[FIX] apply patch end of line extra tab

.github/workflows/bids_validator.yml

@@ -5,7 +5,7 @@ on:
     branches:
       - master
   pull_request:
-    branches: 'master'
+    branches: ['master']
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
@@ -23,27 +23,23 @@ jobs:
     - name: Make jsonread for octave
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave 
+        sudo apt-get -y install octave
         sudo apt-get -y install liboctave-dev
         cd lib/JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
         cd ..
 
     - name: Update octave path
       run: |
+        octave $OCTFLAGS --eval "addpath(pwd); savepath();"
         octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();" 
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
 
     - name: Install BIDS validator
       run: |
         sudo npm install -g bids-validator@1.6.2
 
-    - name: Create dummy dataset and validate it 
+    - name: Create dummy dataset and validate it
       run: |
         cd tests/manualTests
         octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
-
-  
-
-
-

.github/workflows/check_md_links.yml

@@ -7,11 +7,11 @@ on:
     branches:
       - master
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/miss_hit.yml

@@ -5,8 +5,7 @@ on:
     branches:
       - master
   pull_request:
-    branches: '*'
-
+    branches: ['*']
 jobs:
   build:
 

.github/workflows/run_tests.yml

@@ -6,7 +6,7 @@ on:
       - master
       - dev
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   build:
@@ -21,7 +21,7 @@ jobs:
     - name: Make jsonread for octave
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave 
+        sudo apt-get -y install octave
         sudo apt-get -y install liboctave-dev
         cd lib/JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
@@ -30,7 +30,7 @@ jobs:
       uses: joergbrech/moxunit-action@master
       with:
         tests: tests # files or directories containing the MOxUnit test cases
-        src: src # directories to be added to the Octave search path before running the tests. 
+        src: src # directories to be added to the Octave search path before running the tests.
         ext: tests/utils # External resources to add to the search put (excluded from coverage)
         # data: # Directory for test data
         with_coverage: true

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_version
+      name: mh_version
+      entry: mh_style
+      args: [-v]
+      verbose: true
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    # - id: mh_style
+    #   name: mh_style
+    #   entry: mh_style
+    #   args: [--process-slx, --fix]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_metric
+    #   name: mh_metric
+    #   entry: mh_metric
+    #   args: [--ci]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_lint
+    #   name: mh_lint
+    #   entry: mh_lint
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

.readthedocs.yml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt

.zenodo.json

@@ -32,4 +32,4 @@
   ],
   "license": "MIT license",
   "upload_type": "software"
-}
+}

README.md

@@ -19,10 +19,6 @@
 
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS)
 
-**BIDS validator and linter**
-
-[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS)
-
 **Contributors**
 
 [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)

binder/postBuild

@@ -1,3 +1,2 @@
 cd ${HOME}
 cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
-

checkCppBidsDependencies.m

@@ -0,0 +1,65 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function checkCppBidsDependencies(cfg)
+    %
+    % Adds dependencies to the Matlab / Octave path and make sure we got all of them.
+    %
+    % USAGE::
+    %
+    %   checkCppBidsDependencies(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+
+    if nargin < 1
+        cfg.verbose = 2;
+    end
+
+    global CPP_BIDS_INITIALIZED
+
+    if isempty(CPP_BIDS_INITIALIZED)
+
+        GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
+
+        if strcmp(GITHUB_WORKSPACE, '/github/workspace')
+
+            pth = GITHUB_WORKSPACE;
+            addpath(genpath(fullfile(pth, 'lib')));
+
+        elseif isempty(GITHUB_WORKSPACE)  % local
+
+            pth = fullfile(fileparts(mfilename('fullpath')));
+
+            addpath(pth);
+
+            addpath(fullfile(pth, 'lib', 'utils'));
+
+            checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
+            checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
+
+            addpath(genpath(fullfile(pth, 'src')));
+
+        end
+
+        printCreditsCppBids(cfg);
+
+        CPP_BIDS_INITIALIZED = true();
+
+    else
+        fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
+
+    end
+
+end
+
+function checkSubmodule(pth)
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir(pth)) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned!', ...
+               'Try this in your terminal:', ...
+               ' git submodule update --recursive ']);
+    else
+        addpath(pth);
+    end
+end

docs/Makefile

@@ -18,3 +18,6 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+doc:
+	@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)"

docs/source/conf.py

@@ -31,7 +31,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinxcontrib.matlab', 
+    'sphinxcontrib.matlab',
     'sphinx.ext.autodoc']
 matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
 primary_domain = 'mat'
@@ -88,4 +88,4 @@
         'searchbox.html',
         'donate.html',
     ]
-}
+}

docs/source/contributing.rst

@@ -48,7 +48,7 @@ Template proposal
 
    end
 
-.. autofunction:: templateFunction  
+.. autofunction:: templateFunction
 
 
 Example code in the help section
@@ -100,6 +100,3 @@ Example code in the help section
    end
 
 .. autofunction:: templateFunctionExample
-
-
-