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

[ENH] Update bids matlab

.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

docs/.gitignore

@@ -0,0 +1 @@
+build

docs/Makefile

@@ -18,6 +18,3 @@ 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/README.md

@@ -3,8 +3,8 @@
 ## Set up virtual environment
 
 ```bash
-virtualenv -p python3 your_repo_name
-source your_repo_name/bin/activate
+virtualenv -p python3.8 env
+source env/bin/activate
 
 pip install -r requirements.txt
 ```

docs/requirements.txt

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

docs/source/conf.py

@@ -17,12 +17,11 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'your repo name'
-copyright = 'you'
-author = 'you'
+project = 'spm_2_bids'
+author = 'Rémi Gau'
 
 # The full version, including alpha/beta/rc tags
-release = 'v0.0.0'
+release = 'v0.1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,7 +30,7 @@
 # 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'
@@ -53,6 +52,8 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
+autodoc_member_order = 'bysource'
+
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -64,7 +65,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # html_logo = '_static/logo.png'
 
@@ -82,4 +83,4 @@
         'searchbox.html',
         'donate.html',
     ]
-}
+}

docs/source/index.rst

@@ -1,7 +1,7 @@
 .. cpp_bids documentation master file
 
-Welcome to CPP BIDS documentation!
-**********************************
+Welcome to spm_2_bids documentation!
+************************************
 
 .. toctree::
    :maxdepth: 2
@@ -12,11 +12,18 @@ Welcome to CPP BIDS documentation!
 ``spm_2_bids`` only provides names to use but does not actually rename the files.
 
 .. automodule:: src
+
 .. autofunction:: spm_2_bids
 
 .. automodule:: src.defaults
+
 .. autofunction:: check_cfg
 
+.. autoclass:: Mapping
+    :members:
+
+
+
 
 Indices and tables
 ==================

init_env.m → init_spm_2_bids.m

@@ -1,4 +1,4 @@
-function init_env
+function init_spm_2_bids
     %
     % 1 - Check if version requirements
     % are satisfied and the packages are
@@ -18,10 +18,12 @@
     OCTAVE_VER = '4.0.3';
     MATLAB_VER = '8.6.0';
 
-    INSTALL_LIST = {'io', 'statistics', 'image'};
+    INSTALL_LIST = {};
 
     if is_octave
 
+        more off;
+
         % Exit if min version is not satisfied
         if ~compare_versions(OCTAVE_VERSION, OCTAVE_VER, '>=')
             error('Minimum required Octave version: %s', OCTAVE_VER);

lib/README.md

@@ -4,8 +4,4 @@ This code requires:
 
 -   SPM12 for some actions ???
 
--   [BIDS-matlab](https://github.com/bids-standard/bids-matlab) from commi
-    [b7732b0cb](https://github.com/bids-standard/bids-matlab/commit/b7732b0cb2103ee0cfa095ee604bee4086844cad)
-    or later. In doubt use the `dev` branch of bids-matlab.
-
-
+-   [BIDS-matlab](https://github.com/bids-standard/bids-matlab) ; version 0.1.0

miss_hit.cfg

@@ -4,15 +4,18 @@ project_root
 line_length: 100
 
 regex_function_name: "[a-z]+(_[a-z0-9]+)*"
-regex_script_name: "[a-z]+(_[a-z0-9]+)*"
+regex_class_name: "[A-Z]{1}[a-z]+"
+regex_script_name: "[a-z]+(_[a-z]+)*"
+
+# suppress_rule: "naming_parameters"
 # regex_parameter_name: "[a-z]+(_[a-z0-9]+)*"
 
 exclude_dir: "lib"
 
 copyright_entity: "spm_2_bids developers"
 
 # metric for code quality
-metric "cnest": limit 6
+metric "cnest": limit 5
 metric "file_length": limit 500
-metric "cyc": limit 25
-metric "parameters": limit 5
+metric "cyc": limit 13
+metric "parameters": limit 5

notebooks/.gitignore

@@ -0,0 +1 @@
+.ipynb_checkpoints