Merge branch 'dev' into cer-imcalcDefaultOpt

Author: CerenB

.github/workflows/run_system_tests.yml

@@ -60,5 +60,5 @@ jobs:
     - name: Run system tests
       run: |
         cd manualTests/
-        octave $OCTFLAGS --eval "systemTestMoAE"                  
+        octave $OCTFLAGS --eval "test_moae"                  
 

.gitignore

@@ -1,39 +1,61 @@
-
+# General
 .DS_Store
-*.asv
-*.m~
-*.mat
+
 *.xml
 *.log
-*.html
 *.zip
+*.html
 *.ps
 
+*.mat
+
+# Project specific
 options_task-*date*.json
 onsets*_events.mat
 
-# files in the demo folder related to running the demo analysis
-demos/*/outputs/
-demos/*/inputs/
-demos/*/*.nii
-demos/*/cfg/*.json
-
-# test folder and dummy data
-tests/*.png
-tests/group/*
-tests/*/*.json
-tests/dummyData/derivatives/cpp_spm*/sub-*/
-
-# ignore content of the build folder of the doc
-docs/build/*
-
-# ignore virtual env
+## virtual env
 cpp_spm/*
 env/*
+venv/*
 
-# visual studio code stuff
+## visual studio code
 .vscode
 
+## MATLAB / OCTAVE gitignore template
+
+# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
+
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
 
+# Octave session info
+octave-workspace
 
 

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - 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]

README.md

@@ -145,6 +145,23 @@ Scripts names in general and as well functions related to the demos use a
 
 Constant are written in `UPPERCASE`.
 
+#### Pre-commit
+
+There is a [pre-commit hook](https://pre-commit.com/) that you can use to
+reformat files as you commit them.
+
+Install pre-commit by using our `requirements.txt` file 
+```bash
+pip install -r requirements.txt
+```
+
+Install the hook
+```bash
+pre-commit install
+```
+
+You're done. `mh_style --fix` will now be run every time you commit.
+
 ## Contributors
 
 Thanks goes to these wonderful people

demos/.gitignore

@@ -0,0 +1,5 @@
+# files in the demo folder related to running the demo analysis
+*/outputs/
+*/inputs/
+*/*.nii
+*/cfg/*.json

demos/openneuro/ds000114_get_option.m

@@ -16,8 +16,7 @@
   opt.taskName = 'linebisection';
 
   opt.anatReference.type = 'T1w';
-  opt.anatReference.session = 'test';
-
+  opt.anatReference.session = 'retest';
   % Uncomment the lines below to run preprocessing
   % - don't use realign and unwarp
   %   opt.realign.useUnwarp = false;

demos/openneuro/ds001168_get_option.m

@@ -20,7 +20,7 @@
   opt.taskName = 'rest';
 
   opt.anatReference.type = 'T1w';
-  opt.anatReference.session = 1;
+  opt.anatReference.session = '1';
 
   % Uncomment the lines below to run preprocessing
   % - don't use realign and unwarp

docs/.gitignore

@@ -0,0 +1,2 @@
+# documentation
+build/*

manualTests/test_moae.m

@@ -28,7 +28,7 @@
 
 run ../../initCppSpm.m;
 
-dowload_moae_ds(downloadData);
+download_moae_ds(downloadData);
 
 %% Set up
 optionsFilesList = { ...

requirements.txt

@@ -2,4 +2,5 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
-miss_hit==0.9.20
+miss_hit==0.9.20
+pre-commit