Merge pull request #147 from cpp-lln-lab/release_candidate_1.2

Release candidate 1.2

Author: Remi-Gau

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.github/workflows/check_markdown.yml

@@ -0,0 +1,31 @@
+name: Check Markdown
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - uses: actions/setup-node@v2
+      with:
+        node-version: '10'
+
+    - name: Install dependencies and check markdown
+      run: |
+        npm install `cat npm-requirements.txt`
+        npx remark . --frail  
+
+

.github/workflows/check_md_links.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 

.github/workflows/miss_hit.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 
@@ -28,12 +27,16 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install install miss_hit
+        pip3 install -r requirements.txt
 
-    - name: Miss_hit code quality
+    - name: MISS_HIT Code style
       run: |
-        mh_metric . --ci
+        mh_style --process-slx
 
-    - name: Miss_hit code style
+    - name: MISS_HIT Metrics
       run: |
-        mh_style .
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint

.github/workflows/moxunit.yml

@@ -1,4 +1,4 @@
-name: CI
+name: MOxUnit
 
 on:
   push:

.gitignore

@@ -3,7 +3,19 @@
 *.m~
 *octave-workspace
 
+.vscode/*
+
 # exclude content of logfiles folders
 *.tsv
 *.mat
-check_my_code_report.txt
+check_my_code_report.txt
+
+# exclude content of files for virtual env (mostly for the doc)
+cpp_ptb
+
+# ignore file created by sphynx
+/docs/build
+
+# exclude node js stuff
+node_modules/*
+package-lock.json

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt

.travis.yml

@@ -0,0 +1,29 @@
+{
+  "title": "CPP_PTB",
+  "description": "A lightweight toolbox to facilitate setting up experiments with PsychToolBox.",
+  "creators": [
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Gau, Rémi",
+      "orcid": "0000-0002-1535-9767"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Barilari, Marco",
+      "orcid": "0000-0002-3313-3120"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Battal, Ceren",
+      "orcid": "0000-0002-9844-7630"
+    }
+  ],
+  "keywords": [
+    "PsychToolBox",
+    "neuroscience",
+    "MATLAB",
+    "Octave"
+  ],
+  "license": "MIT license",
+  "upload_type": "software"
+}

.zenodo.json

@@ -1,10 +1,24 @@
+<!-- lint disable -->
+
+**Documentation**
+
+[![Documentation Status: stable](https://readthedocs.org/projects/cpp-ptb/badge/?version=stable)](https://cpp-ptb.readthedocs.io/en/stable/?badge=stable)
+
+**Cite it**
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4007672.svg)](https://doi.org/10.5281/zenodo.4007672)
+
+**Unit tests and coverage**
+
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_PTB/actions)
 ![](https://github.com/cpp-lln-lab/CPP_PTB/workflows/CI/badge.svg)
 
 [![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_PTB.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_PTB)
 
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_PTB/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_PTB)
 
+**Contributors**
+
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 
 [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
@@ -13,20 +27,11 @@
 
 # CPP_PTB
 
-<!-- lint disable -->
-
 <!-- TOC -->
 
 -   [CPP_PTB](#cpp_ptb)
-    -   [Requirements](#requirements)
     -   [Documentation](#documentation)
     -   [Content](#content)
-    -   [How to install](#how-to-install)
-        -   [Download with git](#download-with-git)
-        -   [Add as a submodule](#add-as-a-submodule)
-            -   [Example for submodule usage](#example-for-submodule-usage)
-        -   [Direct download](#direct-download)
-        -   [Add CPP_PTB globally to the matlab path](#add-cpp_ptb-globally-to-the-matlab-path)
     -   [Code style guide](#code-style-guide)
     -   [Unit tests](#unit-tests)
     -   [Contributors ✨](#contributors-)
@@ -41,36 +46,15 @@ toolbox.
 Those functions are mostly wrappers around some PTB functions to facilitate
 their use and their reuse (#DontRepeatYourself)
 
-## Requirements
-
-Make sure that the following toolboxes are installed and added to the matlab /
-octave path.
-
-For instructions see the following links:
-
-<!-- lint disable -->
-
-| Requirements                                             | Used version |
-| -------------------------------------------------------- | ------------ |
-| [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
-| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2015b      |
-| or [Octave](https://www.gnu.org/software/octave/)        | 4.?          |
-
-<!-- lint enable -->
-
-Tested:
-
--   matlab 2015b or octave 4.2.2 and PTB 3.0.14.
-
 ## Documentation
 
-All the documentation is accessible [here](./docs/00-index.md).
+All the documentation and installtion information is accessible
+[here](https://cpp-ptb.readthedocs.io/en/stable/index.html#).
 
 ## Content
 
 ```bash
 ├── demos # quick demo of how to use some functions
-├── dev # templates for experiment (will be moved out soon)
 ├── docs # documentation
 ├── manualTests # all the tests that cannot be automated (yet)
 ├── src # actual code of the CPP_PTB
@@ -84,104 +68,6 @@ All the documentation is accessible [here](./docs/00-index.md).
 └── tests # all the tests that that can be run by github actions
 ```
 
-## How to install
-
-### Download with git
-
-```bash
-cd fullpath_to_directory_where_to_install
-# use git to download the code
-git clone https://github.com/cpp-lln-lab/CPP_PTB.git
-# move into the folder you have just created
-cd CPP_PTB
-```
-
-Then get the latest commit to stay up to date:
-
-```bash
-# from the directory where you downloaded the code
-git pull origin master
-```
-
-To work with a specific version, create a branch at a specific version tag
-number
-
-```bash
-# creating and checking out a branch that will be called version1 at the version tag v1.0.0
-git checkout -b version1 v1.0.0
-```
-
-### Add as a submodule
-
-Add it as a submodule in the repo you are working on.
-
-```bash
-cd fullpath_to_directory_where_to_install
-# use git to download the code
-git submodule add https://github.com/cpp-lln-lab/CPP_PTB.git
-```
-
-To get the latest commit you then need to update the submodule with the
-information on its remote repository and then merge those locally.
-
-```bash
-git submodule update --remote --merge
-```
-
-Remember that updates to submodules need to be committed as well.
-
-#### Example for submodule usage
-
-So say you want to clone a repo that has some nested submodules, then you would
-type this to get the content of all the submodules at once (here with my
-experiment repo):
-
-```bash
-git clone --recurse-submodules https://github.com/user_name/yourExperiment.git
-```
-
-This would be the way to do it "by hand"
-
-```bash
-# clone the repo
-git clone https://github.com/user_name/yourExperiment.git
-
-# go into the directory
-cd yourExperiment
-
-# initialize and get the content of the first level of submodules  (CPP_PTB and CPP_BIDS)
-git submodule init
-git submodule update
-
-# get the nested submodules JSONio and BIDS-matlab for CPP_BIDS
-git submodule foreach --recursive 'git submodule init'
-git submodule foreach --recursive 'git submodule update'
-```
-
-### Direct download
-
-Download the code. Unzip. And add to the matlab path.
-
-Pick a specific version from
-[here](https://github.com/cpp-lln-lab/CPP_PTB/releases).
-
-Or take
-[the latest commit](https://github.com/cpp-lln-lab/CPP_PTB/archive/master.zip) -
-NOT RECOMMENDED.
-
-### Add CPP_PTB globally to the matlab path
-
-This is NOT RECOMMENDED as this might create conflicts if you use different
-versions of CPP_PTB as sub-modules.
-
-Also note that this might not work at all if you have not set a command line
-alias to start Matlab from a terminal window by just typing `matlab`. :wink:
-
-```bash
-# from within the CPP_PTB folder
-matlab -nojvm -nosplash -r "addpath(genpath(fullfile(pwd, 'src'))); savepath(); path(); exit();"
-```
-
 ## Code style guide
 
 We use the `camelCase` to more easily differentiates our functions from the ones
@@ -209,7 +95,7 @@ We use the
 to automatically fix some linting issues.
 
 The code style and quality is also checked during the
-[continuous integration](./.travis.yml).
+[continuous integration](.github/workflows/miss_hit.yml).
 
 ## Unit tests