[INFRA] MATLAB test automation

.github/workflows/run_demos.m

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+root_dir = getenv('GITHUB_WORKSPACE');
+
+cd(fullfile(root_dir));
+
+setup();
+
+run matlab/examples/example1;
+run matlab/examples/example2;

.github/workflows/run_demos_matlab.yml

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+name: run matlab demos
+
+# Uses the cron schedule for github actions
+#
+#   will run at 00H00 run on the 1 and 15 of every month
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#         ┌───────────── minute (0 - 59)
+#         │ ┌───────────── hour (0 - 23)
+#         │ │ ┌───────────── day of the month (1 - 31)
+#         │ │ │    ┌───────────── month (1 - 12 or JAN-DEC): * means all
+#         │ │ │    │ ┌───────────── day of the week (0 - 6 or SUN-SAT): * means all
+#         │ │ │    │ │
+#         │ │ │    │ │
+#         │ │ │    │ │
+# 
+# - cron "0 0 1,15 * *"
+
+on:
+  schedule:
+    - cron: "0 0 1,15 * *"
+
+jobs:
+  demos:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          # MATLAB release to set up R2020a
+          release: R2020a
+
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: Run commands
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+            cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+            run run_demos;

.github/workflows/run_tests_matlab.yml

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+name: tests and coverage with MATLAB
+
+# Installs
+# - MATLAB github action
+# - MOXunit
+# - MOcov
+# Get test data
+# cd into .github/workflows
+# run .github/workflows/tests_matlab.m
+# If tests pass, uploads coverage to codecov
+
+on:
+  push:
+    # TODO only run on master branch on push 
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          release: R2020a
+
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0 # 0 means we only get the last commit, not the whole git history
+
+      - name: Install Moxunit and MOcov
+        run: |
+          git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+          git clone https://github.com/MOcov/MOcov.git --depth 1
+
+      - name: Download data
+        run: make tests/data/nsdcoreexampledataset.mat
+
+      - name: Run commands
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+            cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+            run tests_matlab;
+
+      - name: Run tests
+        run: |
+          cat test_report.log | grep 0
+          bash <(curl -s https://codecov.io/bash)
+
+      - name: Code coverage
+        uses: codecov/codecov-action@v1
+        with:
+          file: coverage.xml # optional
+          flags: matlab # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)

.github/workflows/tests_matlab.m

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+root_dir = getenv('GITHUB_WORKSPACE');
+
+% MOxUnit and MOcov need to be in the matlab path
+addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
+cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
+run moxunit_set_path();
+
+% adds GLM single to the path and runs all the tests
+cd(fullfile(root_dir));
+setup();
+run run_tests();

.gitignore

@@ -1,8 +1,10 @@
-#
+# vscode files
 .vscode/
 
+# test related
+tests/outputs/
 
-# data folder
+# data folders
 data/
 
 # example output folders
@@ -13,6 +15,9 @@ figures/
 report.html
 ##*.png
 
+# pyenv
+Pipfile
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -54,6 +59,7 @@ pip-delete-this-directory.txt
 htmlcov/
 .tox/
 .coverage
+coverage_html
 .coverage.*
 .cache
 nosetests.xml
@@ -153,4 +159,3 @@ codegen/
 
 # Octave session info
 octave-workspace
-

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-yaml

CONTRIBUTING.md

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+# CONTRIBUTING
+
+Information for anyone who would like to contribute to this repository.
+
+## Repository map
+
+```bash
+├── .git
+├── .github
+│   └── workflows         # Github continuous integration set up
+├── examples
+│   ├── data
+│   ├── example1outputs
+│   ├── example2outputs
+├── glmsingle             # Python implementation
+│   ├── cod
+│   ├── design
+│   ├── gmm
+│   ├── hrf
+│   ├── ols
+│   ├── ssq
+│   └── utils
+├── matlab                # Matlab implementation
+│   ├── examples
+│   ├── fracridge
+│   └── utilities
+└── tests                 # Python and Matlab tests
+    └── data
+
+```
+
+## Generic
+
+### Makefile
+
+A `Makefile` is used to help set / and automate some things.
+
+In a terminal type `make help` to see what are the different "recipes" you can
+run with this `Makefile`.
+
+### pre-commit
+
+## Matlab
+
+### Style guide
+
+### Tests
+
+Running the tests require to have the following toolboes in your MATLAB path:
+
+- the [MOxUnit testing framework](https://github.com/MOxUnit/MOxUnit) to run the
+  tests
+  ([see installation procedure](https://github.com/MOxUnit/MOxUnit#installation))
+- [MOcov](https://github.com/MOcov/MOcov)) to get a code coverage estimate
+  ([see installation procedure](https://github.com/MOcov/MOcov#installation))
+
+All the tests are in the `tests` folder in files starting with `test_*.m`.
+
+To Download the data required for running the tests (this data is common for
+MATLAB and python tests), type:
+
+```bash
+make tests/data/nsdcoreexampledataset.mat
+```
+
+To run **all** the tests and get code coverage, you can
+
+1. type the following in a terminal
+
+```
+make test-matlab
+```
+
+2. run the `run_tests.m` in MATLAB
+
+You can also run all the tests contained in a specific `test_*.m` file directly,
+by running that file only.
+
+#### Adding new tests
+
+A typical MoxUnit test file starts with with `test_` and would look something
+like this.
+
+```matlab
+function test_suite=test_sum_of_squares
+
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite();
+
+end
+
+function test_sum_of_squares_basic
+
+    % given
+    a = 2;
+    b = 3;
+
+    % when
+    result = sum_of_squares([a, b])
+
+    % then
+    expected = 13;
+    assertEqual(result, expected);
+
+end
+
+% New tests can added as new sub functions
+
+```
+
+#### Demos
+
+### Continuous integration
+
+## Python
+
+### Style guide
+
+### Tests
+
+#### Demos
+
+### Continuous integration