[INFRA] MATLAB test automation

.github/workflows/miss_hit.cfg

@@ -0,0 +1,23 @@
+# miss_hit configuration
+# for matlab linting and static analysis
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+
+project_root
+
+octave: false
+
+line_length: 100
+
+suppress_rule: "copyright_notice"
+
+tab_width: 2
+
+# snake_case
+regex_script_name: "[a-zA-Z]+(_[a-zA-Z0-9]*)*"
+regex_function_name: "[a-zA-Z]+(_[a-zA-Z0-9]*)*"
+
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 10
+metric "parameters": limit 5

.github/workflows/run_demos_ci.m

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+% run demos with moxunit in github CI
+
+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();
+
+% add glm single to path
+cd(root_dir);
+setup();
+
+this_folder = fileparts(mfilename('fullpath'));
+test_folder = this_folder;
+success = moxunit_runtests(test_folder, '-verbose', '-recursive');
+
+if success
+  system('echo 0 > test_report.log');
+else
+  system('echo 1 > test_report.log');
+end

.github/workflows/run_demos_matlab.yaml

@@ -0,0 +1,54 @@
+name: 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:
+          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: Run commands
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+              cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+              run run_demos_ci;
+
+      - name: Check logs
+        run: |
+          cat test_report.log | grep 0

.github/workflows/run_tests_ci.m

@@ -0,0 +1,11 @@
+% run tests with code coverage via the run_tests scripts in the root folder.
+
+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();
+
+cd(root_dir);
+run run_tests();

.github/workflows/run_tests_matlab.yaml

@@ -0,0 +1,68 @@
+name: MATLAB tests
+
+# 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: ["main"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  tests:
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest] # "macos-latest" or "windows-latest" don't work (yet?)
+        matlab-version: ["R2020a"] # add more versions if needed: "R2021a"
+      fail-fast: false  # Don't cancel all jobs if one fails
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Install MATLAB ${{ matrix.matlab-version }}
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          release: ${{ matrix.matlab-version }}
+
+      - 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 tests
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+            cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+            run run_tests_ci;
+
+      - name: Check logs
+        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/test_demos.m

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+function test_suite = test_demos %#ok<*STOUT>
+
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+
+  initTestSuite;
+
+end
+
+function test_demo1()
+
+  run(fullfile(root_dir(), 'matlab', 'examples', 'example1'));
+
+end
+
+function test_demo2()
+
+  run(fullfile(root_dir(), 'matlab', 'examples', 'example2'));
+
+end
+
+function value = root_dir()
+
+  value = getenv('GITHUB_WORKSPACE');
+
+  if isempty(value)
+    value =  fullfile(fileparts(mfilename('fullpath')), '..', '..');
+  end
+
+end

.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