[INFRA] Python test automation

.github/workflows/run_demos_python.yml

@@ -0,0 +1,57 @@
+name: Python 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:
+    continue-on-error: true
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9"]
+
+    steps:
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: "recursive"
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .
+          pip install -r requirements_dev.txt
+
+      - name: Display Python version and packages
+        run: |
+          python -c "import sys; print(sys.version)"
+          pip list
+
+      - name: Run notebooks
+        run: pytest --nbmake --nbmake-timeout=3000 "./examples"

.github/workflows/run_tests_python.yml

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+name: Python tests
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+        python-version: ["3.7", "3.8", "3.9"] # fails on 3.10
+      fail-fast: true  # cancel all jobs if one fails
+
+    steps:
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: "recursive"
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .
+          pip install -r requirements_dev.txt
+
+      - name: Display Python version and packages
+        run: | 
+          python -c "import sys; print(sys.version)"
+          pip list
+
+      - name: Prepare data
+        run: make tests/data/nsdcoreexampledataset.mat          
+
+      - name: Run tests and generate coverage report
+        run: pytest -v --cov glmsingle --cov-report xml tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: python
+          name: codecov-umbrella
+          fail_ci_if_error: true
+          verbose: true

.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              # Python demos: jupyter notebooks
+│   ├── data
+│   ├── example1outputs
+│   ├── example2outputs
+├── glmsingle             # Python implementation
+│   ├── cod
+│   ├── design
+│   ├── gmm
+│   ├── hrf
+│   ├── ols
+│   ├── ssq
+│   └── utils
+├── matlab                # MATLAB implementation
+│   ├── examples          # MATLAB demos
+│   ├── fracridge
+│   └── utilities
+└── tests                 # Python and MATLAB tests
+    └── data
+
+```
+
+## Generic
+
+### Makefile
+
+### pre-commit
+
+## Matlab
+
+### Style guide
+
+### Tests
+
+#### Demos
+
+### Continuous integration
+
+## Python
+
+All the packages required to help with the python development of GLMsingle can
+be installed with:
+
+```bash
+pip install -r requirements_dev.txt
+```
+
+### Style guide
+
+[black](https://black.readthedocs.io/en/stable/) (code formater) and
+[flake8](https://flake8.pycqa.org/en/latest/) (style guide enforcement) are used
+on the test code base.
+
+Ypu can use make to run them automatically with
+
+```bash
+make lint/black # to run black
+make lint/flake8 # to run flake8
+make lint # to run both
+```
+
+### Tests
+
+The tests can be run with with pytest via the make command:
+
+```bash
+make test-python
+```
+
+#### Demos
+
+The jupyter notebook are tested with the
+[`nbmake` plugin for pytest](https://pypi.org/project/nbmake/).
+
+They can be run with the make command:
+
+```bash
+make test-notebooks
+```
+
+### Continuous integration
+
+We use Github to run several workflows for continuous integration.
+
+#### Tests
+
+The python tests are run by the workflow:
+`.github/workflows/run_tests_python.yaml`.
+
+Those tests should be run with every push on the `master` branch and on pull
+request that target the `master` branch.
+
+#### Demos
+
+The demos in the `examples` folder are run automatically in Github CI at regular
+intervals.
+
+The jupyter notebooks are run by the workflow
+`.github/workflows/run_demos_python.yaml`.

Makefile

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+.DEFAULT_GOAL := help
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+# TODO make more general to use the local matlab version
+MATLAB = /usr/local/MATLAB/R2017a/bin/matlab
+MATLAB_ARG    = -nodisplay -nosplash -nodesktop
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+# determines what "make help" will show
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+################################################################################
+# 	GENERIC
+.PHONY: help clean clean-test lint install_dev
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage artifacts
+
+clean-test: ## remove test and coverage artifacts
+	rm -rf .tox/
+	rm -rf .coverage
+	rm -rf htmlcov/
+	rm -rf .pytest_cache
+	rm -rf tests/data
+	rm -rf test/outputs
+
+install_dev: ## install for both matlab and python developpers
+	pip install -e .
+	pip install -r requirements_dev.txt
+
+lint: lint/black lint/flake8 lint/miss_hit ## check style
+
+test: test-matlab test-python
+
+tests/data/nsdcoreexampledataset.mat: 
+	mkdir tests/data
+	curl -fsSL --retry 5 -o "tests/data/nsdcoreexampledataset.mat" https://osf.io/k89b2/download
+
+################################################################################
+
+################################################################################
+# 	MATLAB
+
+.PHONY: lint/miss_hit
+
+lint/miss_hit: ## lint and checks matlab code
+	mh_style --fix tests && mh_metric --ci tests && mh_lint tests
+
+test-matlab: tests/data/nsdcoreexampledataset.mat
+	$(MATLAB) $(MATLAB_ARG) -r "run_tests; exit()"
+
+coverage-matlab: test-matlab
+	$(BROWSER) coverage_html/index.html
+
+################################################################################
+
+################################################################################
+# 	PYTHON
+
+.PHONY: clean-build clean-pyc coverage-python install lint/flake8 lint/black
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+lint/flake8: ## check style with flake8
+	flake8 tests
+lint/black: ## check style with black
+	black tests
+
+test-python: tests/data/nsdcoreexampledataset.mat ## run tests quickly with the default Python
+	pytest -vv
+
+test-notebooks:
+	pytest -vv --nbmake --nbmake-timeout=3000 "./examples"
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage-python: ## check code coverage quickly with the default Python
+	pytest -vv --cov glmsingle --cov-report html:htmlcov 
+	$(BROWSER) htmlcov/index.html
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install
+
+################################################################################