[INFRA] Python test automation

.github/workflows/run_demos_python.yml

@@ -0,0 +1,60 @@
+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 * *"
+
+  push:
+    branches: ["*"]
+
+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

@@ -0,0 +1,54 @@
+name: Python tests
+
+on:
+  push:
+    branches: ["*"]
+  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

CONTRIBUTING.md

@@ -8,7 +8,7 @@ Information for anyone who would like to contribute to this repository.
 ├── .git
 ├── .github
 │   └── workflows         # Github continuous integration set up
-├── examples
+├── examples              # Python demos: jupyter notebooks
 │   ├── data
 │   ├── example1outputs
 │   ├── example2outputs
@@ -20,11 +20,11 @@ Information for anyone who would like to contribute to this repository.
 │   ├── ols
 │   ├── ssq
 │   └── utils
-├── matlab                # Matlab implementation
-│   ├── examples
+├── matlab                # MATLAB implementation
+│   ├── examples          # MATLAB demos
 │   ├── fracridge
 │   └── utilities
-└── tests                 # Python and Matlab tests
+└── tests                 # Python and MATLAB tests
     └── data
 
 ```
@@ -47,10 +47,62 @@ Information for anyone who would like to contribute to this repository.
 
 ## 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
 
-### Continuous integration
+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

@@ -97,17 +97,15 @@ lint/black: ## check style with black
 	black tests
 
 test-python: tests/data/nsdcoreexampledataset.mat ## run tests quickly with the default Python
-	pytest 
+	pytest -vv
 
 test-notebooks:
-	pytest  --nbmake --nbmake-timeout=3000 "./examples"
+	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
-	coverage run --source glmsingle -m pytest
-	coverage report -m
-	coverage html
+	pytest -vv --cov glmsingle --cov-report html:htmlcov 
 	$(BROWSER) htmlcov/index.html
 
 install: clean ## install the package to the active Python's site-packages

README.md

@@ -1,3 +1,8 @@
+
+
+[![Python tests](https://github.com/cvnlab/GLMsingle/actions/workflows/run_tests_python.yml/badge.svg)](https://github.com/cvnlab/GLMsingle/actions/workflows/run_tests_python.yml)
+[![Python demos](https://github.com/cvnlab/GLMsingle/actions/workflows/run_demos_python.yml/badge.svg)](https://github.com/cvnlab/GLMsingle/actions/workflows/run_demos_python.yml)
+[![Python-coverage](https://codecov.io/gh/Remi-Gau/GLMsingle/branch/main/graph/badge.svg?token=H75TAAUVSW)](https://codecov.io/gh/Remi-Gau/GLMsingle)
 # GLMsingle
 
 ![image](https://user-images.githubusercontent.com/35503086/151108958-24479034-c7f7-4734-b903-9046ba6a78ac.png)

examples/example1.ipynb

@@ -85,7 +85,9 @@
     "\n",
     "# note: the fracridge repository is also necessary to run this code\n",
     "# for example, you could do:\n",
-    "#      git clone https://github.com/nrdg/fracridge.git"
+    "#      git clone https://github.com/nrdg/fracridge.git\n",
+    "\n",
+    "raise NameError('test')"
    ]
   },
   {

requirements.txt

@@ -1,8 +1,8 @@
-numpy
-scipy
-sklearn
-matplotlib
-tqdm
-fracridge
-nibabel
-h5py
+fracridge>=1.4.3
+h5py>=3.1.0
+matplotlib>=3.3.4
+nibabel>=3.2.2
+numpy>=1.17.0
+scikit-learn>=0.23.2
+scipy>=1.5.4
+tqdm>=4.63.1

requirements_dev.txt

@@ -1,11 +1,13 @@
+# Base requirements
+-r requirements.txt
+
 # Matlab dev
 miss_hit 
 
 # Python dev
+black
 flake8
-tox
-coverage
 pytest
-black
-nbmake
 pytest-cov
+nbmake
+tox

setup.cfg

@@ -0,0 +1,18 @@
+[flake8]
+max-line-length = 99
+
+ignore = D203, W503
+
+exclude =
+    .git,
+    docs,
+    __pycache__,
+    old,
+    build,
+    dist
+    'matlab/fracridge'
+
+max-complexity = 10
+
+[tool:pytest]
+testpaths = tests

setup.py

@@ -10,7 +10,7 @@
 
 setup(
     name='GLMsingle',
-    version='0.0.1',
+    version='1.0.0',
     description='Python GLMsingle',
     url='https://github.com/kendrickkay/GLMsingle',
     long_description=long_description,
@@ -28,5 +28,6 @@
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,
-    install_requires=requires
+    install_requires=requires,
+    python_requires='>=3.6, <3.10'
 )

tests/__init__.py

@@ -0,0 +1 @@
+"""Unit test package for glmsingle."""

tests/expected/python/README.md

@@ -0,0 +1,52 @@
+# Generate expected data
+
+Generated from the output of one run from the files in `tests/outputs/python`
+
+```python
+import numpy as np
+
+tmp = np.load("TYPEB_FITHRF.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+np.save("TYPEB_FITHRF_HRFindex.npy", results)
+
+tmp = np.load("TYPEC_FITHRF_GLMDENOISE.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+np.save("TYPEC_FITHRF_HRFindex.npy", results)
+
+tmp = np.load("TYPED_FITHRF_GLMDENOISE_RR.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+np.save("TYPED_FITHRF_HRFindex.npy", results)
+
+results = tmp.item(0)["R2"]
+np.save("TYPED_FITHRF_R2.npy", results)
+```
+
+<!-- TODO ?
+## For CSV
+
+```python
+import numpy as np
+
+tmp = np.load("TYPEB_FITHRF.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+results = results.squeeze();
+np.savetxt("TYPEB_FITHRF_HRFindex.csv", results, delimiter=",", fmt="%i")
+
+tmp = np.load("TYPEC_FITHRF_GLMDENOISE.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+results = results.squeeze();
+np.savetxt("TYPEC_FITHRF_HRFindex.csv", results, delimiter=",", fmt="%i")
+
+tmp = np.load("TYPED_FITHRF_GLMDENOISE_RR.npy", allow_pickle=True)
+results = tmp.item(0)["HRFindex"]
+results = results.squeeze();
+np.savetxt("TYPED_FITHRF_HRFindex.csv", results, delimiter=",", fmt="%i")
+```
+
+Read from csv
+
+```python
+from numpy import genfromtxt
+
+my_data = genfromtxt('TYPEB_FITHRF_HRFindex.csv', delimiter=',')
+``` -->