Merge branch 'ci' into 'main'

ci: implement ci pipeline

See merge request !2

.gitlab-ci.yml

+image: python:3.9-slim-buster
+
+stages:
+  - qc
+  - test
+
+qc_1:
+  stage: qc
+
+  before_script:
+    - pip install -r requirements.txt
+    - pip install -r requirements_dev.txt
+    - pip install -e .
+
+  script:
+    - flake8 src/ setup.py
+    - coverage run --source src/ -m pytest
+    - coverage report --fail-under=100
+    - mypy src/
+
+test_1:
+  stage: test
+
+  before_script:
+    - pip install -r requirements.txt
+    - pip install -r requirements_dev.txt
+    - pip install -e .
+
+  script:
+    - python -m pytest
+

requirements_dev.txt

+flake8
+flake8-docstrings
+pytest
+mypy
+coverage

setup.cfg

+[flake8]
+max-line-length = 120
+docstring-convention = google
\ No newline at end of file

setup.py

+"""Setup the package."""
+
+from setuptools import setup, find_packages
+import src
+
+
+setup(
+    name='src',
+    author='Zavolan Lab, Biozentrum, University of Basel',
+    url='https://git.scicore.unibas.ch/zavolan_group/pipelines/scrna-seq-simulation',
+    license='MIT',
+    version=src.__version__,
+    install_requires=[],
+    entrypoints={},
+    packages=find_packages()
+)

src/__init__.py

+"""Placeholder package."""
+
+__version__ = '0.0.0'

tests/__init__.py

+"""Tests for the package src."""

tests/test_dummy.py

+"""Placeholder test for pipeline."""
+
+import src
+import re
+
+
+def test_version():
+    """Assert that version matches semantic versioning format."""
+
+    assert re.match(r'\d\.\d\.\d', src.__version__)