Migrate to pytest.

Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

.coveragerc

+# .coveragerc to control coverage.py
+[run]
+branch = False
+concurrency = multiprocessing
+parallel = True
+omit = */site-packages/*,*/tests/*,*/.eggs/*
+
+[report]
+show_missing = True
+
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+ignore_errors = True
+
+[html]
+directory = htmlcov

.gitlab-ci.yml

@@ -12,18 +12,28 @@ test_pyrsr:
   coverage: '/TOTAL\s+\d+\s+\d+\s+(\d+%)/'
   script:
     - source /root/mambaforge/bin/activate ci_env
-    - make nosetests
+
+    - pip install pytest pytest-cov pytest-reporter-html1 sphinx_rtd_theme sphinx-autodoc-typehints  # TODO remove after recreating CI runner
+
+    # run tests
+    - make pytest
 
     # create the docs
-    - pip install sphinx_rtd_theme  # Read-the-docs theme for SPHINX documentation
-    - pip install sphinx-autodoc-typehints
     - make docs
+
   artifacts:
+    expose_as: 'Test and coverage report'
     paths:
     - htmlcov/
+    - report.html
     - docs/_build/html/
-    - nosetests.html
-    - nosetests.xml
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+      junit: report.xml
+
+    expire_in: 30 days
     when: always
 
 
@@ -82,7 +92,7 @@ pages:  # this job must be called 'pages' to advise GitLab to upload content to
     - mkdir public
     - mkdir -p public/doc
     - mkdir -p public/coverage
-    - mkdir -p public/nosetests_reports
+    - mkdir -p public/test_reports
 
     # Copy over the docs
     - cp -r docs/_build/html/* public/doc/
@@ -90,14 +100,14 @@ pages:  # this job must be called 'pages' to advise GitLab to upload content to
     # Copy over the coverage reports
     - cp -r htmlcov/* public/coverage/
 
-    # Copy over the nosetests reports
-    - cp nosetests.* public/nosetests_reports/
+    # Copy over the test reports
+    - cp report.html public/test_reports/
 
     # Check if everything is working great
     - ls -al public
     - ls -al public/doc
     - ls -al public/coverage
-    - ls -al public/nosetests_reports
+    - ls -al public/test_reports
   artifacts:
     paths:
       - public

Makefile

-.PHONY: clean clean-test clean-pyc clean-build docs help
+.PHONY: clean clean-test clean-pyc clean-build docs help pytest
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -51,8 +51,11 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr .coverage.*
 	rm -fr htmlcov/
-	rm -fr nosetests.html
-	rm -fr nosetests.xml
+	rm -fr report.html
+	rm -fr report.xml
+	rm -fr coverage.xml
+	rm -fr .pytest_cache
+
 
 lint: ## check style with flake8
 	flake8 --max-line-length=120 pyrsr tests > ./tests/linting/flake8.log || \
@@ -78,12 +81,22 @@ coverage: ## check code coverage quickly with the default Python
 	coverage html
 	# $(BROWSER) htmlcov/index.html
 
-nosetests: clean-test ## Runs nosetests with coverage, xUnit and nose-html-output
+pytest: clean-test ## Runs pytest with coverage and creates coverage and test report
 	## - puts the coverage results in the folder 'htmlcov'
-	## - generates 'nosetests.html' (--with-html)
-	## - generates 'nosetests.xml' (--with-xunit) which is currently not visualizable by GitLab
-	nosetests -vv --with-coverage --cover-package=pyrsr --cover-package=bin --cover-erase --cover-html \
-		--cover-html-dir=htmlcov --with-html --with-xunit --rednose --force-color
+	## - generates cobertura 'coverage.xml' (needed to show coverage in GitLab MR changes)
+	## - generates 'report.html' based on pytest-reporter-html1
+	## - generates JUnit 'report.xml' to show the test report as a new tab in a GitLab MR
+	## NOTE: additional options pytest and coverage (plugin pytest-cov) are defined in .pytest.ini and .coveragerc
+	pytest tests \
+		--verbosity=3 \
+		--color=yes \
+		--tb=short \
+		--cov=pyrsr \
+		--cov-report html:htmlcov \
+		--cov-report term-missing \
+		--cov-report xml:coverage.xml \
+		--template=html1/index.html --report=report.html \
+		--junitxml report.xml
 
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/pyrsr.rst

README.rst

@@ -25,7 +25,7 @@ Status
 .. image:: https://img.shields.io/pypi/dm/pyrsr.svg
         :target: https://pypi.python.org/pypi/pyrsr
 
-See also the latest coverage_ report and the nosetests_ HTML report.
+See also the latest coverage_ report and the pytest_ HTML report.
 
 
 Features
@@ -97,4 +97,4 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
 .. _coverage: https://geomultisens.git-pages.gfz-potsdam.de/pyrsr/coverage/
-.. _nosetests: https://geomultisens.git-pages.gfz-potsdam.de/pyrsr/nosetests_reports/nosetests.html
+.. _pytest: https://geomultisens.git-pages.gfz-potsdam.de/pyrsr/test_reports/report.html

setup.py

@@ -42,7 +42,7 @@ requirements = ['numpy', 'pandas', 'matplotlib', 'scipy']
 
 setup_requirements = ['setuptools-git']  # needed for package_data version controlled by GIT
 
-test_requirements = ['coverage', 'nose', 'nose-htmloutput', 'rednose', 'urlchecker']
+test_requirements = ['pytest', 'pytest-cov', 'pytest-reporter-html1', 'urlchecker']
 
 
 setup(

tests/CI_docker/context/environment_pyrsr.yml

@@ -14,14 +14,14 @@ dependencies:
     - scipy
 
     # test and doc dependencies
-    - coverage
     - flake8
-    - nose
-    - nose2
-    - nose-htmloutput
     - pycodestyle
     - pylint
     - pydocstyle
-    - rednose
+    - pytest
+    - pytest-cov
+    - pytest-reporter-html1
     - sphinx-argparse
+    - sphinx_rtd_theme
+    - sphinx-autodoc-typehints
     - urlchecker

tests/test_pyrsr.py

@@ -125,3 +125,8 @@ class Test_get_LayerBandsAssignment(unittest.TestCase):
         LBA = get_LayerBandsAssignment('Sentinel-2A', 'MSI', after_ac=True)
         self.assertEqual(len(LBA), 11)
         self.assertEqual(LBA, ['1', '2', '3', '4', '5', '6', '7', '8', '8A', '11', '12'])
+
+
+if __name__ == '__main__':
+    import pytest
+    pytest.main()