Commit d619c19c authored by Daniel Scheffler's avatar Daniel Scheffler
Browse files

Migrate test calls from nosetests to pytest.


Signed-off-by: Daniel Scheffler's avatarDaniel Scheffler <danschef@gfz-potsdam.de>
parent f6b00607
Pipeline #36277 passed with stage
in 8 minutes and 28 seconds
# .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
......@@ -11,16 +11,25 @@ test_specclassify:
stage: test
script:
- source /root/mambaforge/bin/activate ci_env
- make nosetests
- pip install pytest pytest-cov pytest-reporter-html1 # TODO remove after recreating CI runner
# run tests
- make pytest
# create the docs
- make docs
artifacts:
expose_as: 'Test and coverage report'
paths:
- htmlcov/
- report.html
- docs/_build/html/
- nosetests.html
- nosetests.xml
reports:
cobertura: coverage.xml
junit: report.xml
expire_in: 30 days
when: always
......@@ -79,7 +88,7 @@ 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/
......@@ -87,14 +96,14 @@ 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
......
.PHONY: clean clean-test clean-pyc clean-build docs help nosetests
.PHONY: clean clean-test clean-pyc clean-build docs help pytest
.DEFAULT_GOAL := help
define BROWSER_PYSCRIPT
......@@ -51,8 +51,10 @@ 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 specclassify tests > ./tests/linting/flake8.log || \
......@@ -78,12 +80,22 @@ 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=specclassify --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=specclassify \
--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/specclassify.rst
......
......@@ -42,7 +42,7 @@ requirements = ['numpy', 'tqdm', 'matplotlib', 'scikit-learn', 'geoarray>=0.15.0
setup_requirements = []
test_requirements = ['coverage', 'nose', 'nose2', 'nose-htmloutput', 'rednose', 'dill', 'urlchecker']
test_requirements = ['pytest', 'pytest-cov', 'pytest-reporter-hmtl1', 'dill', 'urlchecker']
setup(
author="Daniel Scheffler",
......
......@@ -109,6 +109,8 @@ class _ImageClassifier(object):
if self.CPUs is None or self.CPUs > 1:
with Pool(self.CPUs, initializer=_mp_initializer, initargs=(self.train_spectra, image_cube_gA)) as pool:
tiles_results = list(pool.imap_unordered(self._predict_tilewise, bounds_alltiles))
pool.close() # needed to make coverage work in multiprocessing
pool.join()
else:
_mp_initializer(self.train_spectra, image_cube_gA)
......
......@@ -16,15 +16,13 @@ dependencies:
- tqdm
# test and doc dependencies
- coverage
- flake8
- nose
- nose2
- nose-htmloutput
- pycodestyle
- pylint
- pydocstyle
- rednose
- pytest
- pytest-cov
- pytest-reporter-html1
- sphinx-argparse
- sphinx-autodoc-typehints
- sphinx_rtd_theme
......
......@@ -417,3 +417,8 @@ class Test_RF_Classifier(unittest.TestCase):
RFC = RF_Classifier(cluster_centers, cluster_labels, CPUs=None, **dict(random_state=0))
cmap_mp = RFC.classify(test_gA_pure_endmembers, in_nodataVal=-9999, tiledims=(400, 200))
self.assertTrue(np.array_equal(cmap_mp.flatten(), cluster_labels))
if __name__ == '__main__':
import pytest
pytest.main()
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