Merge branch 'enhancement/migrate_to_pytest' into 'master'

Enhancement/migrate to pytest

See merge request !6

.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

@@ -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

Makefile

-.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

setup.py

@@ -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",

specclassify/_baseclasses.py

@@ -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)

tests/CI_docker/context/environment_specclassify.yml

@@ -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

tests/test_image_classifier.py

@@ -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()