Merge branch 'enhancement/migrate_to_pytest' into 'master'

Enhancement/migrate to pytest

See merge request !24

.coveragerc

@@ -3,8 +3,11 @@
 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

.gitlab-ci.yml

@@ -13,21 +13,28 @@ test_arosics:
   script:
     - source /root/mambaforge/bin/activate ci_env
 
+    - pip install pytest pytest-cov pytest-reporter-html1  # TODO remove after recreating CI runner
+
     # update py_tools_ds and geoarray
     - pip install -U py_tools_ds -q
     - pip install -U geoarray -q
 
     # run tests
-    - make nosetests
+    - 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
 
 
@@ -87,7 +94,7 @@ pages:  # this job must be called 'pages' to advise GitLab to upload content to
     - mkdir -p public/doc
     - mkdir -p public/images/
     - 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/
@@ -96,14 +103,14 @@ 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

HISTORY.rst

@@ -2,6 +2,12 @@
 History
 =======
 
+1.7.4 (2021-12-15)
+------------------
+
+* Migrated test calls from nosetests to pytest and implemented new test report (!24).
+
+
 1.7.3 (2021-12-02)
 ------------------
 

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
 import os, webbrowser, sys
@@ -49,8 +49,11 @@ 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 . tests > ./tests/linting/flake8.log || \
@@ -84,6 +87,23 @@ nosetests: clean-test ## Runs nosetests with coverage, xUnit and nose-html-outpu
 	nosetests -vv --with-coverage --cover-package=arosics --cover-erase --cover-html --cover-html-dir=htmlcov \
 		--with-html --with-xunit --rednose --force-color
 
+pytest: clean-test ## Runs pytest with coverage and creates coverage and test report
+	## - puts the coverage results in the folder 'htmlcov'
+	## - 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=arosics \
+		--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/arosics.rst
 	rm -f docs/modules.rst

README.rst

@@ -100,7 +100,7 @@ Credits
 -------
 
 AROSICS was developed by Daniel Scheffler (German Research Centre of Geosciences) within the context of the
-`GeoMultiSens <http://www.geomultisens.de/>`__ project funded by the German Federal Ministry of Education and Research
+`GeoMultiSens <http://www.geomultisens.gfz-potsdam.de/>`__ project funded by the German Federal Ministry of Education and Research
 (project grant code: 01 IS 14 010 A-C).
 
 This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

arosics/Tie_Point_Grid.py

@@ -403,6 +403,8 @@ class Tie_Point_Grid(object):
                             # COREG and is not raised
                             results = results.get()
                             break
+                pool.close()  # needed to make coverage work in multiprocessing
+                pool.join()
 
         else:
             # declare global variables needed for self._get_spatial_shifts()
@@ -974,6 +976,8 @@ class Tie_Point_Grid(object):
         #
         #     with multiprocessing.Pool() as pool:
         #        self.kriged = pool.map(self.Kriging_mp,args_kwargs_dicts)
+        #        pool.close()  # needed to make coverage work in multiprocessing
+        #        pool.join()
         # else:
         #     self.Kriging_sp(attrName,skip_nodata=skip_nodata,skip_nodata_col=skip_nodata_col,
         #                     outGridRes=outGridRes,fName_out=fName_out,tilepos=tilepos)

setup.py

@@ -67,7 +67,7 @@ req_setup = [
 
 req_intplot = ['holoviews', 'ipython']
 
-req_test = ['coverage', 'nose', 'nose2', 'nose-htmloutput', 'rednose', 'urlchecker'] + req_intplot
+req_test = ['pytest', 'pytest-cov', 'pytest-reporter-hmtl1', 'urlchecker'] + req_intplot
 
 req_doc = ['sphinx-argparse', 'sphinx_rtd_theme', 'sphinx-autodoc-typehints']
 

tests/CI_docker/context/environment_arosics.yml

@@ -31,15 +31,13 @@ dependencies:
     - geojson
 
     # doc requirements
-    - coverage
     - flake8
-    - nose
-    - nose2
-    - nose-htmloutput
     - pycodestyle
     - pydocstyle
     - pylint
-    - rednose
+    - pytest
+    - pytest-cov
+    - pytest-reporter-html1
     - sphinx-argparse
     - sphinx-autodoc-typehints
     - sphinx_rtd_theme

tests/test_COREG.py

@@ -359,5 +359,5 @@ class CompleteWorkflow_INTER1_S2A_S2A(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    import nose2
-    nose2.main()
+    import pytest
+    pytest.main()

tests/test_COREG_LOCAL.py

@@ -201,5 +201,5 @@ class CompleteWorkflow_INTER1_S2A_S2A(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    import nose2
-    nose2.main()
+    import pytest
+    pytest.main()

tests/test_tie_point_grid.py

@@ -134,5 +134,5 @@ class Test_Tie_Point_Grid(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    import nose2
-    nose2.main()
+    import pytest
+    pytest.main()