Merge branch 'master' into enhancement/rasterization

# Conflicts:
#	arosics/Tie_Point_Grid.py

.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

@@ -20,16 +20,21 @@ test_arosics:
     - pip install scipy  # TODO remove as soon as CI runner is rebuilt
 
     # 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
 
 
@@ -89,7 +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/
@@ -98,14 +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

@@ -2,10 +2,26 @@
 History
 =======
 
-1.7.2 (coming soon)
--------------------
+1.7.4 (2021-12-15)
+------------------
+
+* Migrated test calls from nosetests to pytest and implemented new test report (!24).
+* Removed folium 0.12.1 exclusion due to fix on PyPI and conda-forge.
+* Fixed dead link.
+
+
+1.7.3 (2021-12-02)
+------------------
+
+* Avoid folium 0.12.1 as requirement due to https://github.com/python-visualization/folium/issues/1513.
+
+
+1.7.2 (2021-11-09)
+------------------
 
 * Listed dill in package requirements.
+* Resolved inconsistency in documenting boolean default values.
+* Improved error message when trying to compute statistics and all tie points are flagged as false-positives.
 
 
 1.7.1 (2021-10-13)

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 || \
@@ -77,12 +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=arosics --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=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

README.rst

@@ -41,7 +41,7 @@ Status
 .. image:: https://zenodo.org/badge/253474603.svg
         :target: https://zenodo.org/badge/latestdoi/253474603
 
-See also the latest coverage_ report and the nosetests_ HTML report.
+See also the latest coverage_ report and the pytest_ HTML report.
 
 Feature overview
 ----------------
@@ -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.
@@ -110,6 +110,6 @@ documentation have been provided by NASA (Landsat-8) and ESA (Sentinel-2).
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
 .. _coverage: https://danschef.git-pages.gfz-potsdam.de/arosics/coverage/
-.. _nosetests: https://danschef.git-pages.gfz-potsdam.de/arosics/nosetests_reports/nosetests.html
+.. _pytest: https://danschef.git-pages.gfz-potsdam.de/arosics/test_reports/report.html
 .. _conda: https://conda.io/docs/
 

arosics/CoReg.py

@@ -276,10 +276,10 @@ class COREG(object):
 
         :param calc_corners:
              calculate true positions of the dataset corners in order to get a useful matching window position within
-             the actual image overlap (default: 1; deactivated if '-cor0' and '-cor1' are given
+             the actual image overlap (default: True; deactivated if '-cor0' and '-cor1' are given
 
         :param binary_ws:
-            use binary X/Y dimensions for the matching window (default: 1)
+            use binary X/Y dimensions for the matching window (default: True)
 
         :param mask_baddata_ref:
             path to a 2D boolean mask file (or an instance of GeoArray) for the reference image where all bad data
@@ -297,7 +297,7 @@ class COREG(object):
             number of CPUs to use during pixel grid equalization (default: None, which means 'all CPUs available')
 
         :param force_quadratic_win:
-            force a quadratic matching window (default: 1)
+            force a quadratic matching window (default: True)
 
         :param progress:
             show progress bars (default: True)

arosics/CoReg_local.py

@@ -233,7 +233,7 @@ class COREG_LOCAL(object):
             use binary X/Y dimensions for the matching window (default: True)
 
         :param force_quadratic_win:
-            force a quadratic matching window (default: 1)
+            force a quadratic matching window (default: True)
 
         :param mask_baddata_ref:
             path to a 2D boolean mask file (or an instance of BadDataMask) for the reference image where all bad data

arosics/Tie_Point_Grid.py

@@ -404,6 +404,8 @@ 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()
@@ -468,6 +470,9 @@ class Tie_Point_Grid(object):
         tbl = self.CoRegPoints_table
         tbl = tbl if include_outliers else tbl[tbl['OUTLIER'] == 0].copy() if 'OUTLIER' in tbl.columns else tbl
 
+        if not include_outliers and tbl.empty:
+            raise RuntimeError('Cannot compute the RMSE because all tie points are flagged as false-positives.')
+
         shifts = np.array(tbl['ABS_SHIFT'])
         shifts_sq = [i * i for i in shifts if i != self.outFillVal]
 
@@ -488,6 +493,9 @@ class Tie_Point_Grid(object):
         tbl = self.CoRegPoints_table
         tbl = tbl if include_outliers else tbl[tbl['OUTLIER'] == 0].copy()
 
+        if not include_outliers and tbl.empty:
+            raise RuntimeError('Cannot compute the overall SSIM because all tie points are flagged as false-positives.')
+
         ssim_col = np.array(tbl['SSIM_AFTER' if after_correction else 'SSIM_BEFORE'])
         ssim_col = [i * i for i in ssim_col if i != self.outFillVal]
 
@@ -578,6 +586,10 @@ class Tie_Point_Grid(object):
         tbl = tbl if include_outliers else tbl[tbl['OUTLIER'] == 0].copy() if 'OUTLIER' in tbl.columns else tbl
         tbl = tbl.copy().replace(self.outFillVal, np.nan)
 
+        if not include_outliers and tbl.empty:
+            raise RuntimeError('Cannot compute overall statistics '
+                               'because all tie points are flagged as false-positives.')
+
         def RMSE(shifts):
             shifts_sq = shifts ** 2
             return np.sqrt(sum(shifts_sq) / len(shifts_sq))
@@ -1321,6 +1333,8 @@ class Tie_Point_Grid_Interpolator(object):
             #
             # with multiprocessing.Pool() as pool:
             #     data_full = pool.map(self._Kriging_mp, args_kwargs_dicts)
+            #     pool.close()  # needed to make coverage work in multiprocessing
+            #     pool.join()
 
         return data_full
 

arosics/version.py

@@ -24,5 +24,5 @@
 # limitations under the License.
 
 
-__version__ = '1.7.1'
-__versionalias__ = '2021-10-13_01'
+__version__ = '1.7.4'
+__versionalias__ = '2021-12-15_01'

setup.py

@@ -68,7 +68,7 @@ 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

@@ -32,15 +32,13 @@ dependencies:
     - scipy
 
     # 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

@@ -141,5 +141,5 @@ class Test_Tie_Point_Grid(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    import nose2
-    nose2.main()
+    import pytest
+    pytest.main()