diff --git a/tox.ini b/tox.ini index 034ce04..10fb4ab 100644 --- a/tox.ini +++ b/tox.ini @@ -15,9 +15,9 @@ source_paths = wwpdb/apps/seqmodule wwpdb/apps/tests-seqmodule setup.py # test_path_1 = "wwpdb/apps/tests-seqmodule" # These are placeholders valid source directories without tests files -test_path_2 = "wwpdb/apps/seqmodule/templates" -test_path_3 = "wwpdb/apps/seqmodule/templates" -test_path_4 = "wwpdb/apps/seqmodule/templates" +#test_path_2 = "wwpdb/apps/seqmodule/templates" +#test_path_3 = "wwpdb/apps/seqmodule/templates" +#test_path_4 = "wwpdb/apps/seqmodule/templates" # # Comma separate list of directories/patterns for which test coverage will be evaluated coverage_source_paths = "wwpdb/apps/seqmodule,wwpdb/apps/tests-seqmodule" @@ -50,13 +50,14 @@ allowlist_externals = echo deps = commands = echo "Starting default tests in testenv" -basepython = py312: python3.12 +basepython = py313: python3.13 + py312: python3.12 py311: python3.11 py310: python3.10 py39: python3.9 py27: python2.7 -[testenv:py3{9,10,11,12},py27] +[testenv:py3{9,10,11,12,13},py27] description = 'Run unit tests (unittest runner) using {envpython}' platform= macos: darwin @@ -70,13 +71,13 @@ commands = echo "Starting {envname}" {envpython} -V {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_1} --pattern "{[local_settings]test_pattern}" - {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}" - {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}" - {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}" +# {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}" +# {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}" +# {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}" echo "Completed {envname}" # -[testenv:format_pep8-py3{9,10,11,12}] +[testenv:format_pep8-py3{9,10,11,12,13}] description = 'Run selected PEP8 compliance checks (flake8)' platform= macos: darwin @@ -92,7 +93,7 @@ commands = flake8 --max-line-length=185 --ignore=D,I,E203,W503,E501 {[local_settings]source_paths} {[local_settings]flake_exclude_paths} # -[testenv:lint_pylint-py3{9,10,11,12}] +[testenv:lint_pylint-py3{9,10,11,12,13}] description = 'Run linting compliance checks (pylint)' platform= macos: darwin @@ -107,7 +108,7 @@ commands = echo "Completed {envname}" # -[testenv:format_black-py3{9,10,11,12}] +[testenv:format_black-py3{9,10,11,12,13}] description = 'Run format compliance checks (black)' platform= macos: darwin @@ -123,7 +124,7 @@ commands = echo "Completed {envname}" # -[testenv:test_coverage-py3{9,10,11,12}] +[testenv:test_coverage-py3{9,10,11,12,13}] description = 'Run test coverage analysis' platform= macos: darwin @@ -138,9 +139,9 @@ commands = echo "Starting {envname}" coverage erase coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_1} --pattern "{[local_settings]test_pattern}" - coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}" - coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}" - coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}" +# coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}" +# coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}" +# coverage run --parallel-mode --omit="{[local_settings]coverage_exclude_paths}" --source="{[local_settings]coverage_source_paths}" -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}" echo " ------- Consolidating {envname} data ----------" coverage combine echo " ------- Building {envname} reports ----------" diff --git a/wwpdb/apps/seqmodule/util/SequenceLabel.py b/wwpdb/apps/seqmodule/util/SequenceLabel.py index 871341c..2a617ce 100644 --- a/wwpdb/apps/seqmodule/util/SequenceLabel.py +++ b/wwpdb/apps/seqmodule/util/SequenceLabel.py @@ -90,7 +90,7 @@ def updateAuth(self, authFD, refFD): authFD["SOURCE_COMMON_NAME"] = common_name # # - excludedList = [ "PREDICTED PROTEIN", "PROTEIN OF UNCHARACTERIZED FUNCTION", "UNCHARACTERIZED CONSERVED PROTEIN", "UNCHARACTERIZED PROTEIN" ] + excludedList = ["PREDICTED PROTEIN", "PROTEIN OF UNCHARACTERIZED FUNCTION", "UNCHARACTERIZED CONSERVED PROTEIN", "UNCHARACTERIZED PROTEIN"] # for mapTup in mapTupList: if mapTup[0] == "ENTITY_DESCRIPTION":