PEP8 cleanup and update tox configuration to support python 3.13

wwPDB · Sep 10, 2024 · ff74780 · ff74780
1 parent 32bf3f2
commit ff74780
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Showing 2 changed files with 17 additions and 16 deletions.
diff --git 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
@@ -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":