{"repo":"reframe-hpc\/reframe","instance_id":"reframe-0","base_commit":"b7d86b1d777bc3bed7a3d71d95130376ab5d2820","patch":"","test_patch":"diff --git a\/unittests\/test_sanity_functions.py b\/unittests\/test_sanity_functions.py\nindex 7e6368938..0e9367027 100644\n--- a\/unittests\/test_sanity_functions.py\n+++ b\/unittests\/test_sanity_functions.py\n@@ -473,6 +473,18 @@ def test_assert_reference():\n                              r'\\(l=-1\\.2, u=-0\\.9\\)'):\n         sn.evaluate(sn.assert_reference(-0.8, -1, -0.2, 0.1))\n \n+    # Check that bounds are correctly calculated in case that lower bound\n+    # reaches zero (see also GH issue #3430)\n+    with pytest.raises(SanityError,\n+                       match=r'1 is beyond reference value 0\\.1 '\n+                             r'\\(l=0\\.0, u=0\\.1\\)'):\n+        assert sn.assert_reference(1, 0.1, -1.0, 0)\n+\n+    with pytest.raises(SanityError,\n+                       match=r'-1 is beyond reference value -0\\.1 '\n+                             r'\\(l=-0\\.1, u=-0\\.0\\)'):\n+        assert sn.assert_reference(-1, -0.1, 0, 1.0)\n+\n     # Check invalid thresholds\n     with pytest.raises(SanityError,\n                        match=r'invalid high threshold value: -0\\.1'):\n","problem_statement":"Performance threshold goes to -inf when it should be zero.\n\nIn attempting to create a performance test where zero is the correct value, I created the following reference (since a value of zero results in no reference check being performed; see https:\/\/github.com\/reframe-hpc\/reframe\/issues\/2857):\n\n```\n        self.reference = {\n            '*': {\n                'Gflops': (None, None, None, 'Gflops'),\n                'Exponent': (None, None, None, '10exp'),\n                'Time': (None, None, None, 'seconds'),\n                'failed_tests': (.1, -1.0, 0, 'tests'),\n                'skipped_tests': (.1, -1.0, 0, 'tests')\n        }}\n```\nI was thinking for the failed and skipped tests, this would create a lower bound of zero and upper bound of .1, allowing zero to pass, but integers larger than that would fail.\nThis works for me in that values of zero pass, and 1 or greater values fail, but what is unexpected is that the lower bound gets set to -inf:\n\n```\n  * Reason: performance error: failed to meet references: skipped_tests=1 tests, expected 0.1 (l=-inf, u=0.1)\n```\nAs an additional point of information when I set the lower bound values to -2.0 (or anything greater than 1 abs. value, to see what would happen), the following was printed:\n```\n\tinvalid low threshold value: -2.0\n\tinvalid low threshold value: -2.0\n```\nBut when I choose 2.0 as an upper bound, that seems to be fine:\n```\n                'failed_tests': (.1, -1.0, 2.0, 'tests'),\n                'skipped_tests': (.1, -1.0, 2.0, 'tests')\n```\nresults in the range being interpretted as follows:\n```\n  * Reason: performance error: failed to meet references: skipped_tests=1 tests, expected 0.1 (l=-inf, u=0.30000000000000004)\n```\nIt seems to me that the treatment of lower and upper threshold values should be consistent, and this does not seem consistent.\nAlthough when I switch the reference value to a negative, that reverses the issue:\n```\n                'failed_tests': (-1.0, 0, 2.0, 'tests'),\n                'skipped_tests': (-1.0, 0, 2.0, 'tests')\n```\nresults in:\n```\n\tinvalid high threshold value: 2.0\n\tinvalid high threshold value: 2.0\n```\nand to confirm, I set the lower threshold to -2.0 with a negative reference value to check:\n```\n                'failed_tests': (-1.0, -2.0, 1.0, 'tests'),\n                'skipped_tests': (-1.0, -2.0, 1.0, 'tests')\n```\nresults in:\n```\nPASSED\n```\nMeaning there was no error with the -2.0 reference value in this case. I am not sure what value the upper bound was getting set to in this case, since it wasn't printed out, but since there was no error, it must not be getting set to zero. If it matches the pattern, I am thinking it might be set to inf.\nI am thinking there is something odd that happens when the threshold range crosses zero or has one end that is zero.","hint_text":null,"created_at":"2025-03-18 08:54:38","closed_at":"2025-03-18 08:54:38","version":"0.3.88","FAIL_TO_PASS":[],"PASS_TO_PASS":["unittests\/test_sanity_functions.py::test_assert_ge_with_deferrables","unittests\/test_sanity_functions.py::test_assert_in","unittests\/test_sanity_functions.py::test_count_uniq","unittests\/test_sanity_functions.py::test_assert_false_with_deferrables","unittests\/test_sanity_functions.py::test_assert_not_in","unittests\/test_sanity_functions.py::test_assert_eq","unittests\/test_sanity_functions.py::test_print_separator","unittests\/test_sanity_functions.py::test_all","unittests\/test_sanity_functions.py::test_extractall[extractall_s]","unittests\/test_sanity_functions.py::test_assert_gt_with_deferrables","unittests\/test_sanity_functions.py::test_assert_ne_with_deferrables","unittests\/test_sanity_functions.py::test_hasattr","unittests\/test_sanity_functions.py::test_chain","unittests\/test_sanity_functions.py::test_assert_reference","unittests\/test_sanity_functions.py::test_or","unittests\/test_sanity_functions.py::test_print_stderr","unittests\/test_sanity_functions.py::test_extractsingle[extractsingle_s]","unittests\/test_sanity_functions.py::test_map","unittests\/test_sanity_functions.py::test_abs","unittests\/test_sanity_functions.py::test_extractall_encoding","unittests\/test_sanity_functions.py::test_assert_not_in_with_deferrables","unittests\/test_sanity_functions.py::test_path_isdir","unittests\/test_sanity_functions.py::test_extractall_multiple_tags[extractall]","unittests\/test_sanity_functions.py::test_assert_found_encoding","unittests\/test_sanity_functions.py::test_any","unittests\/test_sanity_functions.py::test_glob","unittests\/test_sanity_functions.py::test_assert_found[assert_found_s]","unittests\/test_sanity_functions.py::test_assert_in_with_deferrables","unittests\/test_sanity_functions.py::test_allx","unittests\/test_sanity_functions.py::test_assert_true_with_deferrables","unittests\/test_sanity_functions.py::test_findall_encoding","unittests\/test_sanity_functions.py::test_extractall_multiple_tags[extractall_s]","unittests\/test_sanity_functions.py::test_extractsingle[extractsingle]","unittests\/test_sanity_functions.py::test_avg","unittests\/test_sanity_functions.py::test_extractsingle_encoding","unittests\/test_sanity_functions.py::test_max","unittests\/test_sanity_functions.py::test_findall_invalid_file","unittests\/test_sanity_functions.py::test_extractall_invalid_file","unittests\/test_sanity_functions.py::test_path_exists","unittests\/test_sanity_functions.py::test_print_end","unittests\/test_sanity_functions.py::test_round","unittests\/test_sanity_functions.py::test_findall[findall_s]","unittests\/test_sanity_functions.py::test_assert_le_with_deferrables","unittests\/test_sanity_functions.py::test_assert_eq_with_deferrables","unittests\/test_sanity_functions.py::test_sum","unittests\/test_sanity_functions.py::test_assert_ne","unittests\/test_sanity_functions.py::test_zip","unittests\/test_sanity_functions.py::test_assert_gt","unittests\/test_sanity_functions.py::test_assert_not_found[assert_not_found]","unittests\/test_sanity_functions.py::test_reversed","unittests\/test_sanity_functions.py::test_assert_not_found_encoding","unittests\/test_sanity_functions.py::test_print_stdout","unittests\/test_sanity_functions.py::test_enumerate","unittests\/test_sanity_functions.py::test_assert_not_found[assert_not_found_s]","unittests\/test_sanity_functions.py::test_extractall_error[extractall_s]","unittests\/test_sanity_functions.py::test_len","unittests\/test_sanity_functions.py::test_assert_lt_with_deferrables","unittests\/test_sanity_functions.py::test_sorted","unittests\/test_sanity_functions.py::test_extractall_custom_conv[extractall]","unittests\/test_sanity_functions.py::test_assert_found[assert_found]","unittests\/test_sanity_functions.py::test_findall[findall]","unittests\/test_sanity_functions.py::test_getitem","unittests\/test_sanity_functions.py::test_extractall[extractall]","unittests\/test_sanity_functions.py::test_min","unittests\/test_sanity_functions.py::test_assert_ge","unittests\/test_sanity_functions.py::test_assert_lt","unittests\/test_sanity_functions.py::test_extractall_error[extractall]","unittests\/test_sanity_functions.py::test_assert_bounded","unittests\/test_sanity_functions.py::test_getitem_with_deferrables","unittests\/test_sanity_functions.py::test_count","unittests\/test_sanity_functions.py::test_safe_format","unittests\/test_sanity_functions.py::test_and","unittests\/test_sanity_functions.py::test_extractall_custom_conv[extractall_s]","unittests\/test_sanity_functions.py::test_iglob","unittests\/test_sanity_functions.py::test_path_isfile","unittests\/test_sanity_functions.py::test_setattr","unittests\/test_sanity_functions.py::test_assert_le","unittests\/test_sanity_functions.py::test_path_islink","unittests\/test_sanity_functions.py::test_assert_true","unittests\/test_sanity_functions.py::test_assert_false","unittests\/test_sanity_functions.py::test_filter"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json unittests\/test_sanity_functions.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/reframe\/utility\/sanity.py b\/reframe\/utility\/sanity.py\nindex a4f57a301..1228586ff 100644\n--- a\/reframe\/utility\/sanity.py\n+++ b\/reframe\/utility\/sanity.py\n@@ -8,6 +8,7 @@\n import contextlib\n import glob as pyglob\n import itertools\n+import math\n import os\n import re\n import sys\n@@ -576,8 +577,14 @@ def calc_bound(thres):\n \n         return ref*(1 + thres)\n \n-    lower = calc_bound(lower_thres) or float('-inf')\n-    upper = calc_bound(upper_thres) or float('inf')\n+    lower = calc_bound(lower_thres)\n+    if lower is None:\n+        lower = -math.inf\n+\n+    upper = calc_bound(upper_thres)\n+    if upper is None:\n+        upper = math.inf\n+\n     try:\n         evaluate(assert_bounded(val, lower, upper))\n     except SanityError:\n"}
{"repo":"PyCQA\/pyflakes","instance_id":"pyflakes-1","base_commit":"433dfd001746a69d12597f7c97af78c13e1f662e","patch":"","test_patch":"diff --git a\/pyflakes\/test\/test_other.py b\/pyflakes\/test\/test_other.py\nindex 68c38e95..23990820 100644\n--- a\/pyflakes\/test\/test_other.py\n+++ b\/pyflakes\/test\/test_other.py\n@@ -1744,6 +1744,13 @@ def test_assign_expr(self):\n         print(x)\n         ''')\n \n+    def test_assign_expr_after_annotation(self):\n+        self.flakes(\"\"\"\n+        a: int\n+        print(a := 3)\n+        print(a)\n+        \"\"\")\n+\n     def test_assign_expr_generator_scope(self):\n         \"\"\"Test assignment expressions in generator expressions.\"\"\"\n         self.flakes('''\n","problem_statement":"Walrus operator + annotation can cause F821 in version 3.3.0\n\nIn order to type hint a variable used in a walrus expression, I put the type hint outside of the expression like in the following example (test.py):\n\n```\na: int\nif a := 3:\n    print(a)\n\nprint(a)\n```\n\nVariable \"a\" is defined in both places\n\n```\n$ python3 test.py\n3\n3\n```\n\nIn pyflakes version 3.2.0 this produced no errors\n\n```pip install flake8==7.1.2 pyflakes==3.2.0```\n\n```\n$ flake8 test.py\n```\n\nIn pyflakes version 3.3.0 this produces F821 even though \"a\" is defined\n\n```pip install flake8==7.2.0 pyflakes==3.3.0```\n\n```\n$ flake8 test.py\ntest.py:3:11: F821 undefined name 'a'\ntest.py:5:7: F821 undefined name 'a'\n```\n\nI am on Windows with Python version 3.12.8","hint_text":null,"created_at":"2025-03-30 21:54:34","closed_at":"2025-03-30 21:54:34","version":"0.3.88","FAIL_TO_PASS":["pyflakes\/test\/test_other.py::TestUnusedAssignment::test_unusedReassignedVariable","pyflakes\/test\/test_other.py::Test::test_doubleAssignment"],"PASS_TO_PASS":["pyflakes\/test\/test_other.py::TestStringFormatting::test_invalid_percent_format_calls","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_unusedVariable","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exceptionUnusedInExceptInFunction","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncDefAwait","pyflakes\/test\/test_other.py::Test::test_duplicateArgs","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_variableUsedInLoop","pyflakes\/test\/test_other.py::Test::test_varAugmentedAssignment","pyflakes\/test\/test_other.py::Test::test_unused_global_statement_not_marked_as_used_by_nested_scope","pyflakes\/test\/test_other.py::TestAsyncStatements::test_raise_notimplemented","pyflakes\/test\/test_other.py::Test::test_redefinedInGenerator","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementSubscriptUndefined","pyflakes\/test\/test_other.py::Test::test_classNameUndefinedInClassBody","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementSingleNameRedefined","pyflakes\/test\/test_other.py::Test::test_extendedSlice","pyflakes\/test\/test_other.py::Test::test_modernProperty","pyflakes\/test\/test_other.py::Test::test_containment","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncDef","pyflakes\/test\/test_other.py::Test::test_redefinedIfElseInListComp","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_setComprehensionAndLiteral","pyflakes\/test\/test_other.py::Test::test_continueOutsideLoop","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exceptWithoutNameInFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementSubscript","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementTupleNamesUndefined","pyflakes\/test\/test_other.py::Test::test_starredAssignmentNoError","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementTupleNamesRedefined","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignToGlobal","pyflakes\/test\/test_other.py::Test::test_redefined_function_shadows_variable","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncForUnderscoreLoopVar","pyflakes\/test\/test_other.py::Test::test_classWithYieldFrom","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_print_in_lambda","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assert_without_message","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_dictComprehension","pyflakes\/test\/test_other.py::Test::test_classRedefinedAsFunction","pyflakes\/test\/test_other.py::Test::test_classWithYield","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_print_returned_in_function","pyflakes\/test\/test_other.py::Test::test_classFunctionDecorator","pyflakes\/test\/test_other.py::Test::test_redefinedInDictComprehension","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_unusedVariableNoLocals","pyflakes\/test\/test_other.py::Test::test_continueInsideLoop","pyflakes\/test\/test_other.py::Test::test_function_arguments","pyflakes\/test\/test_other.py::Test::test_redefinedTryExceptFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exceptWithoutNameInFunctionTuple","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_print_function_assignment","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_listUnpacking","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_valid_print","pyflakes\/test\/test_other.py::Test::test_function_arguments_python3","pyflakes\/test\/test_other.py::TestStringFormatting::test_f_string_without_placeholders","pyflakes\/test\/test_other.py::Test::test_redefinedClassFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignmentInsideLoop","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_invalid_print_when_imported_from_future","pyflakes\/test\/test_other.py::Test::test_unused_nonlocal_statement","pyflakes\/test\/test_other.py::Test::test_breakOutsideLoop","pyflakes\/test\/test_other.py::Test::test_moduleWithYieldFrom","pyflakes\/test\/test_other.py::Test::test_defaultExceptNotLast","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assert_tuple_empty","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementComplicatedTarget","pyflakes\/test\/test_other.py::Test::test_identity","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementUndefinedInside","pyflakes\/test\/test_other.py::Test::test_attrAugmentedAssignment","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_if_tuple","pyflakes\/test\/test_other.py::Test::test_localReferencedBeforeAssignment","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementNameDefinedInBody","pyflakes\/test\/test_other.py::Test::test_redefinedUnderscoreFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_ifexp","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncFor","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_closedOver","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_debuggerskipSpecialVariable","pyflakes\/test\/test_other.py::TestAsyncStatements::test_formatstring","pyflakes\/test\/test_other.py::TestAsyncStatements::test_matmul","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncDefUndefined","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assert_tuple","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_augmentedAssignmentImportedFunctionCall","pyflakes\/test\/test_other.py::Test::test_redefinedInSetComprehension","pyflakes\/test\/test_other.py::Test::test_moduleWithReturn","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assign_expr_nested","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_tupleUnpacking","pyflakes\/test\/test_other.py::Test::test_loopControl","pyflakes\/test\/test_other.py::Test::test_redefinedIfFunction","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncWith","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementListNames","pyflakes\/test\/test_other.py::Test::test_functionRedefinedAsClass","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_f_string","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementSingleName","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_print_augmented_assign","pyflakes\/test\/test_other.py::Test::test_moduleWithYield","pyflakes\/test\/test_other.py::TestAsyncStatements::test_loopControlInAsyncForElse","pyflakes\/test\/test_other.py::Test::test_comparison","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_generatorExpression","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementTupleNames","pyflakes\/test\/test_other.py::Test::test_redefinedFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementSingleNameUndefined","pyflakes\/test\/test_other.py::Test::test_doubleAssignmentConditionally","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_doubleClosedOver","pyflakes\/test\/test_other.py::TestAsyncStatements::test_asyncWithItem","pyflakes\/test\/test_other.py::TestStringFormatting::test_invalid_dot_format_calls","pyflakes\/test\/test_other.py::Test::test_defaultExceptLast","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assert_static","pyflakes\/test\/test_other.py::Test::test_undefinedBaseClass","pyflakes\/test\/test_other.py::Test::test_unused_global_statement","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assign_expr_generator_scope_reassigns_parameter","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assign_expr_generator_scope","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_yieldFromUndefined","pyflakes\/test\/test_other.py::Test::test_classRedefinition","pyflakes\/test\/test_other.py::Test::test_globalDeclaredInDifferentScope","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignInListComprehension","pyflakes\/test\/test_other.py::Test::test_unaryPlus","pyflakes\/test\/test_other.py::TestStringFormatting::test_ok_percent_format_cannot_determine_element_count","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assign_expr","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignToNonlocal","pyflakes\/test\/test_other.py::Test::test_classNameDefinedPreviously","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementAttributeName","pyflakes\/test\/test_other.py::Test::test_classWithReturn","pyflakes\/test\/test_other.py::Test::test_redefinedTryFunction","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_tracebackhideSpecialVariable","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exceptionUnusedInExcept","pyflakes\/test\/test_other.py::Test::test_starredAssignmentErrors","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_unusedUnderscoreVariable","pyflakes\/test\/test_other.py::Test::test_functionDecorator","pyflakes\/test\/test_other.py::TestIncompatiblePrintOperator::test_print_as_condition_test","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assign_expr_after_annotation","pyflakes\/test\/test_other.py::Test::test_breakInsideLoop","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementUndefinedInExpression","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignToMember","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_withStatementNoNames","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assert_with_message","pyflakes\/test\/test_other.py::Test::test_doubleAssignmentWithUse","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exceptionUsedInExcept","pyflakes\/test\/test_other.py::Test::test_redefinedIfElseFunction","pyflakes\/test\/test_other.py::Test::test_ellipsis","pyflakes\/test\/test_other.py::TestAsyncStatements::test_loopControlInAsyncFor","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_unusedVariableAsLocals","pyflakes\/test\/test_other.py::Test::test_redefinedUnderscoreImportation","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_assignInForLoop","pyflakes\/test\/test_other.py::TestUnusedAssignment::test_exception_unused_in_except_star"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json pyflakes\/test\/test_other.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/pyflakes\/checker.py b\/pyflakes\/checker.py\nindex c7d3e882..9888d7ac 100644\n--- a\/pyflakes\/checker.py\n+++ b\/pyflakes\/checker.py\n@@ -1008,8 +1008,12 @@ def addBinding(self, node, value):\n                     for scope in reversed(self.scopeStack)\n                     if not isinstance(scope, GeneratorScope)\n                 )\n-                # it may be a re-assignment to an already existing name\n-                scope.setdefault(value.name, value)\n+                if value.name in scope and isinstance(scope[value.name], Annotation):\n+                    # re-assignment to name that was previously only an annotation\n+                    scope[value.name] = value\n+                else:\n+                    # it may be a re-assignment to an already existing name\n+                    scope.setdefault(value.name, value)\n             else:\n                 self.scope[value.name] = value\n \n"}
{"repo":"tobymao\/sqlglot","instance_id":"sqlglot-2","base_commit":"08eb7f2032957c2fe3119963f344538b90d8f631","patch":"","test_patch":"diff --git a\/tests\/dialects\/test_mysql.py b\/tests\/dialects\/test_mysql.py\nindex 06638f16c5..4a28176ccf 100644\n--- a\/tests\/dialects\/test_mysql.py\n+++ b\/tests\/dialects\/test_mysql.py\n@@ -83,6 +83,12 @@ def test_ddl(self):\n         self.validate_identity(\n             \"CREATE OR REPLACE VIEW my_view AS SELECT column1 AS `boo`, column2 AS `foo` FROM my_table WHERE column3 = 'some_value' UNION SELECT q.* FROM fruits_table, JSON_TABLE(Fruits, '$[*]' COLUMNS(id VARCHAR(255) PATH '$.$id', value VARCHAR(255) PATH '$.value')) AS q\",\n         )\n+        self.validate_identity(\n+            \"CREATE TABLE test_table (id INT AUTO_INCREMENT, PRIMARY KEY (id) USING BTREE)\"\n+        )\n+        self.validate_identity(\n+            \"CREATE TABLE test_table (id INT AUTO_INCREMENT, PRIMARY KEY (id) USING HASH)\"\n+        )\n         self.validate_identity(\n             \"\/*left*\/ EXPLAIN SELECT \/*hint*\/ col FROM t1 \/*right*\/\",\n             \"\/* left *\/ DESCRIBE \/* hint *\/ SELECT col FROM t1 \/* right *\/\",\n","problem_statement":"MySQL dialect fails to parse PRIMARY KEY USING BTREE syntax\n\n**Before you file an issue**\n- Make sure you specify the \"read\" dialect eg. `parse_one(sql, read=\"spark\")`\n- Make sure you specify the \"write\" dialect eg. `ast.sql(dialect=\"duckdb\")`\n- Check if the issue still exists on main\nyes, the issue still exists. I'v tried the latest version.\n**Fully reproducible code snippet**\nPlease include a fully reproducible code snippet or the input sql, dialect, and expected output.\nmysql:\n`CREATE TABLE test_table (\n\tid INT AUTO_INCREMENT,\n\talarm_category VARCHAR ( 255 ),\n\talarm_rule VARCHAR ( 255 ),\nPRIMARY KEY(id) USING BTREE \n)`\n\n**Official Documentation**\nPlease include links to official SQL documentation related to your issue.\nhttps:\/\/sqlglot.com\/sqlglot.html#parse_one\n\n\nreproduce\n```python\nsql = \"CREATE TABLE test_table ( id INT AUTO_INCREMENT, alarm_category VARCHAR ( 255 ), alarm_rule VARCHAR ( 255 ), PRIMARY KEY(id) USING BTREE )\"\nsqlglot.parse_one(sql,read='mysql')\n\n# result\n\n# sqlglot.errors.ParseError: Expecting ). Line 1, Col: 130.\n#   id INT AUTO_INCREMENT, alarm_category VARCHAR ( 255 ), alarm_rule VARCHAR ( 255 ), PRIMARY KEY(id) USING BTREE )\n```\nthis is the reproducible python code","hint_text":null,"created_at":"2025-03-05 15:49:35","closed_at":"2025-03-05 15:49:35","version":"0.3.88","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/dialects\/test_mysql.py::TestMySQL::test_show_like_or_where","tests\/dialects\/test_mysql.py::TestMySQL::test_identity","tests\/dialects\/test_mysql.py::TestMySQL::test_string_literals","tests\/dialects\/test_mysql.py::TestMySQL::test_show_columns","tests\/dialects\/test_mysql.py::TestMySQL::test_types","tests\/dialects\/test_mysql.py::TestMySQL::test_show_name","tests\/dialects\/test_mysql.py::TestMySQL::test_at_time_zone","tests\/dialects\/test_mysql.py::TestMySQL::test_convert","tests\/dialects\/test_mysql.py::TestMySQL::test_ddl","tests\/dialects\/test_mysql.py::TestMySQL::test_show_simple","tests\/dialects\/test_mysql.py::TestMySQL::test_show_processlist","tests\/dialects\/test_mysql.py::TestMySQL::test_match_against","tests\/dialects\/test_mysql.py::TestMySQL::test_number_format","tests\/dialects\/test_mysql.py::TestMySQL::test_show_db_like_or_where_sql","tests\/dialects\/test_mysql.py::TestMySQL::test_json_value","tests\/dialects\/test_mysql.py::TestMySQL::test_grant","tests\/dialects\/test_mysql.py::TestMySQL::test_date_format","tests\/dialects\/test_mysql.py::TestMySQL::test_timestamp_trunc","tests\/dialects\/test_mysql.py::TestMySQL::test_show_profile","tests\/dialects\/test_mysql.py::TestMySQL::test_show_grants","tests\/dialects\/test_mysql.py::TestMySQL::test_mysql","tests\/dialects\/test_mysql.py::TestMySQL::test_show_index","tests\/dialects\/test_mysql.py::TestMySQL::test_bits_literal","tests\/dialects\/test_mysql.py::TestMySQL::test_hexadecimal_literal","tests\/dialects\/test_mysql.py::TestMySQL::test_mysql_time","tests\/dialects\/test_mysql.py::TestMySQL::test_mysql_time_python311","tests\/dialects\/test_mysql.py::TestMySQL::test_canonical_functions","tests\/dialects\/test_mysql.py::TestMySQL::test_show_engine","tests\/dialects\/test_mysql.py::TestMySQL::test_analyze","tests\/dialects\/test_mysql.py::TestMySQL::test_show_events","tests\/dialects\/test_mysql.py::TestMySQL::test_is_null","tests\/dialects\/test_mysql.py::TestMySQL::test_show_tables","tests\/dialects\/test_mysql.py::TestMySQL::test_json_object","tests\/dialects\/test_mysql.py::TestMySQL::test_monthname","tests\/dialects\/test_mysql.py::TestMySQL::test_explain","tests\/dialects\/test_mysql.py::TestMySQL::test_set_variable","tests\/dialects\/test_mysql.py::TestMySQL::test_show_replica_status","tests\/dialects\/test_mysql.py::TestMySQL::test_show_errors","tests\/dialects\/test_mysql.py::TestMySQL::test_introducers","tests\/dialects\/test_mysql.py::TestMySQL::test_escape","tests\/dialects\/test_mysql.py::TestMySQL::test_safe_div"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/dialects\/test_mysql.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/sqlglot\/parser.py b\/sqlglot\/parser.py\nindex 24bf1492f7..f5ed3a8923 100644\n--- a\/sqlglot\/parser.py\n+++ b\/sqlglot\/parser.py\n@@ -1291,6 +1291,10 @@ class Parser(metaclass=_Parser):\n             \"SIMPLE\",\n         ),\n         \"INITIALLY\": (\"DEFERRED\", \"IMMEDIATE\"),\n+        \"USING\": (\n+            \"BTREE\",\n+            \"HASH\",\n+        ),\n         **dict.fromkeys((\"DEFERRABLE\", \"NORELY\"), tuple()),\n     }\n \n"}
{"repo":"matchms\/matchms","instance_id":"matchms-3","base_commit":"0b1707bd866f56404e4056df678af12a4bc20141","patch":"","test_patch":"diff --git a\/tests\/importing\/test_load_from_msp.py b\/tests\/importing\/test_load_from_msp.py\nindex 891ac002..839b604c 100644\n--- a\/tests\/importing\/test_load_from_msp.py\n+++ b\/tests\/importing\/test_load_from_msp.py\n@@ -2,7 +2,7 @@ import os\n import numpy as np\n import pytest\n from matchms import Spectrum\n-from matchms.importing.load_from_msp import load_from_msp, parse_metadata\n+from matchms.importing.load_from_msp import get_peak_values, load_from_msp, parse_metadata\n from tests.builder_Spectrum import SpectrumBuilder\n \n \n@@ -285,3 +285,13 @@ def test_parse_metadata(input_line, expected_output):\n     params = {}\n     parse_metadata(input_line, params)\n     assert params == expected_output\n+\n+\n+@pytest.mark.parametrize(\"line, expected\", [\n+ [\"496\t7.1E-05\", ([496.0], [7.1E-05])],\n+ [\"496\t7.1e-05\", ([496.0], [7.1e-05])],\n+ [\"85:201 86:55 87:10 88:4 89:315\", ([85.0, 86.0, 87.0, 88.0, 89.0], [201.0, 55.0, 10.0, 4.0, 315.0])],\n+])\n+def test_get_peak_values(line, expected):\n+    actual = get_peak_values(line)\n+    assert actual == expected\n\\ No newline at end of file\n","problem_statement":"matchms fails when reading spectra where abundance is in scientific notation\nExample spectrum - spotted in the MSDial EI RI library.\n\nFunny thing is our regex only handles lower case `e` notation while this uses upper case.\n\nMakes me think if we shouldn't just leave the parsing of stuff to python and try to just identify the tokens based on separator?\n\n``` tokens = re.findall(r\"(\\d+(?:\\.\\d+)?(?:e[-+]?\\d+)?)\", peak)```\n```\nNAME: C10 FAME\nEXACTMASS: 186.16198\nFORMULA: C11H22O2\nONTOLOGY: Fatty acid methyl esters\nINCHIKEY: YRHYCMZPEVDGFQ-UHFFFAOYSA-N\nSMILES: CCCCCCCCCC(=O)OC\nRETENTIONINDEX: 1325\nIONMODE: Positive\nINSTRUMENTTYPE: GC-EI-TOF\nCOMMENT: DB#=FiehnLibVolatile0005; origin=Volatile Fiehn Library for Metabolic Profiling\nNum Peaks: 169\n30\t0.629467\n31\t1.545269\n33\t0.272632\n36\t0.02421\n37\t0.313882\n38\t0.539016\n39\t17.716311\n40\t1.915948\n41\t35.4716\n42\t9.51272\n43\t36.860957\n44\t0.788644\n45\t2.384747\n46\t0.104509\n47\t0.031949\n48\t0.035996\n49\t0.052609\n50\t0.529644\n51\t0.838982\n52\t0.365568\n53\t2.854753\n54\t1.750452\n55\t29.439195\n56\t4.268605\n57\t8.867918\n58\t0.591554\n59\t19.854767\n60\t0.49308\n61\t0.379342\n62\t0.260846\n63\t0.557191\n64\t0.08541\n65\t0.63394\n66\t0.192617\n67\t2.198946\n68\t1.443245\n69\t7.300356\n70\t1.714883\n71\t2.948257\n72\t0.322756\n73\t1.743069\n74\t100\n75\t9.275516\n76\t0.745407\n77\t0.361379\n78\t0.038481\n79\t0.615978\n80\t0.123323\n81\t1.452119\n82\t0.612854\n83\t3.739813\n84\t2.643535\n85\t1.788933\n86\t0.278383\n87\t44.905938\n88\t3.900623\n89\t0.580976\n90\t0.037416\n91\t0.023074\n92\t0.025701\n93\t0.21129\n94\t0.043806\n95\t0.774303\n96\t0.156408\n97\t2.040479\n98\t1.468662\n99\t0.256302\n100\t0.217679\n101\t5.157853\n102\t0.416331\n103\t0.024423\n107\t0.071992\n108\t0.018459\n109\t0.002485\n110\t0.228329\n111\t0.387719\n112\t0.390062\n113\t0.245724\n114\t0.05765\n115\t2.589718\n116\t0.396239\n120\t0.001136\n121\t0.032375\n122\t0.007242\n123\t0.027831\n124\t0.013561\n125\t0.150728\n126\t0.114094\n127\t0.07966\n129\t2.578359\n130\t0.256231\n132\t0.005254\n135\t0.102876\n136\t0.03486\n137\t0.071424\n138\t0.021157\n139\t0.314024\n140\t0.065886\n141\t2.280949\n142\t2.305443\n143\t7.497659\n144\t0.656233\n145\t0.026056\n148\t0.005112\n152\t0.034576\n153\t0.069223\n154\t0.035073\n155\t2.668384\n156\t0.291446\n157\t1.242179\n158\t0.131985\n161\t0.008875\n163\t0.018956\n167\t0.000213\n169\t0.00923\n170\t0.000142\n171\t0.011928\n172\t0.001704\n174\t0.002556\n175\t0.000781\n182\t0.003053\n184\t0.000284\n185\t0.008023\n186\t0.458362\n187\t0.050195\n188\t0.004189\n191\t0.000142\n192\t0.000781\n195\t0.000426\n203\t0.000284\n209\t0.00355\n212\t0.000284\n214\t0.000497\n219\t0.000213\n231\t0.000142\n233\t0.000142\n234\t0.000781\n246\t7.1E-05\n249\t0.00284\n250\t0.00142\n251\t0.000355\n257\t0.000639\n263\t0.000639\n266\t0.000213\n270\t0.000142\n283\t0.000284\n295\t0.000568\n297\t0.000355\n314\t0.000213\n315\t0.000142\n321\t0.000426\n327\t0.001207\n329\t0.000994\n342\t0.001633\n348\t0.000355\n380\t0.000142\n390\t0.000497\n398\t0.000213\n401\t0.006674\n402\t0.001775\n403\t0.000923\n427\t0.00071\n455\t0.000213\n468\t0.000355\n474\t0.00071\n495\t0.000213\n496\t7.1E-05\n497\t0.000355\n500\t0.000497\n```","hint_text":null,"created_at":"2025-06-13T09:27:11Z","closed_at":"2025-06-13T09:27:11Z","version":"0.4.3","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/importing\/test_load_from_msp.py::test_load_from_msp_diverse_spectrum_collection","tests\/importing\/test_load_from_msp.py::test_load_from_msp_spaces_massbank_1","tests\/importing\/test_load_from_msp.py::test_parse_metadata[comments: SMILES=\"CC(O)C(O)=O\"-expected_output1]","tests\/importing\/test_load_from_msp.py::test_load_msp_with_scientific_notation","tests\/importing\/test_load_from_msp.py::test_get_peak_values[496\\t7.1e-05-expected1]","tests\/importing\/test_load_from_msp.py::test_parse_metadata[comments: mass=12.0-expected_output2]","tests\/importing\/test_load_from_msp.py::test_parse_metadata[name: 3,4-DICHLOROPHENOL-expected_output3]","tests\/importing\/test_load_from_msp.py::test_get_peak_values[85:201 86:55 87:10 88:4 89:315-expected2]","tests\/importing\/test_load_from_msp.py::test_load_from_msp_multiline","tests\/importing\/test_load_from_msp.py::test_load_from_msp_spaces_mona_1","tests\/importing\/test_load_from_msp.py::test_load_from_msp_spaces_mona_2","tests\/importing\/test_load_from_msp.py::test_load_golm_style_msp","tests\/importing\/test_load_from_msp.py::test_parse_metadata[comments: \"DB#=JP000001\"-expected_output5]","tests\/importing\/test_load_from_msp.py::test_load_msl","tests\/importing\/test_load_from_msp.py::test_load_msp_with_comments_including_quotes","tests\/importing\/test_load_from_msp.py::test_parse_metadata[comments: \"SMILES=\"-expected_output0]","tests\/importing\/test_load_from_msp.py::test_load_from_msp_tabs","tests\/importing\/test_load_from_msp.py::test_get_peak_values[496\\t7.1E-05-expected0]","tests\/importing\/test_load_from_msp.py::test_parse_metadata[comments: \"SMILES=CC(O)C(O)=O\"-expected_output4]"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/importing\/test_load_from_msp.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/matchms\/importing\/load_from_msp.py b\/matchms\/importing\/load_from_msp.py\nindex cf7726a4..47dbedcc 100644\n--- a\/matchms\/importing\/load_from_msp.py\n+++ b\/matchms\/importing\/load_from_msp.py\n@@ -109,7 +109,7 @@ def _parse_line_with_peaks(rline: str) -> Tuple[List[float], List[float], str]:\n \n def get_peak_values(peak: str) -> Tuple[List[float], List[float]]:\n     \"\"\"Get the m\/z and intensity value from the line containing the peak information.\"\"\"\n-    tokens = re.findall(r\"(\\d+(?:\\.\\d+)?(?:e[-+]?\\d+)?)\", peak)\n+    tokens = re.findall(r\"(\\d+(?:\\.\\d+)?(?:[eE][-+]?\\d+)?)\", peak)\n     if len(tokens) % 2 != 0:\n         raise RuntimeError(\"Wrong peak format detected!\")\n \n"}
{"repo":"DataDog\/guarddog","instance_id":"guarddog-4","base_commit":"4d8b7972885ce111991af01610b24b326dcc1de8","patch":"","test_patch":"diff --git a\/tests\/analyzer\/metadata\/test_bundled_binary.py b\/tests\/analyzer\/metadata\/test_bundled_binary.py\nindex 07f1845..7a01283 100644\n--- a\/tests\/analyzer\/metadata\/test_bundled_binary.py\n+++ b\/tests\/analyzer\/metadata\/test_bundled_binary.py\n@@ -19,6 +19,8 @@ class TestBundleBinary:\n     binary_sample_elf = (\n         b\"\\x7F\\x45\\x4C\\x46\" + b\"0x90\" * 10\n     )  # elf magic number plus nop sled\n+    binary_sample_macho32 = b\"\\xFE\\xED\\xFA\\xCE\" + b\"0x90\" * 10\n+    binary_sample_macho64 = b\"\\xFE\\xED\\xFA\\xCF\" + b\"0x90\" * 10\n \n     @pytest.mark.parametrize(\n         \"detector\",\n@@ -52,6 +54,38 @@ class TestBundleBinary:\n             matches, _ = detector.detect({}, dir)\n             assert matches\n \n+    @pytest.mark.parametrize(\n+        \"detector\",\n+        [\n+            (pypi_detector),\n+            (npm_detector),\n+        ],\n+    )\n+    def test_macho32(self, detector: BundledBinary):\n+        with tempfile.TemporaryDirectory() as dir:\n+            full_path = os.path.join(dir, \"package\")\n+            os.mkdir(full_path)\n+            with open(os.path.join(full_path, \"linux.txt\"), \"wb\") as f:\n+                f.write(self.binary_sample_macho32)\n+            matches, _ = detector.detect({}, dir)\n+            assert matches\n+\n+    @pytest.mark.parametrize(\n+        \"detector\",\n+        [\n+            (pypi_detector),\n+            (npm_detector),\n+        ],\n+    )\n+    def test_macho64(self, detector: BundledBinary):\n+        with tempfile.TemporaryDirectory() as dir:\n+            full_path = os.path.join(dir, \"package\")\n+            os.mkdir(full_path)\n+            with open(os.path.join(full_path, \"linux.txt\"), \"wb\") as f:\n+                f.write(self.binary_sample_macho64)\n+            matches, _ = detector.detect({}, dir)\n+            assert matches\n+\n     @pytest.mark.parametrize(\n         \"detector\",\n         [\n","problem_statement":"Add Mach-O magic bytes to the bundled binary detector\nThe [bundled binary detector](https:\/\/github.com\/DataDog\/guarddog\/blob\/v2.1.0\/guarddog\/analyzer\/metadata\/bundled_binary.py#L17) currently detects **ELF** (Unix) and **exe** (Windows) files, but it does not account for the magic bytes for **Mach-O** (Mac) files. This could lead to malicious packages targeting Macs to go unnoticed.\n\nFor reference:\n\n![Image](https:\/\/github.com\/user-attachments\/assets\/7369b953-b3ea-4d0f-a536-70d84d2056ab)\n\nSee https:\/\/en.wikipedia.org\/wiki\/Mach-O#Mach-O_header for more info.","hint_text":null,"created_at":"2025-01-22T12:07:10Z","closed_at":"2025-01-22T12:07:10Z","version":"0.4.3","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_plain[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_empty[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_macho64[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_empty[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_macho64[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_exe[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_macho32[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_exe[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_plain[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_elf[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_macho32[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_multiplebinaries[detector0]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_multiplebinaries[detector1]","tests\/analyzer\/metadata\/test_bundled_binary.py::TestBundleBinary::test_elf[detector0]"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/analyzer\/metadata\/test_bundled_binary.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/guarddog\/analyzer\/metadata\/bundled_binary.py b\/guarddog\/analyzer\/metadata\/bundled_binary.py\nindex 5b6e875..81ed040 100644\n--- a\/guarddog\/analyzer\/metadata\/bundled_binary.py\n+++ b\/guarddog\/analyzer\/metadata\/bundled_binary.py\n@@ -14,7 +14,12 @@ class BundledBinary(Detector):\n \n     # magic bytes are the first few bytes of a file that can be used to identify the file type\n     # regardless of their extension\n-    magic_bytes = {\"exe\": b\"\\x4D\\x5A\", \"elf\": b\"\\x7F\\x45\\x4C\\x46\"}\n+    magic_bytes = {\n+        \"exe\": b\"\\x4D\\x5A\",\n+        \"elf\": b\"\\x7F\\x45\\x4C\\x46\",\n+        \"macho32\": b\"\\xFE\\xED\\xFA\\xCE\",\n+        \"macho64\": b\"\\xFE\\xED\\xFA\\xCF\",\n+    }\n \n     def __init__(self):\n         super().__init__(\n"}
{"repo":"mitmproxy\/pdoc","instance_id":"pdoc-5","base_commit":"ea2b69a4162226b07f68cd25d92d4d92dbbafaf8","patch":"","test_patch":"diff --git a\/test\/test_render_helpers.py b\/test\/test_render_helpers.py\nindex c17740f..4279725 100644\n--- a\/test\/test_render_helpers.py\n+++ b\/test\/test_render_helpers.py\n@@ -110,6 +110,22 @@ def test_markdown_toc():\n     assert to_html(\"#foo\\n#bar\").toc_html  # type: ignore\n \n \n+def test_mixed_toc():\n+    \"\"\"\n+    markdown2 can handle mixed markdown and HTML headings.\n+\n+    Let's test that this works as expected.\n+    \"\"\"\n+    expected = [\n+        \"<ul>\",\n+        '  <li><a href=\"#foo\">foo<\/a><\/li>',\n+        '  <li><a href=\"#bar\">bar<\/a><\/li>',\n+        \"<\/ul>\",\n+        \"\",\n+    ]\n+    assert to_html(\"#foo\\n<h1>bar<\/h1>\").toc_html == \"\\n\".join(expected)\n+\n+\n @pytest.mark.parametrize(\n     \"md,html\",\n     [\n","problem_statement":"Include HTML headers in ToC\n#### Problem Description\n\nWhen a docstring includes HTML headers (`<h1>`, etc.) for example when I used an `.. include:: some_file.html` (or some markdown file which mixes markdown and HTML headers for some reason) directive, those headers are not included in the table of contents.\n\n#### Proposal\nmarkdown2 already supports this feature: https:\/\/github.com\/trentm\/python-markdown2\/pull\/538.\nAll one would need to do, is set `header-ids[\"mixed\"] = True` for the header-ids extra, which pdoc already uses.\n\n\n#### Additional Context\nEssentially, I would consider this the reverse of the `markdown-in-html` setting, which is already supported by pdoc. So I do not see a reason not to support this.","hint_text":null,"created_at":"2025-05-04T12:43:09Z","closed_at":"2025-05-04T12:43:09Z","version":"0.4.3","FAIL_TO_PASS":[],"PASS_TO_PASS":["test\/test_render_helpers.py::test_markdown_autolink[See https:\/\/www.python.org.-<p>See <a href=\"https:\/\/www.python.org\">https:\/\/www.python.org<\/a>.<\/p>\\n]","test\/test_render_helpers.py::test_qualname_candidates[foo-candidates1]","test\/test_render_helpers.py::test_relative_link[foo.bar-foo.bar.baz-bar\/baz.html]","test\/test_render_helpers.py::test_markdown_autolink[https:\/\/example.com\/-<p><a href=\"https:\/\/example.com\/\">https:\/\/example.com\/<\/a><\/p>\\n]","test\/test_render_helpers.py::test_edit_url[demo-True-mapping2-https:\/\/github.com\/mhils\/pdoc\/blob\/master\/test\/testdata\/demo\/__init__.py]","test\/test_render_helpers.py::test_edit_url[demo-False-mapping0-None]","test\/test_render_helpers.py::test_split_identifier[all_modules1-a.c.b.d-result1]","test\/test_render_helpers.py::test_possible_sources[all_modules1-a.b-result1]","test\/test_render_helpers.py::test_relative_link[foo.foo-foo-..\/foo.html]","test\/test_render_helpers.py::test_relative_link[foo.bar.baz-foo.qux.quux-..\/qux\/quux.html]","test\/test_render_helpers.py::test_markdown_toc","test\/test_render_helpers.py::test_relative_link[foo-bar-bar.html]","test\/test_render_helpers.py::test_module_candidates[foo.bar.baz-foo-candidates2]","test\/test_render_helpers.py::test_qualname_candidates[-candidates0]","test\/test_render_helpers.py::test_split_identifier[all_modules0-a.b.c.d-result0]","test\/test_render_helpers.py::test_possible_sources[all_modules0-a.B-result0]","test\/test_render_helpers.py::test_markdown_autolink[See **https:\/\/www.python.org**.-<p>See <strong>https:\/\/www.python.org<\/strong>.<\/p>\\n]","test\/test_render_helpers.py::test_possible_sources[all_modules3-a.b.c.d-result3]","test\/test_render_helpers.py::test_markdown_autolink[See the [Python home page ](https:\/\/www.python.org) for info.-<p>See the <a href=\"https:\/\/www.python.org\">Python home page <\/a> for info.<\/p>\\n]","test\/test_render_helpers.py::test_qualname_candidates[foo.bar-candidates2]","test\/test_render_helpers.py::test_markdown_autolink[<a href=\"https:\/\/example.com\">link<\/a>-<p><a href=\"https:\/\/example.com\">link<\/a><\/p>\\n]","test\/test_render_helpers.py::test_module_candidates[foo.bar.baz-qux-candidates0]","test\/test_render_helpers.py::test_markdown_autolink[<https:\/\/example.com>-<p><a href=\"https:\/\/example.com\">https:\/\/example.com<\/a><\/p>\\n]","test\/test_render_helpers.py::test_edit_url[demo-False-mapping1-https:\/\/github.com\/mhils\/pdoc\/blob\/master\/test\/testdata\/demo.py]","test\/test_render_helpers.py::test_markdown_autolink[[link](https:\/\/example.com)-<p><a href=\"https:\/\/example.com\">link<\/a><\/p>\\n]","test\/test_render_helpers.py::test_mixed_toc","test\/test_render_helpers.py::test_module_candidates[foo.bar.baz-foo.bar-candidates1]","test\/test_render_helpers.py::test_relative_link[foo-foo-]","test\/test_render_helpers.py::test_possible_sources[all_modules2-a-result2]","test\/test_render_helpers.py::test_relative_link[foo.foo-bar-..\/bar.html]"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json test\/test_render_helpers.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/CHANGELOG.md b\/CHANGELOG.md\nindex 747d22f..3337d33 100644\n--- a\/CHANGELOG.md\n+++ b\/CHANGELOG.md\n@@ -4,6 +4,8 @@\n \n ## Unreleased: pdoc next\n \n+- Include included HTML headers in the ToC by default by enabling markdown2's `mixed=True` option of the `header-ids` extra\n+  (#806, @mrossinek)\n \n ## 2025-04-21: pdoc 15.0.3\n \ndiff --git a\/pdoc\/render_helpers.py b\/pdoc\/render_helpers.py\nindex 5c1f339..c96194b 100644\n--- a\/pdoc\/render_helpers.py\n+++ b\/pdoc\/render_helpers.py\n@@ -61,7 +61,7 @@ markdown_extensions = {\n     \"cuddled-lists\": None,\n     \"fenced-code-blocks\": {\"cssclass\": formatter.cssclass},\n     \"footnotes\": None,\n-    \"header-ids\": None,\n+    \"header-ids\": {\"mixed\": True, \"prefix\": None, \"reset-count\": True},\n     \"link-patterns\": None,\n     \"markdown-in-html\": None,\n     \"mermaid\": None,\n"}
{"repo":"MolSSI\/QCElemental","instance_id":"QCElemental-6","base_commit":"cddc5313ad7a251501b633f119c2cb566885bcc1","patch":"","test_patch":"diff --git a\/qcelemental\/tests\/test_molecule.py b\/qcelemental\/tests\/test_molecule.py\nindex 46d7ced..b2154c0 100644\n--- a\/qcelemental\/tests\/test_molecule.py\n+++ b\/qcelemental\/tests\/test_molecule.py\n@@ -2,6 +2,7 @@\n Tests the imports and exports of the Molecule object.\n \"\"\"\n \n+\n import numpy as np\n import pytest\n \n@@ -798,6 +799,15 @@ _ref_mol_multiplicity_hash = {\n     \"triplet\": \"7caca87a\",\n     \"disinglet\": \"83a85546\",\n     \"ditriplet\": \"71d6ba82\",\n+    # float mult\n+    \"singlet_point1\": \"4e9e2587\",\n+    \"singlet_epsilon\": \"ad3f5fab\",\n+    \"triplet_point1\": \"ad35cc28\",\n+    \"triplet_point1_minus\": \"b63d6983\",\n+    \"triplet_point00001\": \"7107b7ac\",\n+    \"disinglet_epsilon\": \"fb0aaaca\",\n+    \"ditriplet_point1\": \"33d47d5f\",\n+    \"ditriplet_point00001\": \"7f0ac640\",\n }\n \n \n@@ -806,14 +816,26 @@ _ref_mol_multiplicity_hash = {\n     [\n         pytest.param(3, 3, False, \"triplet\"),\n         pytest.param(3, 3, True, \"triplet\"),\n-        # 3.1 -> 3 (validate=False) below documents the present bad behavior where a float mult\n-        #   simply gets cast to int with no error. This will change soon. The validate=True throws a\n-        #   nonspecific error that at least mentions type.\n-        pytest.param(3.1, 3, False, \"triplet\"),\n+        # before float multiplicity was allowed, 3.1 (below) was coerced into 3 with validate=False,\n+        #   and validate=True threw a type-mentioning error. Now, 2.9 is allowed for both validate=T\/F\n+        pytest.param(3.1, 3.1, False, \"triplet_point1\"),\n+        # validate=True counterpart fails b\/c insufficient electrons in He for more than triplet\n+        pytest.param(2.9, 2.9, False, \"triplet_point1_minus\"),\n+        pytest.param(2.9, 2.9, True, \"triplet_point1_minus\"),\n+        pytest.param(3.00001, 3.00001, False, \"triplet_point00001\"),\n+        # validate=True counterpart fails like 3.1 above\n+        pytest.param(2.99999, 2.99999, False, \"triplet_point00001\"),  # hash agrees w\/3.00001 above b\/c <CHARGE_NOISE\n+        pytest.param(2.99999, 2.99999, True, \"triplet_point00001\"),\n         pytest.param(3.0, 3, False, \"triplet\"),\n         pytest.param(3.0, 3, True, \"triplet\"),\n         pytest.param(1, 1, False, \"singlet\"),\n         pytest.param(1, 1, True, \"singlet\"),\n+        pytest.param(1.000000000000000000002, 1, False, \"singlet\"),\n+        pytest.param(1.000000000000000000002, 1, True, \"singlet\"),\n+        pytest.param(1.000000000000002, 1.000000000000002, False, \"singlet_epsilon\"),\n+        pytest.param(1.000000000000002, 1.000000000000002, True, \"singlet_epsilon\"),\n+        pytest.param(1.1, 1.1, False, \"singlet_point1\"),\n+        pytest.param(1.1, 1.1, True, \"singlet_point1\"),\n         pytest.param(None, 1, False, \"singlet\"),\n         pytest.param(None, 1, True, \"singlet\"),\n         # fmt: off\n@@ -841,6 +863,9 @@ def test_mol_multiplicity_types(mult_in, mult_store, validate, exp_hash):\n     [\n         pytest.param(-3, False, \"Multiplicity must be positive\"),\n         pytest.param(-3, True, \"Multiplicity must be positive\"),\n+        pytest.param(0.9, False, \"Multiplicity must be positive\"),\n+        pytest.param(0.9, True, \"Multiplicity must be positive\"),\n+        pytest.param(3.1, True, \"Inconsistent or unspecified chg\/mult\"),  # insufficient electrons in He\n     ],\n )\n def test_mol_multiplicity_types_errors(mult_in, validate, error):\n@@ -859,10 +884,11 @@ def test_mol_multiplicity_types_errors(mult_in, validate, error):\n     [\n         pytest.param(5, [3, 3], [3, 3], False, \"ditriplet\"),\n         pytest.param(5, [3, 3], [3, 3], True, \"ditriplet\"),\n-        # 3.1 -> 3 (validate=False) below documents the present bad behavior where a float mult\n-        #   simply gets cast to int with no error. This will change soon. The validate=True throws a\n-        #   irreconcilable error.\n-        pytest.param(5, [3.1, 3.4], [3, 3], False, \"ditriplet\"),\n+        # before float multiplicity was allowed, [3.1, 3.4] (below) were coerced into [3, 3] with validate=False.\n+        #   Now, [2.9, 2.9] is allowed for both validate=T\/F.\n+        pytest.param(5, [3.1, 3.4], [3.1, 3.4], False, \"ditriplet_point1\"),\n+        pytest.param(5, [2.99999, 3.00001], [2.99999, 3.00001], False, \"ditriplet_point00001\"),\n+        pytest.param(5, [2.99999, 3.00001], [2.99999, 3.00001], True, \"ditriplet_point00001\"),\n         # fmt: off\n         pytest.param(5, [3.0, 3.], [3, 3], False, \"ditriplet\"),\n         pytest.param(5, [3.0, 3.], [3, 3], True, \"ditriplet\"),\n@@ -871,6 +897,18 @@ def test_mol_multiplicity_types_errors(mult_in, validate, error):\n         pytest.param(1, [1, 1], [1, 1], True, \"disinglet\"),\n         # None in frag_mult not allowed for validate=False\n         pytest.param(1, [None, None], [1, 1], True, \"disinglet\"),\n+        pytest.param(1, [1.000000000000000000002, 0.999999999999999999998], [1, 1], False, \"disinglet\"),\n+        pytest.param(1, [1.000000000000000000002, 0.999999999999999999998], [1, 1], True, \"disinglet\"),\n+        pytest.param(\n+            1,\n+            [1.000000000000002, 1.000000000000004],\n+            [1.000000000000002, 1.000000000000004],\n+            False,\n+            \"disinglet_epsilon\",\n+        ),\n+        pytest.param(\n+            1, [1.000000000000002, 1.000000000000004], [1.000000000000002, 1.000000000000004], True, \"disinglet_epsilon\"\n+        ),\n     ],\n )\n def test_frag_multiplicity_types(mol_mult_in, mult_in, mult_store, validate, exp_hash):\n@@ -902,6 +940,9 @@ def test_frag_multiplicity_types(mol_mult_in, mult_in, mult_store, validate, exp\n     [\n         pytest.param([-3, 1], False, \"Multiplicity must be positive\"),\n         pytest.param([-3, 1], True, \"Multiplicity must be positive\"),\n+        pytest.param(\n+            [3.1, 3.4], True, \"Inconsistent or unspecified chg\/mult\"\n+        ),  # insufficient e- for triplet+ on He in frag 1\n     ],\n )\n def test_frag_multiplicity_types_errors(mult_in, validate, error):\ndiff --git a\/qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py b\/qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py\nindex 0c18649..0f85bb0 100644\n--- a\/qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py\n+++ b\/qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py\n@@ -94,6 +94,12 @@ working_chgmults = [\n         (-2.4, [-2.4, 0, 0], 3, [1, 2, 2]),\n         \"a83a3356\",\n     ),  # 166\n+    ((\"He\", None, [None], 2.8, [None]), (0, [0], 2.8, [2.8]), \"3e10e7b5\"),  # 180\n+    ((\"He\", None, [None], None, [2.8]), (0, [0], 2.8, [2.8]), \"3e10e7b5\"),  # 181\n+    ((\"N\/N\/N\", None, [None, None, None], 2.2, [2, 2, 2.2]), (0, [0, 0, 0], 2.2, [2, 2, 2.2]), \"798ee5d4\"),  # 183\n+    ((\"N\/N\/N\", None, [None, None, None], 4.2, [2, 2, 2.2]), (0, [0, 0, 0], 4.2, [2, 2, 2.2]), \"ed6d1f35\"),  # 185\n+    ((\"N\/N\/N\", None, [None, None, None], None, [2, 2, 2.2]), (0, [0, 0, 0], 4.2, [2, 2, 2.2]), \"ed6d1f35\"),  # 186\n+    ((\"N\/N\/N\", None, [2, -2, None], 2.2, [2, 2, 2.2]), (0, [2, -2, 0], 2.2, [2, 2, 2.2]), \"66e655c0\"),  # 187\n ]\n \n \n@@ -153,6 +159,8 @@ def test_validate_and_fill_chgmult_mol_model(systemtranslator, inp, expected, ex\n         (\"Gh\", None, [None], 3, [None]),  # 60\n         (\"Gh\/He\", None, [2, None], None, [None, None]),  # 62\n         (\"Gh\/Ne\", 2, [-2, None], None, [None, None]),  # 65b\n+        (\"He\", None, [None], 3.2, [None]),  # 182\n+        (\"N\/N\/N\", None, [None, None, None], 2.2, [None, None, 2.2]),  # 184\n     ],\n )\n def test_validate_and_fill_chgmult_irreconcilable(systemtranslator, inp):\n@@ -173,6 +181,8 @@ def test_validate_and_fill_chgmult_irreconcilable(systemtranslator, inp):\n # 35 - insufficient electrons\n # 55 - both (1, (1, 0.0, 0.0), 4, (1, 3, 2)) and (1, (0.0, 0.0, 1), 4, (2, 3, 1)) plausible\n # 65 - non-0\/1 on Gh fragment errors normally but reset by zero_ghost_fragments\n+# 182 - insufficient electrons on He\n+# 184 - decline to guess fragment multiplicities when floats involved\n \n \n @pytest.fixture\n","problem_statement":"Floating point number allowed for molecular charge but not molecular multiplicity\n**Describe the bug**\r\n<!-- A clear and concise description of what the bug is. -->\r\nQCElemental allows floating point numbers for molecular charges, however when computing the spin with the fractional electron there is no way to represent the molecular multiplicity with just an integer.\r\n\r\n**To Reproduce**\r\n<!-- Code to reproduce the behavior: Please include the results of:-->\r\n```python\r\nimport qcelemental as qcel\r\nmol = qcel.models.Molecule(\r\n    geometry=[0.0, 0.0, 0.5, 0.0, 0.0, -0.5],\r\n    symbols=[\"H\", \"He\"],\r\n    molecular_charge=0.5,\r\n    molecular_multiplicity=1.5,  # not possible\r\n)\r\n```\r\n\r\n**Expected behavior**\r\n<!-- A clear and concise description of what you expected to happen. -->\r\nConsistent behavior for specifying molecular charge and molecular multiplicity.\r\n\r\n**Additional context**\r\n<!-- Add any other context about the problem here. -->","hint_text":null,"created_at":"2025-01-13T16:47:19Z","closed_at":"2025-01-13T16:47:19Z","version":"0.4.3","FAIL_TO_PASS":["qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp50-expected50-]","qcelemental\/tests\/test_molecule.py::test_show","qcelemental\/tests\/test_molecule.py::test_molecule_serialization[msgpack]","qcelemental\/tests\/test_molecule.py::test_to_from_file_charge_spin[msgpack-msgpack]","qcelemental\/tests\/test_molecule.py::test_to_from_file_simple[msgpack-msgpack]","qcelemental\/tests\/test_molecule.py::test_molecule_serialization[msgpack-ext]"],"PASS_TO_PASS":["qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp3-expected3-bfdcbd63]","qcelemental\/tests\/test_molecule.py::test_fragment_charge_configurations[0-4-0-2-0.0-5]","qcelemental\/tests\/test_molecule.py::test_pretty_print","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp16]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[4He 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0 0 0-extra_keys4]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[5-mult_in1-mult_store1-True-ditriplet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp9]","qcelemental\/tests\/test_molecule.py::test_from_data_kwargs","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp6-expected6-35a61864]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp46-expected46-dfc621eb]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp8]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp47-expected47-c828e6fd]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp4-expected4-bfdcbd63]","qcelemental\/tests\/test_molecule.py::test_sparse_molecule_fields[He4 0 0 0-extra_keys3]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3.0-3-False-triplet0]","qcelemental\/tests\/test_molecule.py::test_to_from_file_complex[psi4]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp25-expected25-809afce3]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp37-expected37-cb147b67]","qcelemental\/tests\/test_molecule.py::test_measurements[measure3-result3]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp56-expected56-798ee5d4]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp7-expected7-cd3a0ecd]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp8-expected8-e3ca63c8]","qcelemental\/tests\/test_molecule.py::test_molecule_compare","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[None-1-True-singlet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp20-expected20-516f623a]","qcelemental\/tests\/test_molecule.py::test_nonphysical_spec","qcelemental\/tests\/test_molecule.py::test_to_from_file_complex[json]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp15-expected15-b3855c64]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp54-expected54-3e10e7b5]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp33-expected33-59c6613a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp10-expected10-cf3e8c41]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[He 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chg\/mult]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp13]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[1.000000000000002-1.000000000000002-True-singlet_epsilon]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp12-expected12-752ec2fe]","qcelemental\/tests\/test_molecule.py::test_molecule_np_constructors","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3.1-3.1-False-triplet_point1]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp51-expected51-684cec20]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp0-expected0-b3855c64]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp55-expected55-3e10e7b5]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[2.9-2.9-False-triplet_point1_minus]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp18-expected18-ad36285a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp42-expected42-38a20a23]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp21-expected21-0f1a1ffc]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp37-expected37-cb147b67]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp17-expected17-e5f7b504]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp56-expected56-798ee5d4]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp39-expected39-b381f350]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp17-expected17-e5f7b504]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp33-expected33-59c6613a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp15-expected15-b3855c64]","qcelemental\/tests\/test_molecule.py::test_molecule_serialization[json-ext]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[He 0 0 0\\n--\\n@He 0 0 5-args7-He2-formula_dict7-4.00260325413-2-0.0]","qcelemental\/tests\/test_molecule.py::test_to_from_file_simple[xyz-xyz]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp19-expected19-3fa264e9]","qcelemental\/tests\/test_molecule.py::test_measurements[measure5-result5]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp35-expected35-3a2ba1ea]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp26-expected26-f91e3c77]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp4]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp31-expected31-59c6613a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp30-expected30-e9b8fe09]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp57-expected57-ed6d1f35]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[1.1-1.1-True-singlet_point1]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp32-expected32-ccd5e698]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp41-expected41-b3e87763]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[1-1-True-singlet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp59-expected59-66e655c0]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp12-expected12-752ec2fe]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp54-expected54-3e10e7b5]","qcelemental\/tests\/test_molecule.py::test_fragment_charge_configurations[1-1-1-1-2.0-1]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[2.99999-2.99999-True-triplet_point00001]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp57-expected57-ed6d1f35]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp2-expected2-ad36285a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp34-expected34-ac9200ac]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3-3-False-triplet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp3-expected3-bfdcbd63]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp11-expected11-9cd54b37]","qcelemental\/tests\/test_molecule.py::test_get_fragment[True-True]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp31-expected31-59c6613a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp2-expected2-ad36285a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp22-expected22-9eb13213]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp58-expected58-ed6d1f35]","qcelemental\/tests\/test_molecule.py::test_hash_canary","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp44-expected44-28064e3e]","qcelemental\/tests\/test_molecule.py::test_molecule_errors_shape","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types_errors[0.9-True-Multiplicity must be positive]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[1-mult_in13-mult_store13-True-disinglet_epsilon]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp5-expected5-e7141038]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp27-expected27-dc9720af]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3.0-3-True-triplet0]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp2]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types_errors[mult_in0-False-Multiplicity must be positive]","qcelemental\/tests\/test_molecule.py::test_fragment_charge_configurations[0-2-1-1-1.0-2]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp52-expected52-7a5fd2d3]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[5-mult_in4-mult_store4-True-ditriplet_point00001]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp27-expected27-dc9720af]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp13-expected13-cc52833f]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp44-expected44-28064e3e]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp26-expected26-f91e3c77]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp11]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp43-expected43-38a20a23]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp29-expected29-dfcb8940]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp38-expected38-7140d169]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[1-mult_in7-mult_store7-False-disinglet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp45-expected45-83330b29]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[5He4 0 0 0-args9-He-formula_dict9-5.012057-2-0.0]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp16-expected16-7caca87a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp48-expected48-54238534]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp29-expected29-dfcb8940]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp7]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[He@3.14 0 0 0-args10-He-formula_dict10-3.14-2-0.0]","qcelemental\/tests\/test_molecule.py::test_sparse_molecule_connectivity","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp6-expected6-35a61864]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3.0-3-True-triplet1]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp16-expected16-7caca87a]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp50-expected50-]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp10-expected10-cf3e8c41]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp14]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp48-expected48-54238534]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp47-expected47-c828e6fd]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp28-expected28-9445d8b9]","qcelemental\/tests\/test_molecule.py::test_get_fragment[False-False]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp32-expected32-ccd5e698]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp23-expected23-512c204f]","qcelemental\/tests\/test_molecule.py::test_water_minima_data","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[2.99999-2.99999-False-triplet_point00001]","qcelemental\/tests\/test_molecule.py::test_nuclearrepulsionenergy_nelectrons","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp53-expected53-a83a3356]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp59-expected59-66e655c0]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[1-mult_in8-mult_store8-True-disinglet]","qcelemental\/tests\/test_molecule.py::test_measurements[measure4-result4]","qcelemental\/tests\/test_molecule.py::test_bad_isotope_spec","qcelemental\/tests\/test_molecule.py::test_molecular_weight[He 0 0 0\\n--\\n@He 0 0 5-args4-He2-formula_dict4-0.0-0-0.0]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp14-expected14-cf3e8c41]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[None-1-False-singlet]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp10]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp46-expected46-dfc621eb]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[5-mult_in5-mult_store5-False-ditriplet]","qcelemental\/tests\/test_molecule.py::test_frag_multiplicity_types[1-mult_in11-mult_store11-True-disinglet]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types_errors[0.9-False-Multiplicity must be positive]","qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp24-expected24-74aba942]","qcelemental\/tests\/test_molecule.py::test_molecular_weight[He 0 0 0\\n--\\n@He 0 0 5-args6-He2-formula_dict6-4.00260325413-2-0.0]","qcelemental\/tests\/test_molecule.py::test_mol_multiplicity_types[3.00001-3.00001-False-triplet_point00001]","qcelemental\/tests\/test_molecule.py::test_measurements[measure2-180.0]"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json qcelemental\/tests\/test_molecule.py qcelemental\/tests\/test_molparse_validate_and_fill_chgmult.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/.github\/workflows\/CI.yaml b\/.github\/workflows\/CI.yaml\nindex aa949f3..8aca4c9 100644\n--- a\/.github\/workflows\/CI.yaml\n+++ b\/.github\/workflows\/CI.yaml\n@@ -17,7 +17,8 @@ jobs:\n       matrix:\n         python-version: [\"3.7\", \"3.9\", \"3.11\", \"3.12\"]\n         pydantic-version: [\"1\", \"2\"]\n-        runs-on: [ubuntu-latest, windows-latest]\n+        # runs-on: [ubuntu-latest, windows-latest]\n+        runs-on: [ubuntu-22.04, windows-latest]  # until drop py37\n         exclude:\n           - runs-on: windows-latest\n             pydantic-version: \"1\"\ndiff --git a\/.github\/workflows\/Lint.yml b\/.github\/workflows\/Lint.yml\nindex c337352..c52ea9a 100644\n--- a\/.github\/workflows\/Lint.yml\n+++ b\/.github\/workflows\/Lint.yml\n@@ -14,7 +14,7 @@ jobs:\n       - name: Set up Python\n         uses: actions\/setup-python@v4\n         with:\n-          python-version: \"3.7\"\n+          python-version: \"3.8\"\n       - name: Install black\n         run: pip install \"black>=22.1.0,<23.0a0\"\n       - name: Print code formatting with black (hints here if next step errors)\n@@ -29,7 +29,7 @@ jobs:\n       - name: Set up Python\n         uses: actions\/setup-python@v4\n         with:\n-          python-version: \"3.7\"\n+          python-version: \"3.8\"\n       - name: Install poetry\n         run: pip install poetry\n       - name: Install repo\ndiff --git a\/docs\/changelog.rst b\/docs\/changelog.rst\nindex 76edbc6..0cd1e4f 100644\n--- a\/docs\/changelog.rst\n+++ b\/docs\/changelog.rst\n@@ -19,18 +19,19 @@ Changelog\n .. Misc.\n .. +++++\n \n-- (:pr:`340`, :issue:`330`) Add molecular charge and multiplicity to Molecule repr formula,\n-  so neutral singlet unchanged but radical cation has '2^formula+'.\n-\n \n 0.29.0 \/ 2024-MM-DD (Unreleased)\n --------------------------------\n \n Breaking Changes\n ++++++++++++++++\n+- (:pr:`341`) `packaging` is now a required dependency.\n \n New Features\n ++++++++++++\n+- (:pr:`350`, :pr:`318`, :issue:`317`) Make behavior consistent between molecular_charge\/\n+  fragment_charges and molecular_multiplicity\/fragment_multiplicities by allowing floating point\n+  numbers for multiplicities. @awvwgk\n - (:pr:`360`) ``Molecule`` learned new functions ``element_composition`` and ``molecular_weight``.\n   The first gives a dictionary of element symbols and counts, while the second gives the weight in amu.\n   Both can access the whole molecule or per-fragment like the existing ``nelectrons`` and\n@@ -38,13 +39,30 @@ New Features\n \n Enhancements\n ++++++++++++\n+- (:pr:`340`, :issue:`330`) Add molecular charge and multiplicity to Molecule repr formula,\n+  so neutral singlet unchanged but radical cation has '2^formula+'. @awvwgk\n+- (:pr:`341`) Use `packaging` instead of deprecated `setuptools` to provide version parsing for\n+  `qcelemental.util.parse_version` and `qcelemental.util.safe_version`. This behaves slightly\n+  different; \"v7.0.0+N\/A\" was processed ok before but fails with newer version. @berquist\n+- (:pr:`343`) Molecular and fragment multiplicities are now always enforced to be >=1.0. Previously\n+  this wasn't checked for `Molecule(..., validate=False)`. Error messages will change sometimes\n+  change for `validate=True` (run by default).\n+- (:pr:`343`) `qcelemental.molparse` newly allows floats that are ints (e.g., 1.0) for multiplicity.\n+  Previously it would raise an error about not being an int.\n+- (:pr:`337`) Solidify the (unchanged) schema_name for `QCInputSpecification` and `AtomicResult`\n+  into Literals where previously they had been regex strings coerced into a single name. The literals\n+  allow pydantic to discriminate models, which benefits GeneralizedOptimizationInput\/Result in\n+  QCManyBody\/QCEngine\/OptKing. The only way this can interfere is if schema producers have whitespace\n+  around `schema_name` for these models or if any `AtomicResult`s are still using \"qc_schema_output\",\n+  which looks to have only been added for compatibility with pre-pydantic QCSchema.\n \n Bug Fixes\n +++++++++\n \n Misc.\n +++++\n-- (:pr:`342`) Update some docs settings and requirements for newer tools.\n+- (:pr:`344`, :issue:`282`) Add a citation file since QCElemental doesn't have a paper. @lilyminium\n+- (:pr:`342`, :issue:`333`) Update some docs settings and requirements for newer tools.\n - (:pr:`353`) copied in pkg_resources.safe_version code as follow-up to Eric switch to packaging as both nwchem and gamess were now working. \n the try_harder_safe_version might be even bettter\n \ndiff --git a\/qcelemental\/models\/molecule.py b\/qcelemental\/models\/molecule.py\nindex 63070d5..215db12 100644\n--- a\/qcelemental\/models\/molecule.py\n+++ b\/qcelemental\/models\/molecule.py\n@@ -185,7 +185,7 @@ class Molecule(ProtoModel):\n         description=\"Additional comments for this molecule. Intended for pure human\/user consumption and clarity.\",\n     )\n     molecular_charge: float = Field(0.0, description=\"The net electrostatic charge of the molecule.\")  # type: ignore\n-    molecular_multiplicity: int = Field(1, description=\"The total multiplicity of the molecule.\")  # type: ignore\n+    molecular_multiplicity: float = Field(1, description=\"The total multiplicity of the molecule.\")  # type: ignore\n \n     # Atom data\n     masses_: Optional[Array[float]] = Field(  # type: ignore\n@@ -257,7 +257,7 @@ class Molecule(ProtoModel):\n         \"if not provided (and :attr:`~qcelemental.models.Molecule.fragments` are specified).\",\n         shape=[\"nfr\"],\n     )\n-    fragment_multiplicities_: Optional[List[int]] = Field(  # type: ignore\n+    fragment_multiplicities_: Optional[List[float]] = Field(  # type: ignore\n         None,\n         description=\"The multiplicity of each fragment in the :attr:`~qcelemental.models.Molecule.fragments` list. The index of this \"\n         \"list matches the 0-index indices of :attr:`~qcelemental.models.Molecule.fragments` list. Will be filled in based on a set of \"\n@@ -421,12 +421,16 @@ class Molecule(ProtoModel):\n             n = len(values[\"fragments_\"])\n             if len(v) != n:\n                 raise ValueError(\"Fragment Multiplicities must be same number of entries as Fragments\")\n+        v = [(int(m) if m.is_integer() else m) for m in v]\n         if any([m < 1.0 for m in v]):\n             raise ValueError(f\"Fragment Multiplicity must be positive: {v}\")\n         return v\n \n     @validator(\"molecular_multiplicity\")\n     def _int_if_possible(cls, v, values, **kwargs):\n+        if v.is_integer():\n+            # preserve existing hashes\n+            v = int(v)\n         if v < 1.0:\n             raise ValueError(\"Molecular Multiplicity must be positive\")\n         return v\n@@ -502,7 +506,7 @@ class Molecule(ProtoModel):\n         return fragment_charges\n \n     @property\n-    def fragment_multiplicities(self) -> List[int]:\n+    def fragment_multiplicities(self) -> List[float]:\n         fragment_multiplicities = self.__dict__.get(\"fragment_multiplicities_\")\n         if fragment_multiplicities is None:\n             fragment_multiplicities = [self.molecular_multiplicity]\n@@ -803,9 +807,7 @@ class Molecule(ProtoModel):\n             data = getattr(self, field)\n             if field == \"geometry\":\n                 data = float_prep(data, GEOMETRY_NOISE)\n-            elif field == \"fragment_charges\":\n-                data = float_prep(data, CHARGE_NOISE)\n-            elif field == \"molecular_charge\":\n+            elif field in [\"fragment_charges\", \"molecular_charge\", \"fragment_multiplicities\", \"molecular_multiplicity\"]:\n                 data = float_prep(data, CHARGE_NOISE)\n             elif field == \"masses\":\n                 data = float_prep(data, MASS_NOISE)\ndiff --git a\/qcelemental\/molparse\/chgmult.py b\/qcelemental\/molparse\/chgmult.py\nindex a311d08..493335c 100644\n--- a\/qcelemental\/molparse\/chgmult.py\n+++ b\/qcelemental\/molparse\/chgmult.py\n@@ -19,7 +19,7 @@ def _high_spin_sum(mult_list):\n \n \n def _mult_ok(m):\n-    return isinstance(m, (int, np.integer)) and m >= 1\n+    return isinstance(m, (int, np.integer, float, np.float64)) and m >= 1\n \n \n def _sufficient_electrons_for_mult(z, c, m):\n@@ -430,7 +430,16 @@ def validate_and_fill_chgmult(\n     if molecular_multiplicity is None:  # unneeded, but shortens the exact lists\n         frag_mult_hi = _high_spin_sum(_apply_default(fragment_multiplicities, 2))\n         frag_mult_lo = _high_spin_sum(_apply_default(fragment_multiplicities, 1))\n-        for m in range(frag_mult_lo, frag_mult_hi + 1):\n+        try:\n+            mult_range = range(frag_mult_lo, frag_mult_hi + 1)\n+        except TypeError:\n+            if frag_mult_lo == frag_mult_hi:\n+                mult_range = [frag_mult_hi]\n+            else:\n+                raise ValidationError(\n+                    f\"Cannot process: please fully specify float multiplicity: m: {molecular_multiplicity} fm: {fragment_multiplicities}\"\n+                )\n+        for m in mult_range:\n             cgmp_exact_m.append(m)\n \n     #   * (S6) suggest range of missing mult = tot - high_spin_sum(frag - 1),\n@@ -450,7 +459,16 @@ def validate_and_fill_chgmult(\n \n     for ifr in range(nfr):\n         if fragment_multiplicities[ifr] is None:  # unneeded, but shortens the exact lists\n-            for m in reversed(range(max(missing_mult_lo, 1), missing_mult_hi + 1)):\n+            try:\n+                mult_range = reversed(range(max(missing_mult_lo, 1), missing_mult_hi + 1))\n+            except TypeError:\n+                if missing_mult_lo == missing_mult_hi:\n+                    mult_range = [missing_mult_hi]\n+                else:\n+                    raise ValidationError(\n+                        f\"Cannot process: please fully specify float multiplicity: m: {molecular_multiplicity} fm: {fragment_multiplicities}\"\n+                    )\n+            for m in mult_range:\n                 cgmp_exact_fm[ifr].append(m)\n             cgmp_exact_fm[ifr].append(1)\n             cgmp_exact_fm[ifr].append(2)\n"}
{"repo":"tobymao\/sqlglot","instance_id":"sqlglot-7","base_commit":"cfa25bb59b4537427aebe93f92c7176e045e7b0c","patch":"","test_patch":"diff --git a\/tests\/dialects\/test_tsql.py b\/tests\/dialects\/test_tsql.py\nindex 738120a2ee..fe1aa9c5dd 100644\n--- a\/tests\/dialects\/test_tsql.py\n+++ b\/tests\/dialects\/test_tsql.py\n@@ -436,6 +436,13 @@ def test_tsql(self):\n             \"'a' + 'b'\",\n         )\n \n+        self.validate_identity(\n+            \"CREATE TABLE db.t1 (a INTEGER, b VARCHAR(50), CONSTRAINT c PRIMARY KEY (a DESC))\",\n+        )\n+        self.validate_identity(\n+            \"CREATE TABLE db.t1 (a INTEGER, b INTEGER, CONSTRAINT c PRIMARY KEY (a DESC, b))\"\n+        )\n+\n     def test_option(self):\n         possible_options = [\n             \"HASH GROUP\",\n","problem_statement":"TSQL: PRIMARY KEY constraint fails to parse if sort option is given\n\nThe following CREATE TABLE statement parses just fine:\r\n```\r\nimport sqlglot\r\n\r\ntest = \"\"\"CREATE TABLE dbo.test (\r\n      id INT,\r\n      name VARCHAR(50),\r\n      CONSTRAINT pk_testTable PRIMARY KEY (id)\r\n      ) ;\"\"\"\r\n        \r\n    parsed_script = sqlglot.parse(test, read=\"tsql\")\r\n```\r\n\r\nHowever, when I add ASC or DESC to the PRIMARY KEY constraint, it fails to parse:\r\n\r\n```\r\nimport sqlglot\r\n\r\ntest = \"\"\"CREATE TABLE dbo.test (\r\n    id INT,\r\n    name VARCHAR(50),\r\n    CONSTRAINT pk_testTable PRIMARY KEY (id DESC)\r\n    ) ;\"\"\"\r\n        \r\n    parsed_script = sqlglot.parse(test, read=\"tsql\")\r\n```\r\n\r\nError Message:\r\n\r\n```\r\nException has occurred: ParseError\r\nExpecting ). Line 4, Col: 45.\r\n  bo.test (\r\n        id INT,\r\n        name VARCHAR(50),\r\n        CONSTRAINT pk_testTable PRIMARY KEY (id \u001b[4mDESC\u001b[0m)\r\n        ) ;\r\n  File \"C:\\*snip*\\main.py\", line 96, in main\r\n    parsed_script = sqlglot.parse(test, read=\"tsql\")\r\n                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n  File \"C:\\*snip*\\main.py\", line 116, in <module>\r\n    main()\r\nsqlglot.errors.ParseError: Expecting ). Line 4, Col: 45.\r\n  bo.test (\r\n        id INT,\r\n        name VARCHAR(50),\r\n        CONSTRAINT pk_testTable PRIMARY KEY (id \u001b[4mDESC\u001b[0m)\r\n        ) ;\r\n```\r\n\r\nOfficial Documentation: https:\/\/learn.microsoft.com\/en-us\/sql\/t-sql\/statements\/create-table-transact-sql?view=sql-server-ver16#constraint\r\n\r\nEdit: sqlglot version is 25.21.3.\r\n","hint_text":null,"created_at":"2025-01-15 15:34:32","closed_at":"2025-01-15 15:34:32","version":"0.3.88","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/dialects\/test_tsql.py::TestTSQL::test_rollback","tests\/dialects\/test_tsql.py::TestTSQL::test_declare","tests\/dialects\/test_tsql.py::TestTSQL::test_datetrunc","tests\/dialects\/test_tsql.py::TestTSQL::test_transaction","tests\/dialects\/test_tsql.py::TestTSQL::test_eomonth","tests\/dialects\/test_tsql.py::TestTSQL::test_option","tests\/dialects\/test_tsql.py::TestTSQL::test_set","tests\/dialects\/test_tsql.py::TestTSQL::test_lateral_subquery","tests\/dialects\/test_tsql.py::TestTSQL::test_types_decimals","tests\/dialects\/test_tsql.py::TestTSQL::test_string","tests\/dialects\/test_tsql.py::TestTSQL::test_parsename","tests\/dialects\/test_tsql.py::TestTSQL::test_replicate","tests\/dialects\/test_tsql.py::TestTSQL::test_commit","tests\/dialects\/test_tsql.py::TestTSQL::test_identifier_prefixes","tests\/dialects\/test_tsql.py::TestTSQL::test_hints","tests\/dialects\/test_tsql.py::TestTSQL::test_types","tests\/dialects\/test_tsql.py::TestTSQL::test_json","tests\/dialects\/test_tsql.py::TestTSQL::test_isnull","tests\/dialects\/test_tsql.py::TestTSQL::test_date_diff","tests\/dialects\/test_tsql.py::TestTSQL::test_types_string","tests\/dialects\/test_tsql.py::TestTSQL::test_current_user","tests\/dialects\/test_tsql.py::TestTSQL::test_datename","tests\/dialects\/test_tsql.py::TestTSQL::test_udf","tests\/dialects\/test_tsql.py::TestTSQL::test_types_ints","tests\/dialects\/test_tsql.py::TestTSQL::test_top","tests\/dialects\/test_tsql.py::TestTSQL::test_lateral_table_valued_function","tests\/dialects\/test_tsql.py::TestTSQL::test_openjson","tests\/dialects\/test_tsql.py::TestTSQL::test_count","tests\/dialects\/test_tsql.py::TestTSQL::test_scope_resolution_op","tests\/dialects\/test_tsql.py::TestTSQL::test_len","tests\/dialects\/test_tsql.py::TestTSQL::test_system_time","tests\/dialects\/test_tsql.py::TestTSQL::test_temporal_table","tests\/dialects\/test_tsql.py::TestTSQL::test_fullproc","tests\/dialects\/test_tsql.py::TestTSQL::test_add_date","tests\/dialects\/test_tsql.py::TestTSQL::test_grant","tests\/dialects\/test_tsql.py::TestTSQL::test_format","tests\/dialects\/test_tsql.py::TestTSQL::test_convert","tests\/dialects\/test_tsql.py::TestTSQL::test_qualify_derived_table_outputs","tests\/dialects\/test_tsql.py::TestTSQL::test_types_date","tests\/dialects\/test_tsql.py::TestTSQL::test_procedure_keywords","tests\/dialects\/test_tsql.py::TestTSQL::test_next_value_for","tests\/dialects\/test_tsql.py::TestTSQL::test_tsql","tests\/dialects\/test_tsql.py::TestTSQL::test_datefromparts","tests\/dialects\/test_tsql.py::TestTSQL::test_datepart","tests\/dialects\/test_tsql.py::TestTSQL::test_ddl","tests\/dialects\/test_tsql.py::TestTSQL::test_types_bin","tests\/dialects\/test_tsql.py::TestTSQL::test_insert_cte","tests\/dialects\/test_tsql.py::TestTSQL::test_charindex"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/dialects\/test_tsql.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/sqlglot\/parser.py b\/sqlglot\/parser.py\nindex 7f310b3b58..ae3f6cde66 100644\n--- a\/sqlglot\/parser.py\n+++ b\/sqlglot\/parser.py\n@@ -5902,7 +5902,7 @@ def _parse_foreign_key(self) -> exp.ForeignKey:\n         )\n \n     def _parse_primary_key_part(self) -> t.Optional[exp.Expression]:\n-        return self._parse_field()\n+        return self._parse_ordered() or self._parse_field()\n \n     def _parse_period_for_system_time(self) -> t.Optional[exp.PeriodForSystemTimeConstraint]:\n         if not self._match(TokenType.TIMESTAMP_SNAPSHOT):\n"}
{"repo":"tobymao\/sqlglot","instance_id":"sqlglot-8","base_commit":"06db2350a1c625cc30212912a73267127fc4f3ea","patch":"","test_patch":"diff --git a\/tests\/dialects\/test_postgres.py b\/tests\/dialects\/test_postgres.py\nindex 957eb9d5b9..c732688e55 100644\n--- a\/tests\/dialects\/test_postgres.py\n+++ b\/tests\/dialects\/test_postgres.py\n@@ -372,6 +372,14 @@ def test_postgres(self):\n             pretty=True,\n         )\n \n+        self.validate_all(\n+            \"SELECT CURRENT_TIMESTAMP + INTERVAL '-3 MONTH'\",\n+            read={\n+                \"mysql\": \"SELECT DATE_ADD(CURRENT_TIMESTAMP, INTERVAL -1 QUARTER)\",\n+                \"postgres\": \"SELECT CURRENT_TIMESTAMP + INTERVAL '-3 MONTH'\",\n+                \"tsql\": \"SELECT DATEADD(QUARTER, -1, GETDATE())\",\n+            },\n+        )\n         self.validate_all(\n             \"SELECT ARRAY[]::INT[] AS foo\",\n             write={\n","problem_statement":"[BUG] Conversion from SQL Server's DATEADD(quarter...) to PostgreSQL not working properly\n\n## Type of issue: Bug Report\nConversion from SQL Server's DATEADD(quarter...) to PostgreSQL not working properly\n\n## Description\nWhen trying to convert SQL on read dialect 'tsql' for SQL Server's DATEADD(quarter...) the conversion is not correct and does not fail\n\n## Steps to reproduce\n```python\nimport sqlglot\n\nexample_query = \"SELECT category, SUM(revenue) as total_revenue FROM events WHERE event_date >= DATEADD(quarter, -1, GETDATE()) GROUP BY category;\"\nparsed_postgres = sqlglot.transpile(example_query , read=\"tsql\", write=\"postgres\")\nprint(parsed_postgres)\n```\n\n## Expected behaviour\nThis conversion should show something like:\n```sql\nSELECT category, SUM(revenue) AS total_revenue FROM events WHERE event_date >= CURRENT_TIMESTAMP + INTERVAL '-3 MONTHS' GROUP BY category\n```\n\n## Actual behavior\nRight now it will show:\n```sql\nSELECT category, SUM(revenue) AS total_revenue FROM events WHERE event_date >= CURRENT_TIMESTAMP + INTERVAL '-1 QUARTER' GROUP BY category\n```\n\n## Notes\n1. The current behavior will fail because, as shown in [postgres docs](https:\/\/www.postgresql.org\/docs\/current\/datatype-datetime.html#DATATYPE-INTERVAL-INPUT), QUARTER is not supported. However, the structure of the query is correct. Changing this \"N QUARTER\" to \"3*N months\" should work.\n2. The number before \"QUARTER\" does not matter, that's why it should always be 3 times the number of quarter months.\n\nThanks for this amazing library I just discovered it and it's coming handy! \ud83d\udcaf ","hint_text":null,"created_at":"2025-04-25 21:40:11","closed_at":"2025-04-25 21:40:11","version":"0.3.88","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/dialects\/test_postgres.py::TestPostgres::test_array_length","tests\/dialects\/test_postgres.py::TestPostgres::test_bool_or","tests\/dialects\/test_postgres.py::TestPostgres::test_json_extract","tests\/dialects\/test_postgres.py::TestPostgres::test_xmlelement","tests\/dialects\/test_postgres.py::TestPostgres::test_regexp_binary","tests\/dialects\/test_postgres.py::TestPostgres::test_postgres","tests\/dialects\/test_postgres.py::TestPostgres::test_unnest_json_array","tests\/dialects\/test_postgres.py::TestPostgres::test_analyze","tests\/dialects\/test_postgres.py::TestPostgres::test_recursive_cte","tests\/dialects\/test_postgres.py::TestPostgres::test_variance","tests\/dialects\/test_postgres.py::TestPostgres::test_ddl","tests\/dialects\/test_postgres.py::TestPostgres::test_operator","tests\/dialects\/test_postgres.py::TestPostgres::test_unnest","tests\/dialects\/test_postgres.py::TestPostgres::test_rows_from","tests\/dialects\/test_postgres.py::TestPostgres::test_array_offset","tests\/dialects\/test_postgres.py::TestPostgres::test_string_concat"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/dialects\/test_postgres.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/sqlglot\/dialects\/postgres.py b\/sqlglot\/dialects\/postgres.py\nindex 97589d5fbd..61a6dba438 100644\n--- a\/sqlglot\/dialects\/postgres.py\n+++ b\/sqlglot\/dialects\/postgres.py\n@@ -742,3 +742,12 @@ def isascii_sql(self, expression: exp.IsAscii) -> str:\n         @unsupported_args(\"this\")\n         def currentschema_sql(self, expression: exp.CurrentSchema) -> str:\n             return \"CURRENT_SCHEMA\"\n+\n+        def interval_sql(self, expression: exp.Interval) -> str:\n+            unit = expression.text(\"unit\").lower()\n+\n+            if unit.startswith(\"quarter\") and isinstance(expression.this, exp.Literal):\n+                expression.this.replace(exp.Literal.number(int(expression.this.to_py()) * 3))\n+                expression.args[\"unit\"].replace(exp.var(\"MONTH\"))\n+\n+            return super().interval_sql(expression)\n"}
{"repo":"matthewwithanm\/python-markdownify","instance_id":"python-markdownify-9","base_commit":"e29de4e75314daf9267f30f47fd7a091ef5f1deb","patch":"","test_patch":"diff --git a\/tests\/test_conversions.py b\/tests\/test_conversions.py\nindex 27951ee..6145411 100644\n--- a\/tests\/test_conversions.py\n+++ b\/tests\/test_conversions.py\n@@ -305,6 +305,11 @@ def test_pre():\n     assert md(\"<p>foo<\/p>\\n<pre>bar<\/pre>\\n<\/p>baz<\/p>\", sub_symbol=\"^\") == \"\\n\\nfoo\\n\\n```\\nbar\\n```\\n\\nbaz\"\n \n \n+def test_q():\n+    assert md('foo <q>quote<\/q> bar') == 'foo \"quote\" bar'\n+    assert md('foo <q cite=\"https:\/\/example.com\">quote<\/q> bar') == 'foo \"quote\" bar'\n+\n+\n def test_script():\n     assert md('foo <script>var foo=42;<\/script> bar') == 'foo  bar'\n \n","problem_statement":"Inline Quotation element ignored\n\nHtml that looks like this:\n\n```html\nHere is <q>A Quote<\/q> from someone.\n```\n\nshould be rendered as:\n\n```\nHere is \u201cA Quote\u201c from someone.\n```\n\nhttps:\/\/developer.mozilla.org\/en-US\/docs\/Web\/HTML\/Reference\/Elements\/q\n\nSolution:\n\n```python\ndef convert_q(self, el, text, parent_tags):\n    return '\u201c' + text + '\u201c'\n```","hint_text":null,"created_at":"2025-04-28 10:37:33","closed_at":"2025-04-28 10:37:33","version":"0.3.88","FAIL_TO_PASS":[],"PASS_TO_PASS":["tests\/test_conversions.py::test_kbd","tests\/test_conversions.py::test_hn_atx_headings","tests\/test_conversions.py::test_b","tests\/test_conversions.py::test_code","tests\/test_conversions.py::test_hn_atx_closed_headings","tests\/test_conversions.py::test_a_spaces","tests\/test_conversions.py::test_blockquote_with_nested_paragraph","tests\/test_conversions.py::test_p","tests\/test_conversions.py::test_q","tests\/test_conversions.py::test_spaces","tests\/test_conversions.py::test_em","tests\/test_conversions.py::test_header_with_space","tests\/test_conversions.py::test_div_section_article","tests\/test_conversions.py::test_i","tests\/test_conversions.py::test_pre","tests\/test_conversions.py::test_a","tests\/test_conversions.py::test_blockquote_nested","tests\/test_conversions.py::test_br","tests\/test_conversions.py::test_hn_chained","tests\/test_conversions.py::test_a_shortcut","tests\/test_conversions.py::test_samp","tests\/test_conversions.py::test_sup","tests\/test_conversions.py::test_hn_nested_tag_heading_style","tests\/test_conversions.py::test_head","tests\/test_conversions.py::test_blockquote_with_paragraph","tests\/test_conversions.py::test_b_spaces","tests\/test_conversions.py::test_s","tests\/test_conversions.py::test_hr","tests\/test_conversions.py::test_img","tests\/test_conversions.py::test_sub","tests\/test_conversions.py::test_script","tests\/test_conversions.py::test_h1","tests\/test_conversions.py::test_video","tests\/test_conversions.py::test_strong","tests\/test_conversions.py::test_h2","tests\/test_conversions.py::test_a_no_autolinks","tests\/test_conversions.py::test_dl","tests\/test_conversions.py::test_lang","tests\/test_conversions.py::test_hn","tests\/test_conversions.py::test_strong_em_symbol","tests\/test_conversions.py::test_blockquote","tests\/test_conversions.py::test_figcaption","tests\/test_conversions.py::test_hn_newlines","tests\/test_conversions.py::test_del","tests\/test_conversions.py::test_hn_nested_simple_tag","tests\/test_conversions.py::test_a_with_title","tests\/test_conversions.py::test_lang_callback","tests\/test_conversions.py::test_hn_nested_img","tests\/test_conversions.py::test_a_in_code","tests\/test_conversions.py::test_style"],"environment_setup_commit":null,"command_build":"pip install -e .;\npip install pytest pytest-json-report;","command_test":"pytest --json-report --json-report-file=report_pytest.json","image_name":"python:3.11","meta":null,"command_test_small":"pytest --json-report --json-report-file=report_pytest.json tests\/test_conversions.py","timeout_build":3000,"timeout_test":600,"gold_patch":"diff --git a\/markdownify\/__init__.py b\/markdownify\/__init__.py\nindex 780761c..a43f3a7 100644\n--- a\/markdownify\/__init__.py\n+++ b\/markdownify\/__init__.py\n@@ -650,6 +650,9 @@ def convert_pre(self, el, text, parent_tags):\n \n         return '\\n\\n```%s\\n%s\\n```\\n\\n' % (code_language, text)\n \n+    def convert_q(self, el, text, parent_tags):\n+        return '\"' + text + '\"'\n+\n     def convert_script(self, el, text, parent_tags):\n         return ''\n \n"}