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2025-01-13 16:47:19
2025-06-13 09:27:11
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2025-06-13 09:27:11
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reframe-hpc/reframe
reframe-hpc__reframe-3433
b7d86b1d777bc3bed7a3d71d95130376ab5d2820
diff --git a/reframe/utility/sanity.py b/reframe/utility/sanity.py index a4f57a301..1228586ff 100644 --- a/reframe/utility/sanity.py +++ b/reframe/utility/sanity.py @@ -8,6 +8,7 @@ import contextlib import glob as pyglob import itertools +import math import os import re import sys @@ -576,8 +577,14 @@ def calc_bound(thres): return ref*(1 + thres) - lower = calc_bound(lower_thres) or float('-inf') - upper = calc_bound(upper_thres) or float('inf') + lower = calc_bound(lower_thres) + if lower is None: + lower = -math.inf + + upper = calc_bound(upper_thres) + if upper is None: + upper = math.inf + try: evaluate(assert_bounded(val, lower, upper)) except SanityError:
diff --git a/unittests/test_sanity_functions.py b/unittests/test_sanity_functions.py index 7e6368938..0e9367027 100644 --- a/unittests/test_sanity_functions.py +++ b/unittests/test_sanity_functions.py @@ -473,6 +473,18 @@ def test_assert_reference(): r'\(l=-1\.2, u=-0\.9\)'): sn.evaluate(sn.assert_reference(-0.8, -1, -0.2, 0.1)) + # Check that bounds are correctly calculated in case that lower bound + # reaches zero (see also GH issue #3430) + with pytest.raises(SanityError, + match=r'1 is beyond reference value 0\.1 ' + r'\(l=0\.0, u=0\.1\)'): + assert sn.assert_reference(1, 0.1, -1.0, 0) + + with pytest.raises(SanityError, + match=r'-1 is beyond reference value -0\.1 ' + r'\(l=-0\.1, u=-0\.0\)'): + assert sn.assert_reference(-1, -0.1, 0, 1.0) + # Check invalid thresholds with pytest.raises(SanityError, match=r'invalid high threshold value: -0\.1'):
Performance threshold goes to -inf when it should be zero. In 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): ``` self.reference = { '*': { 'Gflops': (None, None, None, 'Gflops'), 'Exponent': (None, None, None, '10exp'), 'Time': (None, None, None, 'seconds'), 'failed_tests': (.1, -1.0, 0, 'tests'), 'skipped_tests': (.1, -1.0, 0, 'tests') }} ``` I 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. This 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: ``` * Reason: performance error: failed to meet references: skipped_tests=1 tests, expected 0.1 (l=-inf, u=0.1) ``` As 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: ``` invalid low threshold value: -2.0 invalid low threshold value: -2.0 ``` But when I choose 2.0 as an upper bound, that seems to be fine: ``` 'failed_tests': (.1, -1.0, 2.0, 'tests'), 'skipped_tests': (.1, -1.0, 2.0, 'tests') ``` results in the range being interpretted as follows: ``` * Reason: performance error: failed to meet references: skipped_tests=1 tests, expected 0.1 (l=-inf, u=0.30000000000000004) ``` It seems to me that the treatment of lower and upper threshold values should be consistent, and this does not seem consistent. Although when I switch the reference value to a negative, that reverses the issue: ``` 'failed_tests': (-1.0, 0, 2.0, 'tests'), 'skipped_tests': (-1.0, 0, 2.0, 'tests') ``` results in: ``` invalid high threshold value: 2.0 invalid high threshold value: 2.0 ``` and to confirm, I set the lower threshold to -2.0 with a negative reference value to check: ``` 'failed_tests': (-1.0, -2.0, 1.0, 'tests'), 'skipped_tests': (-1.0, -2.0, 1.0, 'tests') ``` results in: ``` PASSED ``` Meaning 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. I am thinking there is something odd that happens when the threshold range crosses zero or has one end that is zero.
@vkarak: Related to #2857.@vkarak: > This 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: Indeed this is a bug. These checks should check against `None`: https://github.com/reframe-hpc/reframe/blob/b7d86b1d777bc3bed7a3d71d95130376ab5d2820/reframe/utility/sanity.py#L579-L580 As for the rest of the behaviour that you describe, this is documented: http://localhost:8000/deferrable_functions_reference.html#reframe.utility.sanity.assert_reference The assumption made is that the extracted quantity is either positive or negative so the bounds should conform to this. That's why for example, you can't have a lower threshold > 1 for positive references, because this would imply a negative value for positive quantity.
2025-03-18T08:54:38Z
2025-03-18T08:54:38Z
0.3.88
[]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json unittests/test_sanity_functions.py", "issue_number": 3430, "merge_commit": "20fed5da1569a4962bed12510a89f53083aea3ef", "merged_at": "", "pr_number": 3433, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/reframe-hpc/reframe/pull/3433.diff", "issue": "https://github.com/reframe-hpc/reframe/issues/3430", "pr": "https://github.com/reframe-hpc/reframe/pull/3433" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json unittests/test_sanity_functions.py
tobymao/sqlglot
tobymao__sqlglot-4837
08eb7f2032957c2fe3119963f344538b90d8f631
diff --git a/sqlglot/parser.py b/sqlglot/parser.py index 24bf1492f7..f5ed3a8923 100644 --- a/sqlglot/parser.py +++ b/sqlglot/parser.py @@ -1291,6 +1291,10 @@ class Parser(metaclass=_Parser): "SIMPLE", ), "INITIALLY": ("DEFERRED", "IMMEDIATE"), + "USING": ( + "BTREE", + "HASH", + ), **dict.fromkeys(("DEFERRABLE", "NORELY"), tuple()), }
diff --git a/tests/dialects/test_mysql.py b/tests/dialects/test_mysql.py index 06638f16c5..4a28176ccf 100644 --- a/tests/dialects/test_mysql.py +++ b/tests/dialects/test_mysql.py @@ -83,6 +83,12 @@ def test_ddl(self): self.validate_identity( "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", ) + self.validate_identity( + "CREATE TABLE test_table (id INT AUTO_INCREMENT, PRIMARY KEY (id) USING BTREE)" + ) + self.validate_identity( + "CREATE TABLE test_table (id INT AUTO_INCREMENT, PRIMARY KEY (id) USING HASH)" + ) self.validate_identity( "/*left*/ EXPLAIN SELECT /*hint*/ col FROM t1 /*right*/", "/* left */ DESCRIBE /* hint */ SELECT col FROM t1 /* right */",
MySQL dialect fails to parse PRIMARY KEY USING BTREE syntax **Before you file an issue** - Make sure you specify the "read" dialect eg. `parse_one(sql, read="spark")` - Make sure you specify the "write" dialect eg. `ast.sql(dialect="duckdb")` - Check if the issue still exists on main yes, the issue still exists. I'v tried the latest version. **Fully reproducible code snippet** Please include a fully reproducible code snippet or the input sql, dialect, and expected output. mysql: `CREATE TABLE test_table ( id INT AUTO_INCREMENT, alarm_category VARCHAR ( 255 ), alarm_rule VARCHAR ( 255 ), PRIMARY KEY(id) USING BTREE )` **Official Documentation** Please include links to official SQL documentation related to your issue. https://sqlglot.com/sqlglot.html#parse_one
@Gohoy: ```python sql = "CREATE TABLE test_table ( id INT AUTO_INCREMENT, alarm_category VARCHAR ( 255 ), alarm_rule VARCHAR ( 255 ), PRIMARY KEY(id) USING BTREE )" sqlglot.parse_one(sql,read='mysql') # result # sqlglot.errors.ParseError: Expecting ). Line 1, Col: 130. # id INT AUTO_INCREMENT, alarm_category VARCHAR ( 255 ), alarm_rule VARCHAR ( 255 ), PRIMARY KEY(id) USING BTREE ) ``` this is the reproducible python code
2025-03-05T15:49:35Z
2025-03-05T15:49:35Z
0.3.88
[]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_mysql.py", "issue_number": 4833, "merge_commit": "adf2fef27dc341508c3b9c710da0f835277094a1", "merged_at": "", "pr_number": 4837, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/tobymao/sqlglot/pull/4837.diff", "issue": "https://github.com/tobymao/sqlglot/issues/4833", "pr": "https://github.com/tobymao/sqlglot/pull/4837" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_mysql.py
matchms/matchms
matchms__matchms-809
0b1707bd866f56404e4056df678af12a4bc20141
diff --git a/matchms/importing/load_from_msp.py b/matchms/importing/load_from_msp.py index cf7726a4..47dbedcc 100644 --- a/matchms/importing/load_from_msp.py +++ b/matchms/importing/load_from_msp.py @@ -109,7 +109,7 @@ def _parse_line_with_peaks(rline: str) -> Tuple[List[float], List[float], str]: def get_peak_values(peak: str) -> Tuple[List[float], List[float]]: """Get the m/z and intensity value from the line containing the peak information.""" - tokens = re.findall(r"(\d+(?:\.\d+)?(?:e[-+]?\d+)?)", peak) + tokens = re.findall(r"(\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)", peak) if len(tokens) % 2 != 0: raise RuntimeError("Wrong peak format detected!")
diff --git a/tests/importing/test_load_from_msp.py b/tests/importing/test_load_from_msp.py index 891ac002..839b604c 100644 --- a/tests/importing/test_load_from_msp.py +++ b/tests/importing/test_load_from_msp.py @@ -2,7 +2,7 @@ import os import numpy as np import pytest from matchms import Spectrum -from matchms.importing.load_from_msp import load_from_msp, parse_metadata +from matchms.importing.load_from_msp import get_peak_values, load_from_msp, parse_metadata from tests.builder_Spectrum import SpectrumBuilder @@ -285,3 +285,13 @@ def test_parse_metadata(input_line, expected_output): params = {} parse_metadata(input_line, params) assert params == expected_output + + +@pytest.mark.parametrize("line, expected", [ + ["496 7.1E-05", ([496.0], [7.1E-05])], + ["496 7.1e-05", ([496.0], [7.1e-05])], + ["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])], +]) +def test_get_peak_values(line, expected): + actual = get_peak_values(line) + assert actual == expected \ No newline at end of file
matchms fails when reading spectra where abundance is in scientific notation Example spectrum - spotted in the MSDial EI RI library. Funny thing is our regex only handles lower case `e` notation while this uses upper case. Makes me think if we shouldn't just leave the parsing of stuff to python and try to just identify the tokens based on separator? ``` tokens = re.findall(r"(\d+(?:\.\d+)?(?:e[-+]?\d+)?)", peak)``` ``` NAME: C10 FAME EXACTMASS: 186.16198 FORMULA: C11H22O2 ONTOLOGY: Fatty acid methyl esters INCHIKEY: YRHYCMZPEVDGFQ-UHFFFAOYSA-N SMILES: CCCCCCCCCC(=O)OC RETENTIONINDEX: 1325 IONMODE: Positive INSTRUMENTTYPE: GC-EI-TOF COMMENT: DB#=FiehnLibVolatile0005; origin=Volatile Fiehn Library for Metabolic Profiling Num Peaks: 169 30 0.629467 31 1.545269 33 0.272632 36 0.02421 37 0.313882 38 0.539016 39 17.716311 40 1.915948 41 35.4716 42 9.51272 43 36.860957 44 0.788644 45 2.384747 46 0.104509 47 0.031949 48 0.035996 49 0.052609 50 0.529644 51 0.838982 52 0.365568 53 2.854753 54 1.750452 55 29.439195 56 4.268605 57 8.867918 58 0.591554 59 19.854767 60 0.49308 61 0.379342 62 0.260846 63 0.557191 64 0.08541 65 0.63394 66 0.192617 67 2.198946 68 1.443245 69 7.300356 70 1.714883 71 2.948257 72 0.322756 73 1.743069 74 100 75 9.275516 76 0.745407 77 0.361379 78 0.038481 79 0.615978 80 0.123323 81 1.452119 82 0.612854 83 3.739813 84 2.643535 85 1.788933 86 0.278383 87 44.905938 88 3.900623 89 0.580976 90 0.037416 91 0.023074 92 0.025701 93 0.21129 94 0.043806 95 0.774303 96 0.156408 97 2.040479 98 1.468662 99 0.256302 100 0.217679 101 5.157853 102 0.416331 103 0.024423 107 0.071992 108 0.018459 109 0.002485 110 0.228329 111 0.387719 112 0.390062 113 0.245724 114 0.05765 115 2.589718 116 0.396239 120 0.001136 121 0.032375 122 0.007242 123 0.027831 124 0.013561 125 0.150728 126 0.114094 127 0.07966 129 2.578359 130 0.256231 132 0.005254 135 0.102876 136 0.03486 137 0.071424 138 0.021157 139 0.314024 140 0.065886 141 2.280949 142 2.305443 143 7.497659 144 0.656233 145 0.026056 148 0.005112 152 0.034576 153 0.069223 154 0.035073 155 2.668384 156 0.291446 157 1.242179 158 0.131985 161 0.008875 163 0.018956 167 0.000213 169 0.00923 170 0.000142 171 0.011928 172 0.001704 174 0.002556 175 0.000781 182 0.003053 184 0.000284 185 0.008023 186 0.458362 187 0.050195 188 0.004189 191 0.000142 192 0.000781 195 0.000426 203 0.000284 209 0.00355 212 0.000284 214 0.000497 219 0.000213 231 0.000142 233 0.000142 234 0.000781 246 7.1E-05 249 0.00284 250 0.00142 251 0.000355 257 0.000639 263 0.000639 266 0.000213 270 0.000142 283 0.000284 295 0.000568 297 0.000355 314 0.000213 315 0.000142 321 0.000426 327 0.001207 329 0.000994 342 0.001633 348 0.000355 380 0.000142 390 0.000497 398 0.000213 401 0.006674 402 0.001775 403 0.000923 427 0.00071 455 0.000213 468 0.000355 474 0.00071 495 0.000213 496 7.1E-05 497 0.000355 500 0.000497 ```
2025-06-13T09:27:11Z
2025-06-13T09:27:11Z
0.4.3
[]
[ "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]" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/importing/test_load_from_msp.py", "issue_number": 802, "merge_commit": "f54285408f4f6e702545871c126161120106e076", "merged_at": "", "pr_number": 809, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/matchms/matchms/pull/809.diff", "issue": "https://github.com/matchms/matchms/issues/802", "pr": "https://github.com/matchms/matchms/pull/809" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/importing/test_load_from_msp.py
DataDog/guarddog
DataDog__guarddog-523
4d8b7972885ce111991af01610b24b326dcc1de8
diff --git a/guarddog/analyzer/metadata/bundled_binary.py b/guarddog/analyzer/metadata/bundled_binary.py index 5b6e875..81ed040 100644 --- a/guarddog/analyzer/metadata/bundled_binary.py +++ b/guarddog/analyzer/metadata/bundled_binary.py @@ -14,7 +14,12 @@ class BundledBinary(Detector): # magic bytes are the first few bytes of a file that can be used to identify the file type # regardless of their extension - magic_bytes = {"exe": b"\x4D\x5A", "elf": b"\x7F\x45\x4C\x46"} + magic_bytes = { + "exe": b"\x4D\x5A", + "elf": b"\x7F\x45\x4C\x46", + "macho32": b"\xFE\xED\xFA\xCE", + "macho64": b"\xFE\xED\xFA\xCF", + } def __init__(self): super().__init__(
diff --git a/tests/analyzer/metadata/test_bundled_binary.py b/tests/analyzer/metadata/test_bundled_binary.py index 07f1845..7a01283 100644 --- a/tests/analyzer/metadata/test_bundled_binary.py +++ b/tests/analyzer/metadata/test_bundled_binary.py @@ -19,6 +19,8 @@ class TestBundleBinary: binary_sample_elf = ( b"\x7F\x45\x4C\x46" + b"0x90" * 10 ) # elf magic number plus nop sled + binary_sample_macho32 = b"\xFE\xED\xFA\xCE" + b"0x90" * 10 + binary_sample_macho64 = b"\xFE\xED\xFA\xCF" + b"0x90" * 10 @pytest.mark.parametrize( "detector", @@ -52,6 +54,38 @@ class TestBundleBinary: matches, _ = detector.detect({}, dir) assert matches + @pytest.mark.parametrize( + "detector", + [ + (pypi_detector), + (npm_detector), + ], + ) + def test_macho32(self, detector: BundledBinary): + with tempfile.TemporaryDirectory() as dir: + full_path = os.path.join(dir, "package") + os.mkdir(full_path) + with open(os.path.join(full_path, "linux.txt"), "wb") as f: + f.write(self.binary_sample_macho32) + matches, _ = detector.detect({}, dir) + assert matches + + @pytest.mark.parametrize( + "detector", + [ + (pypi_detector), + (npm_detector), + ], + ) + def test_macho64(self, detector: BundledBinary): + with tempfile.TemporaryDirectory() as dir: + full_path = os.path.join(dir, "package") + os.mkdir(full_path) + with open(os.path.join(full_path, "linux.txt"), "wb") as f: + f.write(self.binary_sample_macho64) + matches, _ = detector.detect({}, dir) + assert matches + @pytest.mark.parametrize( "detector", [
Add Mach-O magic bytes to the bundled binary detector The [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. For reference: ![Image](https://github.com/user-attachments/assets/7369b953-b3ea-4d0f-a536-70d84d2056ab) See https://en.wikipedia.org/wiki/Mach-O#Mach-O_header for more info.
@ocku: Let me know if I can work on this :)@sobregosodd: Hello @ocku , the case you point out seems valid as well Please, send the PR well look into it. Thanks again!@ocku: ^ Created. Sorry for the delay! I had some issues with GitHub.
2025-01-22T12:07:10Z
2025-01-22T12:07:10Z
0.4.3
[]
[ "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]" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/analyzer/metadata/test_bundled_binary.py", "issue_number": 498, "merge_commit": "4ddb8c8b437c070dc86f17824b7690b5cd4385fe", "merged_at": "", "pr_number": 523, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/DataDog/guarddog/pull/523.diff", "issue": "https://github.com/DataDog/guarddog/issues/498", "pr": "https://github.com/DataDog/guarddog/pull/523" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/analyzer/metadata/test_bundled_binary.py
mitmproxy/pdoc
mitmproxy__pdoc-806
ea2b69a4162226b07f68cd25d92d4d92dbbafaf8
diff --git a/CHANGELOG.md b/CHANGELOG.md index 747d22f..3337d33 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ## Unreleased: pdoc next +- Include included HTML headers in the ToC by default by enabling markdown2's `mixed=True` option of the `header-ids` extra + (#806, @mrossinek) ## 2025-04-21: pdoc 15.0.3 diff --git a/pdoc/render_helpers.py b/pdoc/render_helpers.py index 5c1f339..c96194b 100644 --- a/pdoc/render_helpers.py +++ b/pdoc/render_helpers.py @@ -61,7 +61,7 @@ markdown_extensions = { "cuddled-lists": None, "fenced-code-blocks": {"cssclass": formatter.cssclass}, "footnotes": None, - "header-ids": None, + "header-ids": {"mixed": True, "prefix": None, "reset-count": True}, "link-patterns": None, "markdown-in-html": None, "mermaid": None,
diff --git a/test/test_render_helpers.py b/test/test_render_helpers.py index c17740f..4279725 100644 --- a/test/test_render_helpers.py +++ b/test/test_render_helpers.py @@ -110,6 +110,22 @@ def test_markdown_toc(): assert to_html("#foo\n#bar").toc_html # type: ignore +def test_mixed_toc(): + """ + markdown2 can handle mixed markdown and HTML headings. + + Let's test that this works as expected. + """ + expected = [ + "<ul>", + ' <li><a href="#foo">foo</a></li>', + ' <li><a href="#bar">bar</a></li>', + "</ul>", + "", + ] + assert to_html("#foo\n<h1>bar</h1>").toc_html == "\n".join(expected) + + @pytest.mark.parametrize( "md,html", [
Include HTML headers in ToC #### Problem Description When 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. #### Proposal markdown2 already supports this feature: https://github.com/trentm/python-markdown2/pull/538. All one would need to do, is set `header-ids["mixed"] = True` for the header-ids extra, which pdoc already uses. #### Additional Context Essentially, 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.
@mhils: Sure, please send a PR!@mrossinek: > Sure, please send a PR! Happy to do so! How should I approach this? 1. Should I simply enable mixed header-ids by default? E.g. through `"header-ids": {"mixed": True}` here: https://github.com/mitmproxy/pdoc/blob/ea2b69a4162226b07f68cd25d92d4d92dbbafaf8/pdoc/render_helpers.py#L64 2. Or should I add a new command-line argument, e.g. `--mixed-header-ids` which indicates this boolean value? One could leave its default to be `False`, therefore not changing the current behavior.@mhils: Definitely 1), we want to keep the CLI surface as small as possible.
2025-05-04T12:43:09Z
2025-05-04T12:43:09Z
0.4.3
[]
[ "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]" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json test/test_render_helpers.py", "issue_number": 805, "merge_commit": "2ab4df12693678439a9063f0e3909c26545241a9", "merged_at": "", "pr_number": 806, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/mitmproxy/pdoc/pull/806.diff", "issue": "https://github.com/mitmproxy/pdoc/issues/805", "pr": "https://github.com/mitmproxy/pdoc/pull/806" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json test/test_render_helpers.py
tobymao/sqlglot
tobymao__sqlglot-4618
cfa25bb59b4537427aebe93f92c7176e045e7b0c
diff --git a/sqlglot/parser.py b/sqlglot/parser.py index 7f310b3b58..ae3f6cde66 100644 --- a/sqlglot/parser.py +++ b/sqlglot/parser.py @@ -5902,7 +5902,7 @@ def _parse_foreign_key(self) -> exp.ForeignKey: ) def _parse_primary_key_part(self) -> t.Optional[exp.Expression]: - return self._parse_field() + return self._parse_ordered() or self._parse_field() def _parse_period_for_system_time(self) -> t.Optional[exp.PeriodForSystemTimeConstraint]: if not self._match(TokenType.TIMESTAMP_SNAPSHOT):
diff --git a/tests/dialects/test_tsql.py b/tests/dialects/test_tsql.py index 738120a2ee..fe1aa9c5dd 100644 --- a/tests/dialects/test_tsql.py +++ b/tests/dialects/test_tsql.py @@ -436,6 +436,13 @@ def test_tsql(self): "'a' + 'b'", ) + self.validate_identity( + "CREATE TABLE db.t1 (a INTEGER, b VARCHAR(50), CONSTRAINT c PRIMARY KEY (a DESC))", + ) + self.validate_identity( + "CREATE TABLE db.t1 (a INTEGER, b INTEGER, CONSTRAINT c PRIMARY KEY (a DESC, b))" + ) + def test_option(self): possible_options = [ "HASH GROUP",
TSQL: PRIMARY KEY constraint fails to parse if sort option is given The following CREATE TABLE statement parses just fine: ``` import sqlglot test = """CREATE TABLE dbo.test ( id INT, name VARCHAR(50), CONSTRAINT pk_testTable PRIMARY KEY (id) ) ;""" parsed_script = sqlglot.parse(test, read="tsql") ``` However, when I add ASC or DESC to the PRIMARY KEY constraint, it fails to parse: ``` import sqlglot test = """CREATE TABLE dbo.test ( id INT, name VARCHAR(50), CONSTRAINT pk_testTable PRIMARY KEY (id DESC) ) ;""" parsed_script = sqlglot.parse(test, read="tsql") ``` Error Message: ``` Exception has occurred: ParseError Expecting ). Line 4, Col: 45. bo.test ( id INT, name VARCHAR(50), CONSTRAINT pk_testTable PRIMARY KEY (id DESC) ) ; File "C:\*snip*\main.py", line 96, in main parsed_script = sqlglot.parse(test, read="tsql") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\*snip*\main.py", line 116, in <module> main() sqlglot.errors.ParseError: Expecting ). Line 4, Col: 45. bo.test ( id INT, name VARCHAR(50), CONSTRAINT pk_testTable PRIMARY KEY (id DESC) ) ; ``` Official Documentation: https://learn.microsoft.com/en-us/sql/t-sql/statements/create-table-transact-sql?view=sql-server-ver16#constraint Edit: sqlglot version is 25.21.3.
@cchambers-rdi: Added version to OP.
2025-01-15T15:34:32Z
2025-01-15T15:34:32Z
0.3.88
[]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_tsql.py", "issue_number": 4610, "merge_commit": "14474ee689025cc67b1f9a07e51d2f414ec5ab49", "merged_at": "", "pr_number": 4618, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/tobymao/sqlglot/pull/4618.diff", "issue": "https://github.com/tobymao/sqlglot/issues/4610", "pr": "https://github.com/tobymao/sqlglot/pull/4618" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_tsql.py
MolSSI/QCElemental
MolSSI__QCElemental-350
cddc5313ad7a251501b633f119c2cb566885bcc1
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index aa949f3..8aca4c9 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -17,7 +17,8 @@ jobs: matrix: python-version: ["3.7", "3.9", "3.11", "3.12"] pydantic-version: ["1", "2"] - runs-on: [ubuntu-latest, windows-latest] + # runs-on: [ubuntu-latest, windows-latest] + runs-on: [ubuntu-22.04, windows-latest] # until drop py37 exclude: - runs-on: windows-latest pydantic-version: "1" diff --git a/.github/workflows/Lint.yml b/.github/workflows/Lint.yml index c337352..c52ea9a 100644 --- a/.github/workflows/Lint.yml +++ b/.github/workflows/Lint.yml @@ -14,7 +14,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" - name: Install black run: pip install "black>=22.1.0,<23.0a0" - name: Print code formatting with black (hints here if next step errors) @@ -29,7 +29,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" - name: Install poetry run: pip install poetry - name: Install repo diff --git a/docs/changelog.rst b/docs/changelog.rst index 76edbc6..0cd1e4f 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -19,18 +19,19 @@ Changelog .. Misc. .. +++++ -- (:pr:`340`, :issue:`330`) Add molecular charge and multiplicity to Molecule repr formula, - so neutral singlet unchanged but radical cation has '2^formula+'. - 0.29.0 / 2024-MM-DD (Unreleased) -------------------------------- Breaking Changes ++++++++++++++++ +- (:pr:`341`) `packaging` is now a required dependency. New Features ++++++++++++ +- (:pr:`350`, :pr:`318`, :issue:`317`) Make behavior consistent between molecular_charge/ + fragment_charges and molecular_multiplicity/fragment_multiplicities by allowing floating point + numbers for multiplicities. @awvwgk - (:pr:`360`) ``Molecule`` learned new functions ``element_composition`` and ``molecular_weight``. The first gives a dictionary of element symbols and counts, while the second gives the weight in amu. Both can access the whole molecule or per-fragment like the existing ``nelectrons`` and @@ -38,13 +39,30 @@ New Features Enhancements ++++++++++++ +- (:pr:`340`, :issue:`330`) Add molecular charge and multiplicity to Molecule repr formula, + so neutral singlet unchanged but radical cation has '2^formula+'. @awvwgk +- (:pr:`341`) Use `packaging` instead of deprecated `setuptools` to provide version parsing for + `qcelemental.util.parse_version` and `qcelemental.util.safe_version`. This behaves slightly + different; "v7.0.0+N/A" was processed ok before but fails with newer version. @berquist +- (:pr:`343`) Molecular and fragment multiplicities are now always enforced to be >=1.0. Previously + this wasn't checked for `Molecule(..., validate=False)`. Error messages will change sometimes + change for `validate=True` (run by default). +- (:pr:`343`) `qcelemental.molparse` newly allows floats that are ints (e.g., 1.0) for multiplicity. + Previously it would raise an error about not being an int. +- (:pr:`337`) Solidify the (unchanged) schema_name for `QCInputSpecification` and `AtomicResult` + into Literals where previously they had been regex strings coerced into a single name. The literals + allow pydantic to discriminate models, which benefits GeneralizedOptimizationInput/Result in + QCManyBody/QCEngine/OptKing. The only way this can interfere is if schema producers have whitespace + around `schema_name` for these models or if any `AtomicResult`s are still using "qc_schema_output", + which looks to have only been added for compatibility with pre-pydantic QCSchema. Bug Fixes +++++++++ Misc. +++++ -- (:pr:`342`) Update some docs settings and requirements for newer tools. +- (:pr:`344`, :issue:`282`) Add a citation file since QCElemental doesn't have a paper. @lilyminium +- (:pr:`342`, :issue:`333`) Update some docs settings and requirements for newer tools. - (: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. the try_harder_safe_version might be even bettter diff --git a/qcelemental/models/molecule.py b/qcelemental/models/molecule.py index 63070d5..215db12 100644 --- a/qcelemental/models/molecule.py +++ b/qcelemental/models/molecule.py @@ -185,7 +185,7 @@ class Molecule(ProtoModel): description="Additional comments for this molecule. Intended for pure human/user consumption and clarity.", ) molecular_charge: float = Field(0.0, description="The net electrostatic charge of the molecule.") # type: ignore - molecular_multiplicity: int = Field(1, description="The total multiplicity of the molecule.") # type: ignore + molecular_multiplicity: float = Field(1, description="The total multiplicity of the molecule.") # type: ignore # Atom data masses_: Optional[Array[float]] = Field( # type: ignore @@ -257,7 +257,7 @@ class Molecule(ProtoModel): "if not provided (and :attr:`~qcelemental.models.Molecule.fragments` are specified).", shape=["nfr"], ) - fragment_multiplicities_: Optional[List[int]] = Field( # type: ignore + fragment_multiplicities_: Optional[List[float]] = Field( # type: ignore None, description="The multiplicity of each fragment in the :attr:`~qcelemental.models.Molecule.fragments` list. The index of this " "list matches the 0-index indices of :attr:`~qcelemental.models.Molecule.fragments` list. Will be filled in based on a set of " @@ -421,12 +421,16 @@ class Molecule(ProtoModel): n = len(values["fragments_"]) if len(v) != n: raise ValueError("Fragment Multiplicities must be same number of entries as Fragments") + v = [(int(m) if m.is_integer() else m) for m in v] if any([m < 1.0 for m in v]): raise ValueError(f"Fragment Multiplicity must be positive: {v}") return v @validator("molecular_multiplicity") def _int_if_possible(cls, v, values, **kwargs): + if v.is_integer(): + # preserve existing hashes + v = int(v) if v < 1.0: raise ValueError("Molecular Multiplicity must be positive") return v @@ -502,7 +506,7 @@ class Molecule(ProtoModel): return fragment_charges @property - def fragment_multiplicities(self) -> List[int]: + def fragment_multiplicities(self) -> List[float]: fragment_multiplicities = self.__dict__.get("fragment_multiplicities_") if fragment_multiplicities is None: fragment_multiplicities = [self.molecular_multiplicity] @@ -803,9 +807,7 @@ class Molecule(ProtoModel): data = getattr(self, field) if field == "geometry": data = float_prep(data, GEOMETRY_NOISE) - elif field == "fragment_charges": - data = float_prep(data, CHARGE_NOISE) - elif field == "molecular_charge": + elif field in ["fragment_charges", "molecular_charge", "fragment_multiplicities", "molecular_multiplicity"]: data = float_prep(data, CHARGE_NOISE) elif field == "masses": data = float_prep(data, MASS_NOISE) diff --git a/qcelemental/molparse/chgmult.py b/qcelemental/molparse/chgmult.py index a311d08..493335c 100644 --- a/qcelemental/molparse/chgmult.py +++ b/qcelemental/molparse/chgmult.py @@ -19,7 +19,7 @@ def _high_spin_sum(mult_list): def _mult_ok(m): - return isinstance(m, (int, np.integer)) and m >= 1 + return isinstance(m, (int, np.integer, float, np.float64)) and m >= 1 def _sufficient_electrons_for_mult(z, c, m): @@ -430,7 +430,16 @@ def validate_and_fill_chgmult( if molecular_multiplicity is None: # unneeded, but shortens the exact lists frag_mult_hi = _high_spin_sum(_apply_default(fragment_multiplicities, 2)) frag_mult_lo = _high_spin_sum(_apply_default(fragment_multiplicities, 1)) - for m in range(frag_mult_lo, frag_mult_hi + 1): + try: + mult_range = range(frag_mult_lo, frag_mult_hi + 1) + except TypeError: + if frag_mult_lo == frag_mult_hi: + mult_range = [frag_mult_hi] + else: + raise ValidationError( + f"Cannot process: please fully specify float multiplicity: m: {molecular_multiplicity} fm: {fragment_multiplicities}" + ) + for m in mult_range: cgmp_exact_m.append(m) # * (S6) suggest range of missing mult = tot - high_spin_sum(frag - 1), @@ -450,7 +459,16 @@ def validate_and_fill_chgmult( for ifr in range(nfr): if fragment_multiplicities[ifr] is None: # unneeded, but shortens the exact lists - for m in reversed(range(max(missing_mult_lo, 1), missing_mult_hi + 1)): + try: + mult_range = reversed(range(max(missing_mult_lo, 1), missing_mult_hi + 1)) + except TypeError: + if missing_mult_lo == missing_mult_hi: + mult_range = [missing_mult_hi] + else: + raise ValidationError( + f"Cannot process: please fully specify float multiplicity: m: {molecular_multiplicity} fm: {fragment_multiplicities}" + ) + for m in mult_range: cgmp_exact_fm[ifr].append(m) cgmp_exact_fm[ifr].append(1) cgmp_exact_fm[ifr].append(2)
diff --git a/qcelemental/tests/test_molecule.py b/qcelemental/tests/test_molecule.py index 46d7ced..b2154c0 100644 --- a/qcelemental/tests/test_molecule.py +++ b/qcelemental/tests/test_molecule.py @@ -2,6 +2,7 @@ Tests the imports and exports of the Molecule object. """ + import numpy as np import pytest @@ -798,6 +799,15 @@ _ref_mol_multiplicity_hash = { "triplet": "7caca87a", "disinglet": "83a85546", "ditriplet": "71d6ba82", + # float mult + "singlet_point1": "4e9e2587", + "singlet_epsilon": "ad3f5fab", + "triplet_point1": "ad35cc28", + "triplet_point1_minus": "b63d6983", + "triplet_point00001": "7107b7ac", + "disinglet_epsilon": "fb0aaaca", + "ditriplet_point1": "33d47d5f", + "ditriplet_point00001": "7f0ac640", } @@ -806,14 +816,26 @@ _ref_mol_multiplicity_hash = { [ pytest.param(3, 3, False, "triplet"), pytest.param(3, 3, True, "triplet"), - # 3.1 -> 3 (validate=False) below documents the present bad behavior where a float mult - # simply gets cast to int with no error. This will change soon. The validate=True throws a - # nonspecific error that at least mentions type. - pytest.param(3.1, 3, False, "triplet"), + # before float multiplicity was allowed, 3.1 (below) was coerced into 3 with validate=False, + # and validate=True threw a type-mentioning error. Now, 2.9 is allowed for both validate=T/F + pytest.param(3.1, 3.1, False, "triplet_point1"), + # validate=True counterpart fails b/c insufficient electrons in He for more than triplet + pytest.param(2.9, 2.9, False, "triplet_point1_minus"), + pytest.param(2.9, 2.9, True, "triplet_point1_minus"), + pytest.param(3.00001, 3.00001, False, "triplet_point00001"), + # validate=True counterpart fails like 3.1 above + pytest.param(2.99999, 2.99999, False, "triplet_point00001"), # hash agrees w/3.00001 above b/c <CHARGE_NOISE + pytest.param(2.99999, 2.99999, True, "triplet_point00001"), pytest.param(3.0, 3, False, "triplet"), pytest.param(3.0, 3, True, "triplet"), pytest.param(1, 1, False, "singlet"), pytest.param(1, 1, True, "singlet"), + pytest.param(1.000000000000000000002, 1, False, "singlet"), + pytest.param(1.000000000000000000002, 1, True, "singlet"), + pytest.param(1.000000000000002, 1.000000000000002, False, "singlet_epsilon"), + pytest.param(1.000000000000002, 1.000000000000002, True, "singlet_epsilon"), + pytest.param(1.1, 1.1, False, "singlet_point1"), + pytest.param(1.1, 1.1, True, "singlet_point1"), pytest.param(None, 1, False, "singlet"), pytest.param(None, 1, True, "singlet"), # fmt: off @@ -841,6 +863,9 @@ def test_mol_multiplicity_types(mult_in, mult_store, validate, exp_hash): [ pytest.param(-3, False, "Multiplicity must be positive"), pytest.param(-3, True, "Multiplicity must be positive"), + pytest.param(0.9, False, "Multiplicity must be positive"), + pytest.param(0.9, True, "Multiplicity must be positive"), + pytest.param(3.1, True, "Inconsistent or unspecified chg/mult"), # insufficient electrons in He ], ) def test_mol_multiplicity_types_errors(mult_in, validate, error): @@ -859,10 +884,11 @@ def test_mol_multiplicity_types_errors(mult_in, validate, error): [ pytest.param(5, [3, 3], [3, 3], False, "ditriplet"), pytest.param(5, [3, 3], [3, 3], True, "ditriplet"), - # 3.1 -> 3 (validate=False) below documents the present bad behavior where a float mult - # simply gets cast to int with no error. This will change soon. The validate=True throws a - # irreconcilable error. - pytest.param(5, [3.1, 3.4], [3, 3], False, "ditriplet"), + # before float multiplicity was allowed, [3.1, 3.4] (below) were coerced into [3, 3] with validate=False. + # Now, [2.9, 2.9] is allowed for both validate=T/F. + pytest.param(5, [3.1, 3.4], [3.1, 3.4], False, "ditriplet_point1"), + pytest.param(5, [2.99999, 3.00001], [2.99999, 3.00001], False, "ditriplet_point00001"), + pytest.param(5, [2.99999, 3.00001], [2.99999, 3.00001], True, "ditriplet_point00001"), # fmt: off pytest.param(5, [3.0, 3.], [3, 3], False, "ditriplet"), pytest.param(5, [3.0, 3.], [3, 3], True, "ditriplet"), @@ -871,6 +897,18 @@ def test_mol_multiplicity_types_errors(mult_in, validate, error): pytest.param(1, [1, 1], [1, 1], True, "disinglet"), # None in frag_mult not allowed for validate=False pytest.param(1, [None, None], [1, 1], True, "disinglet"), + pytest.param(1, [1.000000000000000000002, 0.999999999999999999998], [1, 1], False, "disinglet"), + pytest.param(1, [1.000000000000000000002, 0.999999999999999999998], [1, 1], True, "disinglet"), + pytest.param( + 1, + [1.000000000000002, 1.000000000000004], + [1.000000000000002, 1.000000000000004], + False, + "disinglet_epsilon", + ), + pytest.param( + 1, [1.000000000000002, 1.000000000000004], [1.000000000000002, 1.000000000000004], True, "disinglet_epsilon" + ), ], ) def test_frag_multiplicity_types(mol_mult_in, mult_in, mult_store, validate, exp_hash): @@ -902,6 +940,9 @@ def test_frag_multiplicity_types(mol_mult_in, mult_in, mult_store, validate, exp [ pytest.param([-3, 1], False, "Multiplicity must be positive"), pytest.param([-3, 1], True, "Multiplicity must be positive"), + pytest.param( + [3.1, 3.4], True, "Inconsistent or unspecified chg/mult" + ), # insufficient e- for triplet+ on He in frag 1 ], ) def test_frag_multiplicity_types_errors(mult_in, validate, error): diff --git a/qcelemental/tests/test_molparse_validate_and_fill_chgmult.py b/qcelemental/tests/test_molparse_validate_and_fill_chgmult.py index 0c18649..0f85bb0 100644 --- a/qcelemental/tests/test_molparse_validate_and_fill_chgmult.py +++ b/qcelemental/tests/test_molparse_validate_and_fill_chgmult.py @@ -94,6 +94,12 @@ working_chgmults = [ (-2.4, [-2.4, 0, 0], 3, [1, 2, 2]), "a83a3356", ), # 166 + (("He", None, [None], 2.8, [None]), (0, [0], 2.8, [2.8]), "3e10e7b5"), # 180 + (("He", None, [None], None, [2.8]), (0, [0], 2.8, [2.8]), "3e10e7b5"), # 181 + (("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", 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", None, [None, None, None], None, [2, 2, 2.2]), (0, [0, 0, 0], 4.2, [2, 2, 2.2]), "ed6d1f35"), # 186 + (("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 ] @@ -153,6 +159,8 @@ def test_validate_and_fill_chgmult_mol_model(systemtranslator, inp, expected, ex ("Gh", None, [None], 3, [None]), # 60 ("Gh/He", None, [2, None], None, [None, None]), # 62 ("Gh/Ne", 2, [-2, None], None, [None, None]), # 65b + ("He", None, [None], 3.2, [None]), # 182 + ("N/N/N", None, [None, None, None], 2.2, [None, None, 2.2]), # 184 ], ) def test_validate_and_fill_chgmult_irreconcilable(systemtranslator, inp): @@ -173,6 +181,8 @@ def test_validate_and_fill_chgmult_irreconcilable(systemtranslator, inp): # 35 - insufficient electrons # 55 - both (1, (1, 0.0, 0.0), 4, (1, 3, 2)) and (1, (0.0, 0.0, 1), 4, (2, 3, 1)) plausible # 65 - non-0/1 on Gh fragment errors normally but reset by zero_ghost_fragments +# 182 - insufficient electrons on He +# 184 - decline to guess fragment multiplicities when floats involved @pytest.fixture
Floating point number allowed for molecular charge but not molecular multiplicity **Describe the bug** <!-- A clear and concise description of what the bug is. --> QCElemental 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. **To Reproduce** <!-- Code to reproduce the behavior: Please include the results of:--> ```python import qcelemental as qcel mol = qcel.models.Molecule( geometry=[0.0, 0.0, 0.5, 0.0, 0.0, -0.5], symbols=["H", "He"], molecular_charge=0.5, molecular_multiplicity=1.5, # not possible ) ``` **Expected behavior** <!-- A clear and concise description of what you expected to happen. --> Consistent behavior for specifying molecular charge and molecular multiplicity. **Additional context** <!-- Add any other context about the problem here. -->
@loriab: I'll make sure to bring this up to @bennybp to see if the database is ready for a type change.
2025-01-13T16:47:19Z
2025-01-13T16:47:19Z
0.4.3
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"qcelemental/tests/test_molecule.py::test_mol_multiplicity_types_errors[3.1-True-Inconsistent or unspecified chg/mult]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types_errors[mult_in1-True-Multiplicity must be positive]", "qcelemental/tests/test_molecule.py::test_measurements[measure1-37.98890673587713]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp40-expected40-2d17a8fd]", "qcelemental/tests/test_molecule.py::test_molecule_data_constructor_numpy", "qcelemental/tests/test_molecule.py::test_molecule_errors_extra", "qcelemental/tests/test_molecule.py::test_molecule_repeated_hashing", "qcelemental/tests/test_molecule.py::test_water_orient", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp45-expected45-83330b29]", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types[2.9-2.9-True-triplet_point1_minus]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp8-expected8-e3ca63c8]", "qcelemental/tests/test_molecule.py::test_to_from_file_charge_spin[json-json]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp9-expected9-8d70c7ec]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp21-expected21-0f1a1ffc]", "qcelemental/tests/test_molecule.py::test_molecular_weight[He 0 0 0\\n--\\n@He 0 0 5-args5-He2-formula_dict5-8.00520650826-4-0.4233417684]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types[1-mult_in12-mult_store12-False-disinglet_epsilon]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp0-expected0-b3855c64]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types[5-mult_in3-mult_store3-False-ditriplet_point00001]", "qcelemental/tests/test_molecule.py::test_good_isotope_spec", "qcelemental/tests/test_molecule.py::test_water_minima_fragment", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types[1.000000000000002-1.000000000000002-False-singlet_epsilon]", "qcelemental/tests/test_molecule.py::test_charged_fragment", "qcelemental/tests/test_molecule.py::test_molecule_repr_chgmult", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp1-expected1-b3855c64]", "qcelemental/tests/test_molecule.py::test_fragment_charge_configurations[0-2-0-2-0.0-3]", "qcelemental/tests/test_molecule.py::test_molecule_data_constructor_error", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp1]", "qcelemental/tests/test_molecule.py::test_fragment_charge_configurations[1-1-0-2-1.0-2]", "qcelemental/tests/test_molecule.py::test_sparse_molecule_fields[He@3.14 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 0 0 0\\n--\\nHe 0 0 5-args1-He2-formula_dict1-8.00520650826-4-0.4233417684]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp18-expected18-ad36285a]", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types[1.0-1-True-singlet]", "qcelemental/tests/test_molecule.py::test_molecule_connectivity", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types[1.0-1-False-singlet]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types[5-mult_in0-mult_store0-False-ditriplet]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp20-expected20-516f623a]", "qcelemental/tests/test_molecule.py::test_sparse_molecule_fields[He 0 0 0\\n--\\nHe 0 0 5-extra_keys1]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp38-expected38-7140d169]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp41-expected41-b3e87763]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp5]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp43-expected43-38a20a23]", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types[1.1-1.1-False-singlet_point1]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types[5-mult_in2-mult_store2-False-ditriplet_point1]", "qcelemental/tests/test_molecule.py::test_extras", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp5-expected5-e7141038]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp4-expected4-bfdcbd63]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp1-expected1-b3855c64]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp14-expected14-cf3e8c41]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types[1-mult_in9-mult_store9-True-disinglet]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp17]", "qcelemental/tests/test_molecule.py::test_molecule_json_serialization", "qcelemental/tests/test_molecule.py::test_molecule_data_constructor_dict", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult[inp11-expected11-9cd54b37]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp49-expected49-ffe022cd]", "qcelemental/tests/test_molecule.py::test_mol_multiplicity_types_errors[-3-True-Multiplicity must be positive]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_irreconcilable[inp3]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp9-expected9-8d70c7ec]", "qcelemental/tests/test_molparse_validate_and_fill_chgmult.py::test_validate_and_fill_chgmult_mol_model[inp40-expected40-2d17a8fd]", "qcelemental/tests/test_molecule.py::test_frag_multiplicity_types_errors[mult_in2-True-Inconsistent or unspecified 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]", 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"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]" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json qcelemental/tests/test_molparse_validate_and_fill_chgmult.py qcelemental/tests/test_molecule.py", "issue_number": 317, "merge_commit": "1908ccc4228544f7c5dd02be7b660f2fc4e73ade", "merged_at": "", "pr_number": 350, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/MolSSI/QCElemental/pull/350.diff", "issue": "https://github.com/MolSSI/QCElemental/issues/317", "pr": "https://github.com/MolSSI/QCElemental/pull/350" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json qcelemental/tests/test_molparse_validate_and_fill_chgmult.py qcelemental/tests/test_molecule.py
PyCQA/pyflakes
PyCQA__pyflakes-831
433dfd001746a69d12597f7c97af78c13e1f662e
diff --git a/pyflakes/checker.py b/pyflakes/checker.py index c7d3e882..9888d7ac 100644 --- a/pyflakes/checker.py +++ b/pyflakes/checker.py @@ -1008,8 +1008,12 @@ def addBinding(self, node, value): for scope in reversed(self.scopeStack) if not isinstance(scope, GeneratorScope) ) - # it may be a re-assignment to an already existing name - scope.setdefault(value.name, value) + if value.name in scope and isinstance(scope[value.name], Annotation): + # re-assignment to name that was previously only an annotation + scope[value.name] = value + else: + # it may be a re-assignment to an already existing name + scope.setdefault(value.name, value) else: self.scope[value.name] = value
diff --git a/pyflakes/test/test_other.py b/pyflakes/test/test_other.py index 68c38e95..23990820 100644 --- a/pyflakes/test/test_other.py +++ b/pyflakes/test/test_other.py @@ -1744,6 +1744,13 @@ def test_assign_expr(self): print(x) ''') + def test_assign_expr_after_annotation(self): + self.flakes(""" + a: int + print(a := 3) + print(a) + """) + def test_assign_expr_generator_scope(self): """Test assignment expressions in generator expressions.""" self.flakes('''
Walrus operator + annotation can cause F821 in version 3.3.0 In 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): ``` a: int if a := 3: print(a) print(a) ``` Variable "a" is defined in both places ``` $ python3 test.py 3 3 ``` In pyflakes version 3.2.0 this produced no errors ```pip install flake8==7.1.2 pyflakes==3.2.0``` ``` $ flake8 test.py ``` In pyflakes version 3.3.0 this produces F821 even though "a" is defined ```pip install flake8==7.2.0 pyflakes==3.3.0``` ``` $ flake8 test.py test.py:3:11: F821 undefined name 'a' test.py:5:7: F821 undefined name 'a' ``` I am on Windows with Python version 3.12.8
@sigmavirus24: Thanks for reporting and fixing!
2025-03-30T21:54:34Z
2025-03-30T21:54:34Z
0.3.88
[ "pyflakes/test/test_other.py::TestUnusedAssignment::test_unusedReassignedVariable", "pyflakes/test/test_other.py::Test::test_doubleAssignment" ]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json pyflakes/test/test_other.py", "issue_number": 830, "merge_commit": "87051d20e2f5054302f1a5785c6b5a2c83a39cba", "merged_at": "", "pr_number": 831, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/PyCQA/pyflakes/pull/831.diff", "issue": "https://github.com/PyCQA/pyflakes/issues/830", "pr": "https://github.com/PyCQA/pyflakes/pull/831" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json pyflakes/test/test_other.py
tobymao/sqlglot
tobymao__sqlglot-5015
06db2350a1c625cc30212912a73267127fc4f3ea
diff --git a/sqlglot/dialects/postgres.py b/sqlglot/dialects/postgres.py index 97589d5fbd..61a6dba438 100644 --- a/sqlglot/dialects/postgres.py +++ b/sqlglot/dialects/postgres.py @@ -742,3 +742,12 @@ def isascii_sql(self, expression: exp.IsAscii) -> str: @unsupported_args("this") def currentschema_sql(self, expression: exp.CurrentSchema) -> str: return "CURRENT_SCHEMA" + + def interval_sql(self, expression: exp.Interval) -> str: + unit = expression.text("unit").lower() + + if unit.startswith("quarter") and isinstance(expression.this, exp.Literal): + expression.this.replace(exp.Literal.number(int(expression.this.to_py()) * 3)) + expression.args["unit"].replace(exp.var("MONTH")) + + return super().interval_sql(expression)
diff --git a/tests/dialects/test_postgres.py b/tests/dialects/test_postgres.py index 957eb9d5b9..c732688e55 100644 --- a/tests/dialects/test_postgres.py +++ b/tests/dialects/test_postgres.py @@ -372,6 +372,14 @@ def test_postgres(self): pretty=True, ) + self.validate_all( + "SELECT CURRENT_TIMESTAMP + INTERVAL '-3 MONTH'", + read={ + "mysql": "SELECT DATE_ADD(CURRENT_TIMESTAMP, INTERVAL -1 QUARTER)", + "postgres": "SELECT CURRENT_TIMESTAMP + INTERVAL '-3 MONTH'", + "tsql": "SELECT DATEADD(QUARTER, -1, GETDATE())", + }, + ) self.validate_all( "SELECT ARRAY[]::INT[] AS foo", write={
[BUG] Conversion from SQL Server's DATEADD(quarter...) to PostgreSQL not working properly ## Type of issue: Bug Report Conversion from SQL Server's DATEADD(quarter...) to PostgreSQL not working properly ## Description When trying to convert SQL on read dialect 'tsql' for SQL Server's DATEADD(quarter...) the conversion is not correct and does not fail ## Steps to reproduce ```python import sqlglot example_query = "SELECT category, SUM(revenue) as total_revenue FROM events WHERE event_date >= DATEADD(quarter, -1, GETDATE()) GROUP BY category;" parsed_postgres = sqlglot.transpile(example_query , read="tsql", write="postgres") print(parsed_postgres) ``` ## Expected behaviour This conversion should show something like: ```sql SELECT category, SUM(revenue) AS total_revenue FROM events WHERE event_date >= CURRENT_TIMESTAMP + INTERVAL '-3 MONTHS' GROUP BY category ``` ## Actual behavior Right now it will show: ```sql SELECT category, SUM(revenue) AS total_revenue FROM events WHERE event_date >= CURRENT_TIMESTAMP + INTERVAL '-1 QUARTER' GROUP BY category ``` ## Notes 1. 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. 2. The number before "QUARTER" does not matter, that's why it should always be 3 times the number of quarter months. Thanks for this amazing library I just discovered it and it's coming handy! 💯
2025-04-25T21:40:11Z
2025-04-25T21:40:11Z
0.3.88
[]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_postgres.py", "issue_number": 5013, "merge_commit": "60103020879db5f23a6c4a1775848e31cce13415", "merged_at": "", "pr_number": 5015, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/tobymao/sqlglot/pull/5015.diff", "issue": "https://github.com/tobymao/sqlglot/issues/5013", "pr": "https://github.com/tobymao/sqlglot/pull/5015" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/dialects/test_postgres.py
matthewwithanm/python-markdownify
matthewwithanm__python-markdownify-217
e29de4e75314daf9267f30f47fd7a091ef5f1deb
diff --git a/markdownify/__init__.py b/markdownify/__init__.py index 780761c..a43f3a7 100644 --- a/markdownify/__init__.py +++ b/markdownify/__init__.py @@ -650,6 +650,9 @@ def convert_pre(self, el, text, parent_tags): return '\n\n```%s\n%s\n```\n\n' % (code_language, text) + def convert_q(self, el, text, parent_tags): + return '"' + text + '"' + def convert_script(self, el, text, parent_tags): return ''
diff --git a/tests/test_conversions.py b/tests/test_conversions.py index 27951ee..6145411 100644 --- a/tests/test_conversions.py +++ b/tests/test_conversions.py @@ -305,6 +305,11 @@ def test_pre(): assert md("<p>foo</p>\n<pre>bar</pre>\n</p>baz</p>", sub_symbol="^") == "\n\nfoo\n\n```\nbar\n```\n\nbaz" +def test_q(): + assert md('foo <q>quote</q> bar') == 'foo "quote" bar' + assert md('foo <q cite="https://example.com">quote</q> bar') == 'foo "quote" bar' + + def test_script(): assert md('foo <script>var foo=42;</script> bar') == 'foo bar'
Inline Quotation element ignored Html that looks like this: ```html Here is <q>A Quote</q> from someone. ``` should be rendered as: ``` Here is “A Quote“ from someone. ``` https://developer.mozilla.org/en-US/docs/Web/HTML/Reference/Elements/q Solution: ```python def convert_q(self, el, text, parent_tags): return '“' + text + '“' ```
@chrispy-snps: @colinrobinsonuib - good catch! We should probably use straight ASCII quotes for wider compatibility with downstream flows. Are you interested in opening a pull request and officially becoming a contributor?@colinrobinsonuib: Sure https://github.com/matthewwithanm/python-markdownify/pull/217
2025-04-28T10:37:33Z
2025-04-28T10:37:33Z
0.3.88
[]
[ "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" ]
pip install -e .; pip install pytest pytest-json-report;
pytest --json-report --json-report-file=report_pytest.json
python:3.11
{ "command_test_small": "pytest --json-report --json-report-file=report_pytest.json tests/test_conversions.py", "issue_number": 216, "merge_commit": "0e1a849346f24e9b15eefb11752feaf7b4b821fa", "merged_at": "", "pr_number": 217, "score": { "complexity": -1, "task_correctness": -1, "test_completeness": -1, "test_correctness": -1 }, "tag": "swb25_250629", "task_id": null, "type": "python pytest", "url": { "diff": "https:///github.com/matthewwithanm/python-markdownify/pull/217.diff", "issue": "https://github.com/matthewwithanm/python-markdownify/issues/216", "pr": "https://github.com/matthewwithanm/python-markdownify/pull/217" } }
3,000
600
pytest --json-report --json-report-file=report_pytest.json tests/test_conversions.py

SWE-MERA

Continuously updated SWE-MERA dataset

SWE-MERA splits:

  • dev: for testing (10 samples)
  • lite: presented at the leaderboard here (750 samples)
  • full: continuously updated to collect more data (2738 samples)

Load dataset

from datasets import load_dataset
ds = load_dataset("MERA-evaluation/SWE-MERA", split='dev')

Evaluation

Description

The main tool to validate tasks is repotest (available at PyPI or GitHub)

data.jsonl - dataset file, where after the agent run, the patch column was changed

Install dependencies

pip install repositorytest

Run evaluation

swemera --fn_input=data.jsonl --fn_output=submission.jsonl --column_patch=patch --mode=docker

If you don't want to use Docker and prefer Conda or local execution:

swemera --fn_input=data.jsonl --fn_output=submission.jsonl --column_patch=patch --mode=local

Schema

Column Name Type Description Is New Column
repo VARCHAR Repository name (e.g., GitHub repository) False
instance_id VARCHAR Unique identifier for task: f"{repo.replace('/', '_') + '' + pr_number}" False
base_commit VARCHAR Commit hash of the base code before patch applied False
patch VARCHAR Code patch or diff applied to the base_commit to be the correct solution False
test_patch VARCHAR Patch for test code, if separate from main code patch False
problem_statement VARCHAR Description or statement of the problem to solve False
hint_text VARCHAR Hints or tips for solving the problem from GitHub issue comments False
created_at VARCHAR Date when the instance was created False
closed_at VARCHAR Date when the instance was closed or resolved True
version VARCHAR Version identifier for the instance or dataset False
FAIL_TO_PASS LIST[VARCHAR] Test cases which were failing but later passed False
PASS_TO_PASS LIST[VARCHAR] Test cases which passed at all times False
environment_setup_commit VARCHAR Commit hash for environment setup configuration False
command_build VARCHAR Command used to build the repo True
command_test VARCHAR Command used to run the tests inside repo True
image_name VARCHAR Docker or container image name used for testing environment True
command_test_small VARCHAR Command to run a smaller subset of tests True
timeout_build INTEGER Timeout limit in seconds for build command True
timeout_test INTEGER Timeout limit in seconds for test command True
meta DICT[STR,ANY] Additional metadata about the instance*

*meta field description:

{
  "score": {
    "task_correctness": "INTEGER",
    "test_correctness": "INTEGER",
    "complexity": "INTEGER",
    "test_completeness": "INTEGER"
  },
  "type": "VARCHAR",
  "pr_number": "INTEGER",
  "issue_number": "INTEGER",
  "merged_at": "VARCHAR",
  "tag": "VARCHAR // Information on how data was collected",
  "merge_commit": "VARCHAR",
  "task_id": "VARCHAR // Latency identifier of the task",
  "url": {
    "issue": "VARCHAR",
    "pr": "VARCHAR",
    "diff": "VARCHAR"
  },
  "command_test_small": "VARCHAR // Command to run only a small number of tests"
}

Dev tasks Examples

Instances

Instance ID Short Title
reframe-0 Performance threshold goes to -inf when it should be zero.
pyflakes-1 Walrus operator + annotation can cause F821
sqlglot-2 MySQL dialect fails to parse PRIMARY KEY USING BTREE syntax
matchms-3 matchms fails when reading spectra where abundance is in scientific notation #809
guarddog-4 Add Mach-O magic bytes to bundled binary detector #523
pdoc-5 Include HTML headers in ToC
QCElemental-6 QCElemental 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.
sqlglot-7 TSQL: PRIMARY KEY constraint fails to parse if
sqlglot-8 [BUG] Conversion from SQL Server's DATEADD(quarter...) to PostgreSQL not working properly
python-markdownify-9 Inline Quotation element ignored
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