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CI: update pytest results
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‎tests/pytest_results_py3.12.txt‎

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
Pytest results (Python 3.12) - 2026-03-05T16:23:06Z
1+
Pytest results (Python 3.12) - 2026-03-09T16:26:59Z
22

33
============================= test session starts ==============================
44
platform linux -- Python 3.12.12, pytest-9.0.2, pluggy-1.6.0 -- /opt/hostedtoolcache/Python/3.12.12/x64/bin/python
@@ -275,7 +275,7 @@ tests/test_virus.py::TestVirus::test_virus_with_source_database_filter PASSED [1
275275
=================================== FAILURES ===================================
276276
________________________ TestSearch.test_search_octopus ________________________
277277

278-
self = <pandas.io.sql.SQLiteDatabase object at 0x7f814c61c200>
278+
self = <pandas.io.sql.SQLiteDatabase object at 0x7fc0a47b0ef0>
279279
sql = "\n SELECT gene.stable_id AS 'ensembl_id', xref.display_label AS 'gene_name', gene.description AS 'ensembl_...lay_label LIKE '%methi%' OR external_synonym.synonym LIKE '%methi%' OR gene_attrib.value LIKE '%methi%')\n "
280280
params = None
281281

@@ -294,7 +294,7 @@ params = None
294294
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/pandas/io/sql.py:2668:
295295
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
296296

297-
self = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
297+
self = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
298298

299299
def rollback(self) -> None:
300300
"""Rollback current transaction"""
@@ -306,7 +306,7 @@ self = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
306306
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/connection.py:1463:
307307
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
308308

309-
self = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
309+
self = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
310310
query = 'ROLLBACK'
311311

312312
def _execute_query(self, query: str) -> None:
@@ -324,7 +324,7 @@ query = 'ROLLBACK'
324324
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/connection.py:1475:
325325
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
326326

327-
cnx = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
327+
cnx = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
328328
args = ('ROLLBACK',), kwargs = {}
329329

330330
def wrapper(cnx: "MySQLConnectionAbstract", *args: Any, **kwargs: Any) -> Any:
@@ -337,7 +337,7 @@ args = ('ROLLBACK',), kwargs = {}
337337
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/opentelemetry/context_propagation.py:97:
338338
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
339339

340-
cnx = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
340+
cnx = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
341341
args = ('ROLLBACK',), kwargs = {}
342342

343343
@functools.wraps(cnx_method)
@@ -354,7 +354,7 @@ args = ('ROLLBACK',), kwargs = {}
354354
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/_decorating.py:89:
355355
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
356356

357-
cnx = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
357+
cnx = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
358358
args = ('ROLLBACK',), kwargs = {}
359359

360360
@functools.wraps(cnx_method)
@@ -368,7 +368,7 @@ args = ('ROLLBACK',), kwargs = {}
368368
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/_decorating.py:85:
369369
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
370370

371-
self = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
371+
self = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
372372
query = b'ROLLBACK', raw = False, buffered = False, raw_as_string = False
373373
kwargs = {}, charset = 'utf8', packet = bytearray(b'ROLLBACK')
374374

@@ -489,7 +489,7 @@ kwargs = {}, charset = 'utf8', packet = bytearray(b'ROLLBACK')
489489
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/connection.py:984:
490490
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
491491

492-
cnx = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
492+
cnx = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
493493
args = (bytearray(b"M\x00\x00\t\x10GeneID_128249166\x0cTrnam-cau-22\'transfer RNA methionine (anticodon CAU)\xfb\x04tRNA\xfb"), None, None)
494494
kwargs = {}
495495

@@ -507,7 +507,7 @@ kwargs = {}
507507
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/_decorating.py:89:
508508
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
509509

510-
cnx = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
510+
cnx = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
511511
args = (bytearray(b"M\x00\x00\t\x10GeneID_128249166\x0cTrnam-cau-22\'transfer RNA methionine (anticodon CAU)\xfb\x04tRNA\xfb"), None, None)
512512
kwargs = {}
513513

@@ -522,7 +522,7 @@ kwargs = {}
522522
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/mysql/connector/_decorating.py:85:
523523
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
524524

525-
self = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
525+
self = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
526526
packet = bytearray(b"M\x00\x00\t\x10GeneID_128249166\x0cTrnam-cau-22\'transfer RNA methionine (anticodon CAU)\xfb\x04tRNA\xfb")
527527
read_timeout = None, write_timeout = None
528528

@@ -614,7 +614,7 @@ self = <tests.test_search.TestSearch testMethod=test_search_octopus>
614614
tests/from_json.py:87:
615615
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
616616

617-
func = <function search at 0x7f81642bf2e0>
617+
func = <function search at 0x7fc0bd2d7060>
618618
args = {'limit': 1, 'searchwords': 'methi', 'species': 'octopus_bimaculoides'}
619619

620620
def do_call(func, args):
@@ -845,7 +845,7 @@ gget/gget_search.py:244:
845845
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
846846

847847
sql = "\n SELECT gene.stable_id AS 'ensembl_id', xref.display_label AS 'gene_name', gene.description AS 'ensembl_...lay_label LIKE '%methi%' OR external_synonym.synonym LIKE '%methi%' OR gene_attrib.value LIKE '%methi%')\n "
848-
con = <mysql.connector.connection.MySQLConnection object at 0x7f814c61c380>
848+
con = <mysql.connector.connection.MySQLConnection object at 0x7fc0a47b0110>
849849
index_col = None, coerce_float = True, params = None, parse_dates = None
850850
columns = None, chunksize = None, dtype_backend = 'numpy', dtype = None
851851

@@ -999,7 +999,7 @@ columns = None, chunksize = None, dtype_backend = 'numpy', dtype = None
999999
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/pandas/io/sql.py:708:
10001000
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
10011001

1002-
self = <pandas.io.sql.SQLiteDatabase object at 0x7f814c61c200>
1002+
self = <pandas.io.sql.SQLiteDatabase object at 0x7fc0a47b0ef0>
10031003
sql = "\n SELECT gene.stable_id AS 'ensembl_id', xref.display_label AS 'gene_name', gene.description AS 'ensembl_...lay_label LIKE '%methi%' OR external_synonym.synonym LIKE '%methi%' OR gene_attrib.value LIKE '%methi%')\n "
10041004
index_col = None, coerce_float = True, parse_dates = None, params = None
10051005
chunksize = None, dtype = None, dtype_backend = 'numpy'
@@ -1021,7 +1021,7 @@ chunksize = None, dtype = None, dtype_backend = 'numpy'
10211021
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/pandas/io/sql.py:2728:
10221022
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
10231023

1024-
self = <pandas.io.sql.SQLiteDatabase object at 0x7f814c61c200>
1024+
self = <pandas.io.sql.SQLiteDatabase object at 0x7fc0a47b0ef0>
10251025
sql = "\n SELECT gene.stable_id AS 'ensembl_id', xref.display_label AS 'gene_name', gene.description AS 'ensembl_...lay_label LIKE '%methi%' OR external_synonym.synonym LIKE '%methi%' OR gene_attrib.value LIKE '%methi%')\n "
10261026
params = None
10271027

@@ -1166,7 +1166,7 @@ gget/gget_8cube.py 83 28 66% 26-27, 34-43, 93, 105, 112, 115
11661166
gget/gget_alphafold.py 362 321 11% 86-108, 115-116, 123-149, 181-186, 233-867
11671167
gget/gget_archs4.py 79 13 84% 75-78, 84, 107, 123-126, 139-142, 148, 170, 198-201, 207
11681168
gget/gget_bgee.py 56 6 89% 60, 83, 103, 130, 154, 175
1169-
gget/gget_blast.py 127 36 72% 92, 124-142, 163-165, 204, 207, 246-248, 296-299, 302-303, 322-325, 332-333, 336-341, 346, 351-354
1169+
gget/gget_blast.py 127 36 72% 92, 124-142, 163-165, 204, 207, 251-255, 296-299, 302-303, 322-325, 332-333, 336-341, 346, 351-354
11701170
gget/gget_blat.py 86 10 88% 58-62, 95, 136, 139, 168, 232-233, 239
11711171
gget/gget_cbio.py 524 403 23% 28, 39-67, 77-87, 136-137, 143-147, 154-157, 161, 164, 172-177, 208, 226, 265, 271-275, 278, 282-294, 296, 322-331, 334, 376-389, 393-416, 420-441, 447-450, 454-473, 477, 494-537, 540-757, 760-789, 802-1164, 1218-1254
11721172
gget/gget_cellxgene.py 53 9 83% 21-22, 140-149, 176, 215, 231, 247
@@ -1190,16 +1190,16 @@ gget/utils.py 448 77 83% 31, 36-42, 72, 95, 119, 122, 18
11901190
--------------------------------------------------------
11911191
TOTAL 8233 4240 48%
11921192
============================= slowest 10 durations =============================
1193-
79.09s call tests/test_blast.py::TestBlast::test_blast_nt
1194-
53.28s call tests/test_virus.py::TestVirus::test_virus_with_length_filters
1195-
32.97s call tests/test_virus.py::TestVirus::test_virus_integer_virus_id
1196-
30.37s call tests/test_virus.py::TestVirus::test_virus_with_source_database_filter
1197-
29.62s call tests/test_virus.py::TestVirus::test_virus_with_has_proteins_filter
1198-
29.54s call tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata
1199-
29.52s call tests/test_virus.py::TestVirus::test_virus_with_lab_passaged_filter
1200-
29.50s call tests/test_virus.py::TestVirus::test_virus_with_max_ambiguous_chars_filter
1201-
27.87s call tests/test_search.py::TestSearch::test_search_gene_two_sw_limit
1202-
26.06s call tests/test_virus.py::TestVirus::test_virus_with_protein_count_filters
1193+
76.07s call tests/test_blast.py::TestBlast::test_blast_nt
1194+
38.50s call tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata
1195+
34.94s call tests/test_search.py::TestSearch::test_search_gene_two_sw_limit
1196+
29.16s call tests/test_virus.py::TestVirus::test_virus_with_max_ambiguous_chars_filter
1197+
25.31s call tests/test_virus.py::TestVirus::test_virus_integer_virus_id
1198+
24.72s call tests/test_virus.py::TestVirus::test_virus_with_source_database_filter
1199+
23.80s call tests/test_virus.py::TestVirus::test_virus_with_annotated_filter
1200+
23.61s call tests/test_virus.py::TestVirus::test_virus_with_has_proteins_filter
1201+
23.60s call tests/test_virus.py::TestVirus::test_virus_with_lab_passaged_filter
1202+
22.79s call tests/test_virus.py::TestVirus::test_virus_with_protein_count_filters
12031203
=========================== short test summary info ============================
12041204
FAILED tests/test_search.py::TestSearch::test_search_octopus - pandas.errors.DatabaseError: Execution failed on sql:
12051205
SELECT gene.stable_id AS 'ensembl_id', xref.display_label AS 'gene_name', gene.description AS 'ensembl_description', xref.description AS 'ext_ref_description', gene.biotype AS 'biotype', external_synonym.synonym AS 'synonym'
@@ -1211,4 +1211,4 @@ FAILED tests/test_search.py::TestSearch::test_search_octopus - pandas.errors.Dat
12111211

12121212
Expected EOF packet
12131213
unable to rollback
1214-
=========== 1 failed, 262 passed, 270 warnings in 823.63s (0:13:43) ============
1214+
=========== 1 failed, 262 passed, 270 warnings in 695.57s (0:11:35) ============

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