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start

Mono Color

• 5216add545 Replaced deprecated ruff linter ID master Peter J. A. Cock 2025-10-15 11:38:33 +01:00
• 4c8696aa82 Remove unused or read only globals (flake8 F824) Peter J. A. Cock 2025-10-15 11:37:00 +01:00
• e451db211b update NEWS file Rob Miller 2024-11-04 16:49:08 -04:00
• f7d7ded086 make spheres nicer on first start Rob Miller 2024-11-04 16:40:15 -04:00
• 682eb13373 Add OpenSCAD code to enable multimaterial printer output Rob Miller 2024-11-04 11:48:48 -04:00
• dd1cabc980 Fix markup, update & sort names Peter Cock 2025-10-10 12:30:23 +01:00
• 37f6c5f81d Test on Python 3.10 ~ 3.14 Peter J. A. Cock 2025-10-09 09:35:17 +01:00
• f47393b775 Sort names Peter J. A. Cock 2025-10-09 09:37:27 +01:00
• e763ca5721 Add paragraph about iplotx in Phylo tutorial (#5028) Fabio Zanini 2025-10-09 19:27:43 +11:00
• 9111417121 Stay on mypy 1.16.1 Peter J. A. Cock 2025-10-07 09:34:04 +01:00
• 24b9dba21a B017 - avoid blind exception Peter J. A. Cock 2025-10-07 09:32:22 +01:00
• 2a392a0452 Stay at black 24.10.0 Peter Cock 2025-10-06 20:28:41 +01:00
• 6cf5841fdf [pre-commit.ci] autoupdate pre-commit-ci[bot] 2025-10-06 19:23:00 +00:00
• f2004e04da added test and docstring for #5053 Manuel Lera-Ramirez 2025-09-23 10:48:18 +02:00
• 5d48cf583f SnapGene: Filter out partial binding sites. Damien Goutte-Gattat 2025-09-22 22:12:34 +01:00
• e85f1958ee Make PDB.Chain.__getitem__ more lenient for indexing with int-like values (#5018) Kâmuran İmran 2025-09-29 18:50:29 +10:00
• 20ad9bea6d Handle possible non-existent attributes in clusterbuster.py (#5074) Yen-Chung Chen 2025-09-27 03:03:53 -04:00
• 5a31c3ef74 removing tests for removed modules Michiel de Hoon 2025-09-18 15:41:30 +09:00
• 5a31cfce80 updating the DEPRECATED.rst file Michiel de Hoon 2025-09-18 15:28:14 +09:00
• 5b2a50a9ce removing deprecated code Michiel de Hoon 2025-09-18 15:24:35 +09:00
• a32c56e1a1 Bump tj-actions/changed-files from 46 to 47 dependabot[bot] 2025-09-15 14:31:54 +00:00
• 593114d868 deprecating the SummaryInfo class in Bio.Align.AlignInfo (#5069) mdehoon 2025-09-21 18:06:00 +09:00
• 0c4fae3d61 Fix F824 in Bio.PDB.vectors (#5067) Mikel Martinez Goikoetxea 2025-09-20 20:11:58 +02:00
• ac0216ab12 Delete Tests/BWA/ test data. Étienne Mollier 2025-09-15 19:17:45 +02:00
• be97b2d4e7 Aligner default arguments (#5029) mdehoon 2025-09-16 22:46:35 +09:00
• b4d7c115d2 Bump actions/setup-python from 5 to 6 dependabot[bot] 2025-09-08 12:21:20 +00:00
• 6e43775844 documentation tweaks (#5055) mdehoon 2025-09-04 16:23:53 +09:00
• ad9456f3bb Align: add substitution matrix support to Alignment.format() (#5049) RachelStern20 2025-09-04 08:14:55 +03:00
• d3de878863 Fixes formatting for extremely high B-factor values in PDB files (#5047) Oliver Wissett 2025-09-03 15:05:07 +01:00
• d1c4b3d0e2 pairwisealigner pickle fix (#5041) Arik Mitschang 2025-08-18 20:18:30 -04:00
• a4f7ca03bb Bump actions/checkout from 4 to 5 dependabot[bot] 2025-08-11 17:38:12 +00:00
• 4ceee03dbf typo (#5040) mdehoon 2025-08-12 16:06:49 +09:00
• ff4bed01f5 declare local functions as static (#5037) mdehoon 2025-08-12 00:33:52 +09:00
• 35bdb3f576 Update YN00 docstrings Thomas Walsh 2025-07-24 18:14:34 +01:00
• 053bdc8ed2 Uppercase PAML software names except in run methods Thomas Walsh 2025-07-24 18:12:54 +01:00
• f6e56e5061 Update long docstrings in PAML class methods Thomas Walsh 2025-07-24 15:10:28 +01:00
• aceebefbff Set PAML class names in CamelCase Thomas Walsh 2025-07-24 15:03:01 +01:00
• 392ede471d Fixed flake8 rule D209 violations Franziska Arndt 2020-01-04 01:45:14 +01:00
• b86d003e49 Update CONTRIB.rst Edward Haigh 2018-10-06 10:23:25 +01:00
• 727b5055ff Updated docstrings to use consistent capitalization. paml >> PAML etc. funcylambda 2018-10-06 10:16:14 +01:00
• 95f8119ad9 Updated docstrings to include the output and mention any validation that occurs. Also, changed docstring so they have consistent capitalization. Baseml >> BASEML etc funcylambda 2018-10-06 10:13:58 +01:00
• 6851cd8d03 Drop comment Peter Cock 2025-07-24 17:59:12 +01:00
• b027825127 Prevent side-effect in SeqRecord._per_letter_annotations Michael M 2025-07-18 15:16:53 -05:00
• 66ad0a062e Extend the .counts method of an Alignment (#5011) mdehoon 2025-07-11 14:40:07 +09:00
• 1b5e9ccef5 Stay at black 24.10.0 for trailing whitespace in doctests Peter J. A. Cock 2025-07-11 10:00:36 +09:00
• 116d92b0fe Drop trailing whitespace in some docstrings Peter J. A. Cock 2025-07-11 09:56:33 +09:00
• ed51b11450 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-07-07 18:48:16 +00:00
• 8aaa7ffc41 [pre-commit.ci] autoupdate pre-commit-ci[bot] 2025-07-07 18:45:28 +00:00
• 0969cc24fd Add automatic alignment generation to StructureAlignment Dimitris Kalafatis 2025-07-03 11:33:06 -05:00
• fb837c6c3b Update ci.yml and change windows-2019 to windows-2022 (#5024) João Rodrigues 2025-07-03 08:53:04 -07:00
• 7ada95b6c5 Reset to 3.13 mdehoon 2025-06-30 13:21:37 +09:00
• feeb7283cf Style change only (#5019) mdehoon 2025-06-21 10:16:04 +09:00
• b19a21029a follow recommended style for PyTypeObject (#5014) mdehoon 2025-06-21 01:13:57 +09:00
• f340157030 Also use 3.13.5 when testing on Windows mdehoon 2025-06-20 19:17:20 +09:00
• 2875c9d91d Use 3.13.5 instead of 3.13 mdehoon 2025-06-20 19:08:03 +09:00
• dcc414824d miniconda -> miniforge for AppVeyor Peter J. A. Cock 2025-06-17 10:28:59 +09:00
• 0b41684f14 Fix QCPSuperimposer bug (#5005) Santeri Paajanen 2025-06-10 00:19:55 +03:00
• 17e870f6da Added Documentation to CEAlign and QCPSuperimposer (#5002) Dimitris Kalafatis 2025-06-09 11:00:38 -05:00
• 1172869397 Uniprotxml parse ligand tag (#5001) Ira Horecka 2025-05-30 16:09:26 -07:00
• 91740a7788 Remove unused f-string Peter Cock 2025-05-29 09:45:17 +01:00
• 2cb91f3c73 linting lee-t 2025-05-19 22:04:34 -04:00
• 28f18b2d09 improve coverage of tests lee-t 2025-05-19 21:57:54 -04:00
• 377635ed52 remove urlerror and httperror lee-t 2025-05-19 12:51:39 -04:00
• 6d03848836 change url in test lee-t 2025-05-19 11:48:19 -04:00
• ebcc56b389 add tests for bad url and http error lee-t 2025-05-18 21:47:02 -04:00
• 41fa46f50e format with black lee-t 2025-05-18 21:25:44 -04:00
• 49a3981d75 if error is caught should return None instead of final_file lee-t 2025-05-18 21:12:19 -04:00
• 0e0ede6655 compliance with contrib guide lee-t 2025-05-18 21:05:11 -04:00
• a4b3afbe4a fixed PDBlist.retrieve_pdb_file(); improved error handling, should not show misleading message lee-t 2025-05-18 20:42:44 -04:00
• 137dca3eb9 test: add test to check if Location.fromstring is static Fynn Freyer 2025-03-27 20:09:16 +01:00
• 8e969c418f chore: add name to contrib.rst Fynn Freyer 2025-03-27 15:08:07 +01:00
• 10bb678638 fix(SeqFeature): add missing decorator to Location.fromstring factory method Fynn Freyer 2025-03-27 14:48:04 +01:00
• 32b9648617 use PyOS_double_to_string to prevent locale-specific behavior (#4982) mdehoon 2025-03-26 17:58:08 +09:00
• 180d8a6e69 Added InfernalIO to NEWS.rst Samuel Prince 2025-03-14 21:08:43 -05:00
• 96a734ff9a Remove reference to the fmt override in the documentation Samuel Prince 2025-03-14 19:25:15 -05:00
• 70f553f9c6 Fixed issues in docstring introduced in e477fd8 Samuel Prince 2025-03-14 15:59:36 -05:00
• 11bdb70bac Remove reference to the fmt override in the documentation Samuel Prince 2025-03-14 14:37:09 -05:00
• 2db4d2c4e7 Fixed stype Samuel Prince 2025-01-19 11:03:40 -05:00
• 0304aa8162 Removed support for user-provided --fmt Samuel Prince 2025-02-06 16:01:52 -05:00
• 511648f992 Improved behaviour consistency for the tabular format handling Samuel Prince 2025-01-21 18:11:45 -05:00
• 8663d68cc8 Update documentation Samuel Prince 2025-01-19 10:56:50 -05:00
• 4f39ac9c3b Changed overlapping hit fields (tabular fmt 2) to numeric type Samuel Prince 2025-01-19 10:51:51 -05:00
• 1b186f2670 Use lambda function for inclusion conversion Samuel Prince 2025-01-19 09:51:49 -05:00
• 38f0fed34a Infer the tabular format from the header Samuel Prince 2025-01-19 09:35:33 -05:00
• c30a15fbae Fix import style Samuel Prince 2025-01-17 10:50:10 -05:00
• 4f6fb06665 Fix typo in documentation Samuel Prince 2025-01-17 10:49:22 -05:00
• ce0d90d133 Update NEWS.rst Samuel Prince 2024-10-25 13:00:12 -04:00
• 00868673f6 Update docstring Samuel Prince 2024-10-25 12:39:58 -04:00
• 86decf2df1 Fixed docstring Samuel Prince 2024-10-02 04:23:14 -04:00
• 1cec609d6c Added testing for notextw plain text output Samuel Prince 2024-09-26 08:56:20 -04:00
• 2e45868a64 Standardized assertion format Samuel Prince 2024-09-25 08:10:51 -04:00
• ecc4136d22 Moved model information to the HSP in the tabular format parser Samuel Prince 2024-09-25 07:58:23 -04:00
• 981e136ac2 Added InfernalIO module doc string Samuel Prince 2024-09-25 07:48:01 -04:00
• 164fdf0163 Fixed issues in text format testing Samuel Prince 2024-09-24 09:58:47 -04:00
• 71f13fc2b7 Removed unused code in the tabular format parser Samuel Prince 2024-09-24 09:09:21 -04:00
• 7f4b9eaf44 Fixed formatting Samuel Prince 2024-09-24 08:59:50 -04:00
• f9f871a5b4 Removed a change introduced earlier in Blast parser Samuel Prince 2024-09-24 08:47:41 -04:00
• b7f1782578 Tests names standardization Samuel Prince 2024-09-20 08:10:51 -04:00
• 35a3324e21 Added infernal text indexer Samuel Prince 2024-09-20 08:10:42 -04:00
• 9757867b6b Corrected testing function name Samuel Prince 2024-09-20 07:46:07 -04:00