b86d003e49
Update CONTRIB.rst
2025-07-30 16:28:38 +01:00
727b5055ff
Updated docstrings to use consistent capitalization. paml >> PAML etc.
2025-07-30 16:28:38 +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
2025-07-30 16:28:38 +01:00
6851cd8d03
Drop comment
2025-07-24 18:13:30 +01:00
b027825127
Prevent side-effect in SeqRecord._per_letter_annotations
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Fixes #5015
2025-07-24 18:13:30 +01:00
66ad0a062e
Extend the .counts method of an Alignment ( #5011 )
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* replace precompiler #defines by inline functions
* update
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* add tests
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* documentation
* update
* avoid stpcpy
* pointer printing
* compiler warning
* testing without codonalign
* testing without codonalign and pairwisealigner
* compiler warning
* adding codonalign and pairwisealigner back in
* remove inline from check_indices
* add inline to check_indices
* update
* add test line 12287 test_pairwise_aligner.py
* update
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* change dtype from int32 to "i"
* all done
* testing
* testing
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* done
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* fix how pointers are printed on Windows
* update
* update
* update
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* fix id printing on pypy
* style change only
* Use Py_uintptr_t instead of uintptr_t
* fix memory leak
* remove double semicolon
* check if GitHub actions are now pickup up Python version 3.13.5 without hardcoding it
---------
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp >
Co-authored-by: Michiel de Hoon <michiel.dehoon@riken.jp >
2025-07-11 14:40:07 +09:00
1b5e9ccef5
Stay at black 24.10.0 for trailing whitespace in doctests
2025-07-11 10:26:05 +09:00
116d92b0fe
Drop trailing whitespace in some docstrings
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Used black 25.1.0 which does this in docstrings too which is bad.
2025-07-11 10:26:05 +09:00
ed51b11450
[pre-commit.ci] auto fixes from pre-commit.com hooks
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for more information, see https://pre-commit.ci
2025-07-11 10:26:05 +09:00
8aaa7ffc41
[pre-commit.ci] autoupdate
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.7 → v0.12.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.7...v0.12.2 )
- [github.com/psf/black: 24.10.0 → 25.1.0](https://github.com/psf/black/compare/24.10.0...25.1.0 )
- [github.com/PyCQA/flake8: 7.1.2 → 7.3.0](https://github.com/PyCQA/flake8/compare/7.1.2...7.3.0 )
- [github.com/pre-commit/mirrors-mypy: v1.15.0 → v1.16.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.15.0...v1.16.1 )
- [github.com/rstcheck/rstcheck: v6.2.4 → v6.2.5](https://github.com/rstcheck/rstcheck/compare/v6.2.4...v6.2.5 )
- [github.com/PyCQA/doc8: v1.1.2 → v2.0.0](https://github.com/PyCQA/doc8/compare/v1.1.2...v2.0.0 )
2025-07-11 10:26:05 +09:00
0969cc24fd
Add automatic alignment generation to StructureAlignment
2025-07-03 09:33:06 -07:00
fb837c6c3b
Update ci.yml and change windows-2019 to windows-2022 ( #5024 )
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Closes #5023
2025-07-03 08:53:04 -07:00
7ada95b6c5
Reset to 3.13
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3.13.5 is now cached on the runners, so specifying 3.13 will resolve to that version, and we don't need to hardcode it here any more.
2025-06-30 13:21:37 +09:00
feeb7283cf
Style change only ( #5019 )
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Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-06-21 10:16:04 +09:00
b19a21029a
follow recommended style for PyTypeObject ( #5014 )
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* follow recommended style for PyTypeObject
* update
---------
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-06-21 01:13:57 +09:00
f340157030
Also use 3.13.5 when testing on Windows
2025-06-20 19:17:20 +09:00
2875c9d91d
Use 3.13.5 instead of 3.13
2025-06-20 19:08:03 +09:00
dcc414824d
miniconda -> miniforge for AppVeyor
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Should fix recent issue with failing to download miniconda.
Using miniforge is recommended by conda-forge.
2025-06-17 10:55:50 +09:00
0b41684f14
Fix QCPSuperimposer bug ( #5005 )
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Addresses a bug in the code that caused the Newton-Raphson optimization to quit earlier than it should, resulting in poorer alignments.
2025-06-09 14:19:55 -07:00
17e870f6da
Added Documentation to CEAlign and QCPSuperimposer ( #5002 )
2025-06-09 09:00:38 -07:00
1172869397
Uniprotxml parse ligand tag ( #5001 )
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* enable handling of <ligand> tags in UniProt XML files
* test parsing of <ligand> in UniProt XML
* add name to CONTRIB.rst
* format with black
* enable capture of multiple ligands from uniprot xml file. update tests accordingly
* add mock UniProt XML file with multiple ligand tags per feature
* test for correct len of all ligands list and multiple ligands per feature
2025-05-31 00:09:26 +01:00
91740a7788
Remove unused f-string
2025-05-29 10:00:50 +01:00
2cb91f3c73
linting
2025-05-29 10:00:50 +01:00
28f18b2d09
improve coverage of tests
2025-05-29 10:00:50 +01:00
377635ed52
remove urlerror and httperror
2025-05-29 10:00:50 +01:00
6d03848836
change url in test
2025-05-29 10:00:50 +01:00
ebcc56b389
add tests for bad url and http error
2025-05-29 10:00:50 +01:00
41fa46f50e
format with black
2025-05-29 10:00:50 +01:00
49a3981d75
if error is caught should return None instead of final_file
2025-05-29 10:00:50 +01:00
0e0ede6655
compliance with contrib guide
2025-05-29 10:00:50 +01:00
a4b3afbe4a
fixed PDBlist.retrieve_pdb_file(); improved error handling, should not show misleading message
2025-05-29 10:00:50 +01:00
137dca3eb9
test: add test to check if Location.fromstring is static
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requested by peterjc
I agree to my contributions being dual licensed under the BSD 3-Clause and Biopython License
Signed-off-by: Fynn Freyer <fynn.freyer@googlemail.com >
2025-03-28 14:47:27 +00:00
8e969c418f
chore: add name to contrib.rst
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I agree to my contributions being dual licensed under the BSD 3-Clause and Biopython License
Signed-off-by: Fynn Freyer <fynn.freyer@googlemail.com >
2025-03-28 14:47:27 +00:00
10bb678638
fix(SeqFeature): add missing decorator to Location.fromstring factory method
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The fromstring method of the abstract Location class is missing a method decorator, which causes the first argument to be interpreted as self.
This doesn't lead to any problems when calling it from the class, but confuses tooling.
Note that the commit that added this (908ee298) speaks of a "fromstring class method", so taking this method in the instance context should be fine.
I agree to my contributions being dual licensed under the BSD 3-Clause and Biopython License
Signed-off-by: Fynn Freyer <fynn.freyer@googlemail.com >
2025-03-28 14:47:27 +00:00
32b9648617
use PyOS_double_to_string to prevent locale-specific behavior ( #4982 )
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* use PyOS_double_to_string to prevent locale-specific behavior
* update
---------
2025-03-26 17:58:08 +09:00
180d8a6e69
Added InfernalIO to NEWS.rst
2025-03-22 06:59:36 +01:00
96a734ff9a
Remove reference to the fmt override in the documentation
2025-03-22 06:59:36 +01:00
70f553f9c6
Fixed issues in docstring introduced in e477fd8
2025-03-22 06:59:36 +01:00
11bdb70bac
Remove reference to the fmt override in the documentation
2025-03-22 06:59:36 +01:00
2db4d2c4e7
Fixed stype
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Co-authored-by: Wibowo Arindrarto <343998+bow@users.noreply.github.com >
2025-03-22 06:59:36 +01:00
0304aa8162
Removed support for user-provided --fmt
2025-03-22 06:59:36 +01:00
511648f992
Improved behaviour consistency for the tabular format handling
2025-03-22 06:59:36 +01:00
8663d68cc8
Update documentation
2025-03-22 06:59:36 +01:00
4f39ac9c3b
Changed overlapping hit fields (tabular fmt 2) to numeric type
2025-03-22 06:59:36 +01:00
1b186f2670
Use lambda function for inclusion conversion
2025-03-22 06:59:36 +01:00
38f0fed34a
Infer the tabular format from the header
2025-03-22 06:59:36 +01:00
c30a15fbae
Fix import style
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Co-authored-by: Wibowo Arindrarto <343998+bow@users.noreply.github.com >
2025-03-22 06:59:36 +01:00
4f6fb06665
Fix typo in documentation
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Co-authored-by: Wibowo Arindrarto <343998+bow@users.noreply.github.com >
2025-03-22 06:59:36 +01:00
ce0d90d133
Update NEWS.rst
2025-03-22 06:59:36 +01:00
00868673f6
Update docstring
2025-03-22 06:59:36 +01:00
