GitHub / biopython/biopython / commits
Official git repository for Biopython (originally converted from CVS)
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| 8b4d499f |
Handle empty QUAL title line without raising IndexError (#5283)
Co-authored-by: Peter Cock <p****k@g****m> |
eeshsaxena <1****a@u****m>
Committed by: GitHub <n****y@g****m> |
9 days ago | |
| 62f83712 | pairwise2 bugfix (#5289) |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
10 days ago | |
| 98d5f570 | Add an example to Bio.codonalign docstring using the newer CodonAligner in Bi... |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
11 days ago | |
| 607b24da | Fixed alphabetical ordering of name addition |
Rohit Kattimani <8****i@u****m>
Committed by: Peter Cock <p****k@g****m> |
11 days ago | |
| 3ad5f920 | Add Rohit Kattimani to contributors list |
Rohit Kattimani <8****i@u****m>
Committed by: Peter Cock <p****k@g****m> |
11 days ago | |
| a9f0274b | DOCS: fix stale param name in Bio.Entrez._open docstring |
Rohit Kattimani <8****i@u****m>
Committed by: Peter Cock <p****k@g****m> |
12 days ago | |
| c9489604 | Post Biopython 1.88 release version bump | Peter J. A. Cock <p****k@g****m> | 23 days ago | |
| d7e4b8b1 | Call this Biopython 1.88 | Peter J. A. Cock <p****k@g****m> | 23 days ago | |
| 611b13dd | Update CircleCI to use latest CodeCov orb 6.0.0 |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
24 days ago | |
| 98d0b3cd | Test on Python 3.15 release candidate (GitHub Action) |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
24 days ago | |
| 4bfd123f | Fix GenBank Record serialization of WGS ranges (#5275) |
Marcus Campbell <2****l@u****m>
Committed by: GitHub <n****y@g****m> |
24 days ago | |
| 98059a63 | Add supported Python versions; sort recent contributors |
Peter Cock <p****k@g****m>
Committed by: GitHub <n****y@g****m> |
24 days ago | |
| 3d79e1d4 | Enable ruff S307 to spot using built-in eval() function | Peter J. A. Cock <p****k@g****m> | 24 days ago | |
| 0e4b36f6 | Use globals() dict to lookup class by name rather than eval function | Peter J. A. Cock <p****k@g****m> | 24 days ago | |
| 23442543 | Use tuple rather than list-as-string in Nexus consensus method. | Peter J. A. Cock <p****k@g****m> | 24 days ago | |
| 1d125360 | Rewrite to avoid using eval in SearchIO HSP init | Peter J. A. Cock <p****k@g****m> | 24 days ago | |
| 0fb1129f | Avoid eval in Nexus parser for NTAX and NCHAR | Peter J. A. Cock <p****k@g****m> | 24 days ago | |
| dafeffb1 | Add missing docstring to TreeElement.__str__ (fixes D105) |
mystical-illusion <m****9@g****m>
Committed by: Peter Cock <p****k@g****m> |
about 1 month ago | |
| 80401d49 |
Don't check the written data byte-by-bute, as the written data may differ bet...
Co-authored-by: Michiel de Hoon <m****n@t****p> |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
about 1 month ago | |
| e136be72 | fix: reshape cel and vector arrays |
stanbot8 <s****8@g****m>
Committed by: Peter Cock <p****k@g****m> |
about 1 month ago | |
| 5d6fe8d2 |
Bump actions/checkout from 6 to 7
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
about 1 month ago | |
| 456c569a |
Bump actions/setup-python from 6 to 7
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
about 1 month ago | |
| dcaa19be |
[pre-commit.ci] autoupdate (#5189)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m>, Peter Cock <p****k@g****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
about 2 months ago | |
| 71ab98b8 | Fix typo |
Brandon Seah <k****h@u****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| b55488a0 | Mark these attributes as array or None for mypy |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| 14550ed1 | Avoid changing type of msa_coordinates variable for mypy |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| c6244d02 | Update mypy ignore-imports for PDB binary CIF work |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| 484c1c29 | Guard Tree.collapse() against children without branch lengths |
Liza <2****z@u****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| 158b2f2a | Preserve small Newick branch lengths |
Joey Dufourd <j****d@g****m>
Committed by: Peter Cock <p****k@g****m> |
2 months ago | |
| ffffe49f | Set expectations on the issue tags (#5229) |
Peter Cock <p****k@g****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 47a6ebeb | Add missing magic method docstrings in SeqIO interfaces (#5230) |
Ishita Goswami <7****s@u****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 8ef75308 | Use curl for miniconda download with retry on AppVeyor (#5223) |
generatedscript <6****L@u****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 175f1b2b | Fix AlphaFoldDB path test on Windows (#5220) |
generatedscript <6****L@u****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| e4470607 | Cope with invalid strand in GenBank LOCUS line |
CameronCat <c****n@y****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 6fc0e887 | Switch some percent formatting to f-strings with pyupgrade v3.19.1 |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
3 months ago | |
| d00e5364 | Fix remaining flake8-docstrings D400, D401 and D402 issues. |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
3 months ago | |
| 95ff2cbb | Add Laura Piñero Roig to CONTRIB.rst and NEWS.rst |
laurapiro17 <1****7@u****m>
Committed by: Peter Cock <p****k@g****m> |
3 months ago | |
| 213e5ba8 | Add docstrings to remaining SeqIO iterator __next__ methods |
laurapiro17 <1****7@u****m>
Committed by: Peter Cock <p****k@g****m> |
3 months ago | |
| 0271a9fc | Update docstrings to refer to the function being described |
John Marshall <j****l@h****m>
Committed by: Peter Cock <p****k@g****m> |
4 months ago | |
| 1043c225 | Add docstrings to SeqIO iterator __next__ methods |
laurapiro17 <1****7@u****m>
Committed by: Peter Cock <p****k@g****m> |
4 months ago | |
| c7f25060 | Add docstrings to FastaIO iterator __next__ methods |
laurapiro17 <1****7@u****m>
Committed by: Peter Cock <p****k@g****m> |
4 months ago | |
| 8dcaccb6 | Update chapter_pairwise.rst |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 324a5ff3 | Drop Jython code from BioSQL tests too |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
5 months ago | |
| ef353228 | Remove Jython specific code in BioSQL |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
5 months ago | |
| 52054714 | Fix Bio.Pathway.Interaction.__init__ and many typos (#5188) |
Suyadi <1****i@u****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 5b3faaf1 | Fix issue with GenBank debug print (#5190) |
Peter Cock <p****k@g****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| d59ab34b | Declare Python 3.10 support deprecated. |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
5 months ago | |
| e0d5ef82 | Remove stray file | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| fc3e2ca2 | Post Biopython 1.87 release version bump | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| 1ab53fe9 | Automatically update the docs symlink for new releases - Take 7 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| b1d8f383 | Automatically update the docs symlink for new releases - Take 6 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| cf6bafda | Automatically update the docs symlink for new releases - Take 5 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| 2a899d94 | Automatically update the docs symlink for new releases - Take 4 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| aef1f21c | Automatically update the docs symlink for new releases - Take 3 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| 817cf045 | Automatically update the docs symlink for new releases - retry | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| 94460272 | Automatically update the docs symlink for new releases | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| 6f611a2d |
Bump codecov/codecov-action from 5 to 6
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
5 months ago | |
| 7a9c76cc | Biopython 1.87 | Peter J. A. Cock <p****k@g****m> | 5 months ago | |
| d76a5581 |
Bump geekyeggo/delete-artifact from 5 to 6
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
6 months ago | |
| a25e8c78 | Stress importance of the PR template | Peter Cock <p****k@g****m> | 6 months ago | |
| 736c96f3 |
Fix `Entrez.Parser.DataHandler` URL security check continuity (related to #51...
Co-authored-by: Peter Cock <p****k@g****m>, Peter Cock <p****k@g****m>, Peter Cock <p****k@g****m> |
Sebastian Pipping <s****n@p****g>
Committed by: GitHub <n****y@g****m> |
6 months ago | |
| ead54d7b | Using np.sin or np.cos was generating return values which were not plain float. |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
6 months ago | |
| 471a866f | Added PERMISSIVE argument to MMCIFParser as in PDBParser. (#5134) |
Pierre <1****e@u****m>
Committed by: GitHub <n****y@g****m> |
6 months ago | |
| 322cd902 | closes #5162 |
Manuel Lera-Ramirez <m****4@g****m>
Committed by: Peter Cock <p****k@g****m> |
6 months ago | |
| a6000cd4 | Fix vector test for NumPy 2.4 |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| 96188bc6 | Drop older commented code lines in PDB vector code |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| 4a209ac2 | Use more typical double indexing with numpy arrays |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| f4d8ae45 | Correctly clean up files generated by the Phylo tutorial. |
alex <a****0@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| f0973f67 | Fix unstable doctest (key order random) |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| 6807e7e0 | Migrate to pyproject.toml |
alex <a****0@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| 6568a976 | Avoid http links in Bio.Entrez (#5114) |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| b4a0d811 | Remove code that was deprecated in 1.85 (#5144) |
mdehoon <m****n@y****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| f948a55b | Add test for run_psea using a temporary directory |
Kiran Dharmar <k****7@g****m>
Committed by: Peter Cock <p****k@g****m> |
7 months ago | |
| 0d829a8d | Replace print statements with warnings/stderr in NCBIXML (#5140) |
chani <7****y@u****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| 156e6b6c | Format Bio/PDB/PSEA.py with black |
Kiran Dharmar <k****7@g****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| d9529227 | Replace Union and Optional with Python 3.10+ typing |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| c489daaf | Stay on mypy 1.16.1 and older black |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| b5bbbfc8 | Ignore B905 in ruff command line too | Peter Cock <p****k@g****m> | 8 months ago | |
| 22a672bf | Ignore B905 | Peter Cock <p****k@g****m> | 8 months ago | |
| e6ddb858 | Silence PDBConstructionWarning in test_PDB_StructureAlignment |
csbiy <k****6@n****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| b8627d61 | Run PSEA in a temporary directory to avoid leftover files |
Kiran Dharmar <k****7@g****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| d7c0fe32 | [pre-commit.ci] autoupdate |
pre-commit-ci[bot] <6****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
8 months ago | |
| 54a8eda8 | Issue 5122 bug fix (#5126) |
Ben Oppenheimer <4****p@u****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 22aa877f |
DOC: Clarify Visual Studio Build Tools workload requirement for Windows (#5118)
Co-authored-by: Peter Cock <p****k@g****m> |
suyash469 <s****5@g****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 845455ce |
Bump actions/cache from 4 to 5
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| 10985991 | Fix parsing of snapgene features with linebreaks in qualifier values (#5117) |
Manuel Lera-Ramirez <m****4@g****m>
Committed by: GitHub <n****y@g****m> |
9 months ago | |
| fb2f3f0d | use an existing pdb file for the test |
Tim Dennis <t****n@g****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| 7f00d026 | README.rst: Mass-replace http:// links with https:// |
Sebastian Pipping <s****n@p****g>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| f4b277ee | Fix typo/bug in biopython.Bio.PDB.vectors vector_to_axis (#5045) |
Mikel Martinez Goikoetxea <4****G@u****m>
Committed by: GitHub <n****y@g****m> |
9 months ago | |
| 59130e06 | Thank Ziyan Rao in NEWS.rst and CONTRIB.rst (#5111) |
Peter Cock <p****k@g****m>
Committed by: GitHub <n****y@g****m> |
9 months ago | |
| 90be93a3 | Remove Python 3.8 support leftovers |
Sebastian Pipping <s****n@p****g>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| d07dde90 |
Bump actions/checkout from 5 to 6
Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| b936f628 | Make pre-commit CI more helpful |
Sebastian Pipping <s****n@p****g>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| 6242fcb0 | test for fixed format string |
Tim Dennis <t****n@g****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| 19788bf9 | add missing space in the format string |
Tim Dennis <t****n@g****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| b2701d40 | fix error message raised when the target is not found in the tree |
Tim Dennis <t****n@g****m>
Committed by: Peter Cock <p****k@g****m> |
9 months ago | |
| fe756122 | Update ScanProsite for new XML format from ScanProsite API (#5099) |
timjden <6****n@u****m>
Committed by: GitHub <n****y@g****m> |
9 months ago | |
| 4b6b4074 | Bump year in license (overdue) |
Peter Cock <p****k@g****m>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| f3690dae | Remove reference to PDF Tutorial |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
10 months ago | |
| 5c4b009a | Update FAQ on latest version of the docs |
Peter J. A. Cock <p****k@g****m>
Committed by: Peter Cock <p****k@g****m> |
10 months ago |