de0bb21fb3
Apply isort (forcing single lines, not sorting by type) via ruff
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$ ruff check --fix --select=I \
--config=lint.isort.force-single-line=true \
--config=lint.isort.order-by-type=false \
BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py
Using ruff version 0.4.10
2024-06-26 15:31:39 +09:00
a47460e59a
Misc spellings flagged by codespell ( #4716 )
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Note the childs to children changes in Bio/Phylo/Consensus.py
included fixing internal variable names only.
Not applying all the catergories ==> categories fixes
to the (deprecated) EMBOSS wrappers as some would be
functional changes.
Also no more LaTeX files (for spell checking)
2024-05-01 14:21:12 +01:00
57056bbfc4
ruff format v0.3.1, black v24.2.0
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Reverted unwanted changes (mostly arrays in tests, but also
some whitespace in doctests).
Remaining changes are standardising spacing between module
docstring and imports, and lower-case \x<hex> in strings.
2024-03-14 11:05:43 +00:00
0938871295
black v23.9.1
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Had to tweak four conflicts with D202
2023-10-05 08:47:54 +01:00
21eb40450d
Doc exonerate ( #4400 )
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* update
* update
2023-08-04 14:40:17 +09:00
1add58c797
Bigbed writer ( #4311 )
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* update
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* Fix alignment iterator length calculation
* Update test_Align_bed.py
* Update bed.py
* Update test_Align_bed.py
---------
Co-authored-by: Michiel de Hoon <mdehoon@MichielMacBook.local >
Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp >
Co-authored-by: Michiel de Hoon <mdehoon@android-549ef7acc3977720.localdomain >
2023-05-22 04:29:31 +09:00
f3a6b43992
Standardize on import numpy as np ( #4259 )
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* Standardize on import numpy as np
* adding name to NEWS.rst and CONTRIB.rst
* NumPy is how the project capitalises their name.
Largely addresses issue #4238
2023-03-23 09:37:07 +00:00
b09394edc5
print alignments when the sequence is unknown ( #4206 )
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* test_Align_a2m
* clustal
* fasta
* msf
* nexus
* phylip
* stockholm
* stockholm
* maf
* emboss
* hhr
* mauve
* bigmaf
* psl
* bed
* sam
* update
* _get_row
* column
* slice
* tests
* shape
* update
* aligned
* update
* indices
* substitutions
* cleanup
* tests
* tests
* tabular
* update
* update
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* substitutions
* cleanup
2022-12-30 23:37:03 +09:00
bcd471318f
Enable Seq and plain string objects for Bio.Align writers ( #4187 )
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* update
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* update
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2022-12-04 16:47:22 +09:00
518c4be6ae
Alignment format ( #4082 )
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* a2m
* bed
* clustal
* exonerate
* fasta
* maf
* mauve
* nexus
* phylip_psl
* sam
* stockholm
* finished
2022-09-18 20:12:00 +09:00
95393f67a3
add parse, read, write functions to Bio.Align ( #4065 )
2022-08-31 09:40:24 +09:00
222fbc4534
Clean up Bio.Align.interfaces ( #3977 )
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* update
* black
* update
2022-07-10 12:04:03 +09:00
2cd7f87040
In Bio.Align, use metadata consistently ( #3974 )
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* use metadata consistently
* black
2022-07-07 22:09:12 +09:00
8d26ba76e4
Add a parser for HHsuite output files ( #3973 )
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* update
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* updare
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* black
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* update
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2022-07-07 11:31:42 +09:00
918dda48ab
Add a parser for Exonerate cigar and vulgar output to Bio.Align ( #3943 )
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* starting
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* bugfix
* black
* flake
* black
* bow suggestions
2022-06-05 10:01:21 +09:00
