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66ad0a062e98f9964a7a4c67ad85291386ef3540
biopython/Tests
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mdehoon 66ad0a062e Extend the .counts method of an Alignment (#5011) 
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* replace precompiler #defines by inline functions

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* add tests

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* documentation

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* avoid stpcpy

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* 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

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* add test line 12287 test_pairwise_aligner.py

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* change dtype from int32 to "i"

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* fix how pointers are printed on Windows

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* fix id printing on pypy

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* 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
..
Abi
Remove executable flags and shebang (#2826)
2020-05-26 13:09:54 +01:00
Ace
Fix ambig typos
2021-08-31 10:41:38 +01:00
Affy
Parser for Affy CEL file version 4
2016-12-09 11:58:05 +00:00
Align
Align codonaligner (#4479)
2023-11-02 09:14:55 +00:00
BioSQL
Change quote style, update BioSQL file
2019-03-15 17:06:51 +00:00
Blast
add psiblast test (#4889)
2024-11-21 17:29:30 +09:00
Blat
bigBed big-endian (#4670)
2024-03-18 11:55:25 +09:00
BWA
Command line wrapper for BWA
2013-04-11 11:59:16 +01:00
CDAO
Converting a tree into a librdf model and then serializing is slow, requires a lot of memory, and is not feasible for large trees. Refactoring CDAOIO.Writer to write triples directly to file instead of using librdf. This also makes the API more similar to other Bio.Phylo modules.
2013-02-26 10:46:47 -05:00
Cellosaurus
Updated the cellosaurus tests:
2024-02-02 14:52:48 +00:00
Clustalw
Bio.Align parser/writer for A2M alignment files (#3966)
2022-06-30 23:29:58 +09:00
Cluster
cyano.txt sample file for Bio.Cluster documentation.
2017-05-26 12:48:43 +01:00
codonalign
Align codonaligner (#4479)
2023-11-02 09:14:55 +00:00
CodonUsage
Removing Mac OS hidden meta data file
2009-03-20 10:33:50 +00:00
Compass
Added Compass parsing code contributed by James Casbon.
2004-05-05 14:45:29 +00:00
EMBL
Ignore but warn on invalid EMBL DR lines (e.g. from RepBase)
2018-04-03 13:35:53 +01:00
Emboss
Support EMBOSS needle/water alignments to the reverse strand (#4142)
2022-10-24 01:24:31 +09:00
Entrez
Entrez parser fix for #3734 (#3738)
2021-09-18 06:34:34 +09:00
Enzymes
Updating these files with the latest version from ExPASy.
2009-03-25 01:57:13 +00:00
Exonerate
Add a parser for Exonerate cigar and vulgar output to Bio.Align (#3943)
2022-06-05 10:01:21 +09:00
ExtendedPhylip
Update tests for extended phylip format
2011-06-18 13:41:30 +01:00
Fasta
Don't allow comments at the beginning of Fasta files (#4780)
2024-09-06 02:44:40 +09:00
FSSP
----------------------------------------------------------------------
2001-06-07 17:43:53 +00:00
Gck
Test the GckIO module against an artificial sample.
2019-08-21 16:46:22 +01:00
GenBank
4775: raise warnings instead of errors if dashes are not in the expected places for dates
2024-12-31 18:44:31 +00:00
Geo
Remove executable flags and shebang (#2826)
2020-05-26 13:09:54 +01:00
GFA
Add SeqIO support for GFA files. (#4598)
2024-01-26 14:27:18 +00:00
GFF
Support files for test_GFF
2002-12-03 18:11:41 +00:00
Graphics
Remove overlooked .cvsignore files
2017-10-20 21:04:55 +01:00
HHsuite
Update hhr.py to consider incomplete confidence (#4344)
2023-07-02 00:51:06 +09:00
Hmmer
regex fix and preliminary test
2023-10-28 17:36:54 +02:00
Infernal
Changed overlapping hit fields (tabular fmt 2) to numeric type
2025-03-22 06:59:36 +01:00
IntelliGenetics
TAT_mase-nuc.txt is an unused identical copy of TAT_mase_nuc.txt (which is used in test_intelligenetics.py)
2008-07-04 13:54:37 +00:00
InterProScan
adding test, handling duplicate hits, handling dbxrefs, and calculating aln_span
2018-03-16 13:11:39 +01:00
KEGG
Remove executable flags and shebang (#2826)
2020-05-26 13:09:54 +01:00
MAF
Bigmaf writer (#4324)
2023-06-07 22:10:42 +09:00
Mauve
Add Mauve section to Bio.Align documentation (#4394)
2023-08-01 11:39:17 +09:00
Medline
PubMed file with multi-line MESH terms (MH lines).
2014-11-13 15:09:22 +09:00
MetaTool
Remove unused files.
2008-07-16 05:40:57 +00:00
motifs
Add support for reading GAP and WEIGHT parameters from Cluster Buster motif file.
2024-08-12 16:20:55 +01:00
msf
Sample problematic GCG MSF file from IPD-IMGT/HLA database
2019-11-05 17:02:32 +00:00
NBRF
Fix NBRF/PIR parsing so that is accepts files produced by Clustalw -- thanks to Ashleigh Smythe for the bug report.
2004-03-02 23:17:13 +00:00
NeuralNetwork
Remove overlooked .cvsignore files
2017-10-20 21:04:55 +01:00
NeXML
Adding basic unit tests for NeXML parser using example files from nexml.org.
2013-02-15 00:07:52 -05:00
Nexus
Added STANDARD datatype support to Nexus parser
2015-10-27 10:59:18 -07:00
Nib
support soft-masking in nib files (#2303)
2019-10-17 06:23:34 +09:00
NMR
Improve test coverage for module Bio.NMR
2019-06-25 12:05:25 +01:00
PAML
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
PDB
Started a_structure.cif with data_
2024-06-26 10:44:57 +09:00
Phd
Adding 454 and Solexa derived PHD files from the Consed author David Gordon (see also Bug 2865)
2009-07-02 09:25:20 +00:00
phenotype
Phenotype: smaller test files
2016-06-03 11:15:51 +01:00
Phylip
Add a parser for the PHYLIP format to Bio.Align. (#3745)
2021-09-23 08:46:50 +09:00
PhyloXML
Preserve root branch length in Phylo.TreeMixin.prune
2024-10-02 13:47:27 +01:00
PopGen
parse error tests and removal of old test files
2017-05-24 10:39:13 +01:00
PQR
PQR Parser (#2338)
2020-01-13 20:32:17 +09:00
Prosite
Adding part of the prosite.doc file, which is used in the Prodoc tests.
2009-03-16 01:04:31 +00:00
Quality
Testing indexing FASTQ file with zero length record (issue #269)
2013-12-12 16:42:55 +00:00
Rebase
*** empty log message ***
2000-09-07 02:28:23 +00:00
Registry
Improved parsing of GN in the SwissProt parser, take 2 (#4162)
2022-11-16 00:09:53 +09:00
Roche
Fixes an issue with how mode is detected from input streams for SFF file parsing. Closes #440
2014-12-10 15:08:16 -05:00
Saf
*** empty log message ***
2002-05-14 07:06:44 +00:00
SamBam
Fix tests for samtools 1.x support
2015-10-07 10:36:30 +01:00
SCOP
Cleaning up the SCOP tests
2010-01-25 20:13:26 +09:00
SeqXML
Support all versions of SeqXML
2024-01-22 09:11:55 +00:00
SnapGene
snapgene: Test parsing a primer.
2023-01-24 13:23:15 +00:00
Stockholm
allow to read and write nonstandard GC, GS, GR lines in Stockholm format (#4504)
2023-12-16 20:06:59 +00:00
SubsMat
15 Nov 00 Brad
2000-11-15 18:34:43 +00:00
SwissProt
Uniprotxml parse ligand tag (#5001)
2025-05-31 00:09:26 +01:00
TreeConstruction
Special cases for minimum alignment matrices in the NJ algorithm (#1891)
2019-02-12 19:09:21 +00:00
TwoBit
Add a parser for 2bit files to Bio.SeqIO (#3388)
2020-12-04 00:28:39 +09:00
UniGene
Updating the UniGene parser to be consistent with current UniGene files.
2009-04-24 12:03:45 +00:00
UniProt
UniProt GOA Added parser for GPI version 1.2 (#3290)
2021-03-23 09:28:27 +00:00
Xdna
Add test cases and sample files for the new parsers.
2019-08-21 16:46:22 +01:00
.coveragerc
Adding coverage configuration file.
2017-04-04 16:19:05 +01:00
biosql.ini.appveyor
Tests do not require postgresql CREATE DATABASE permissions
2017-10-27 14:11:39 +01:00
biosql.ini.sample
Tests do not require postgresql CREATE DATABASE permissions
2017-10-27 14:11:39 +01:00
common_BioSQL_online.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
common_BioSQL.py
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2024-06-26 15:31:39 +09:00
pairwise2_testCases.py
ruff format v0.3.1, black v24.2.0
2024-03-14 11:05:43 +00:00
requires_internet.py
Apply black to last non-formatted tests
2020-07-25 20:56:04 +01:00
run_tests.py
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2024-06-26 15:31:39 +09:00
search_tests_common.py
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2024-06-26 15:31:39 +09:00
seq_tests_common.py
remove deprecated .strand, .ref and .ref_db from Seqfeature (#4916)
2025-01-17 11:04:45 +00:00
test_Ace.py
Fix ambig typos
2021-08-31 10:41:38 +01:00
test_Affy.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_Align_a2m.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_Alignment.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_bed.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_bigbed.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_bigmaf.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_bigpsl.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_chain.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_clustal.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_codonalign.py
update (#4820)
2024-09-02 13:58:03 +09:00
test_Align_emboss.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_exonerate.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_fasta.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_hhr.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_maf.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_mauve.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_msf.py
Generalize the counts attribute of an Alignment (#4924)
2025-02-04 22:45:43 +09:00
test_Align_nexus.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_phylip.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_psl.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_sam.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_Align_stockholm.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_align_substitution_matrices.py
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2024-06-26 15:31:39 +09:00
test_Align_tabular.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_align.py
remove deprecated functionality from Bio.Align.AlignInfo (#4907)
2025-01-15 18:38:28 +00:00
test_AlignIO_ClustalIO.py
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2024-06-26 15:31:39 +09:00
test_AlignIO_convert.py
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2024-06-26 15:31:39 +09:00
test_AlignIO_EmbossIO.py
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2024-06-26 15:31:39 +09:00
test_AlignIO_FastaIO.py
reorder imports for SeqIO and AlignIO
2021-03-06 13:05:10 +00:00
test_AlignIO_MauveIO.py
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2024-06-26 15:31:39 +09:00
test_AlignIO_PhylipIO.py
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2024-06-26 15:31:39 +09:00
test_AlignIO.py
remove deprecated functionality from Bio.Align.AlignInfo (#4907)
2025-01-15 18:38:28 +00:00
test_bgzf.py
Fix byte mode detection on BgzfWriter
2024-05-12 22:15:20 +01:00
test_BioSQL_mysql_connector_online.py
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2024-06-26 15:31:39 +09:00
test_BioSQL_mysql_connector.py
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test_BioSQL_MySQLdb_online.py
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test_BioSQL_MySQLdb.py
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test_BioSQL_psycopg2_online.py
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2024-06-26 15:31:39 +09:00
test_BioSQL_psycopg2.py
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2024-06-26 15:31:39 +09:00
test_BioSQL_sqlite3_online.py
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2024-06-26 15:31:39 +09:00
test_BioSQL_sqlite3.py
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2024-06-26 15:31:39 +09:00
test_Blast_parser.py
update (#4964)
2025-03-02 09:19:37 +09:00
test_Blast_Record.py
New Blast parser and qblast (#4505)
2024-01-02 09:45:48 +09:00
test_CAPS.py
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2024-06-26 15:31:39 +09:00
test_cellosaurus.py
ran black on test_cellosaurus.py
2024-02-02 14:52:48 +00:00
test_Chi2.py
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2024-06-26 15:31:39 +09:00
test_Cluster.py
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2024-06-26 15:31:39 +09:00
test_codonalign.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_CodonTable.py
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2024-06-26 15:31:39 +09:00
test_ColorSpiral.py
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2024-06-26 15:31:39 +09:00
test_Compass.py
remove float (#4109)
2022-09-29 10:21:04 +09:00
test_Consensus.py
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2024-06-26 15:31:39 +09:00
test_EMBL_unittest.py
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test_EmbossPrimer.py
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2024-06-26 15:31:39 +09:00
test_Entrez_online.py
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2024-06-26 15:31:39 +09:00
test_Entrez_parser.py
Drop trailing whitespace in some docstrings
2025-07-11 10:26:05 +09:00
test_Entrez.py
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2024-06-26 15:31:39 +09:00
test_Enzyme.py
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2024-06-26 15:31:39 +09:00
test_ExPASy.py
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test_File.py
ruff format v0.3.1, black v24.2.0
2024-03-14 11:05:43 +00:00
test_GenBank.py
update (#4964)
2025-03-02 09:19:37 +09:00
test_GenomeDiagram.py
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2024-06-26 15:31:39 +09:00
test_geo.py
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2020-05-26 13:02:58 +01:00
test_GraphicsBitmaps.py
ruff fix PIE790 Unnecessary pass statement
2023-11-02 09:34:48 +00:00
test_GraphicsChromosome.py
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test_GraphicsDistribution.py
ruff format v0.3.1, black v24.2.0
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test_GraphicsGeneral.py
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test_HMMCasino.py
ruff format v0.3.1, black v24.2.0
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test_HMMGeneral.py
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test_KEGG_online.py
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test_KEGG.py
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test_KeyWList.py
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test_KGML_graphics_online.py
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2024-06-26 15:31:39 +09:00
test_KGML_graphics.py
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2024-06-26 15:31:39 +09:00
test_KGML_nographics.py
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2024-06-26 15:31:39 +09:00
test_MafIO_index.py
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test_Medline.py
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2020-05-26 15:03:09 +01:00
test_mmtf_online.py
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test_mmtf.py
Skip test_mmtf.py if mmtf is missing
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test_motifs_online.py
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2024-06-26 15:31:39 +09:00
test_motifs.py
remove deprecated code from Bio.motifs (#4915)
2025-01-17 10:48:06 +09:00
test_NCBI_qblast.py
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2024-06-26 15:31:39 +09:00
test_NCBIXML.py
Fix assertAlmostEqual calls in tests, when checking for very small numbers in scientific notation. (#4770)
2024-07-20 08:48:52 +09:00
test_Nexus.py
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2024-06-26 15:31:39 +09:00
test_NMR.py
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test_pairwise2_no_C.py
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2024-06-26 15:31:39 +09:00
test_pairwise2.py
Apply black styling to test_pairwise*.py
2020-07-24 10:08:06 +01:00
test_pairwise_aligner.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_pairwise_alignment_map.py
Extend the .counts method of an Alignment (#5011)
2025-07-11 14:40:07 +09:00
test_PAML_baseml.py
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test_PAML_codeml.py
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test_PAML_tools.py
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2024-06-26 15:31:39 +09:00
test_PAML_yn00.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_Pathway.py
use assertEqual
2020-11-27 12:49:13 +00:00
test_PDB_alphafold_db.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_binary_cif.py
Add BinaryCIF parser (#4707)
2024-06-11 04:35:46 +01:00
test_PDB_CEAligner.py
Fix QCPSuperimposer bug (#5005)
2025-06-09 14:19:55 -07:00
test_PDB_Dice.py
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2024-06-26 15:31:39 +09:00
test_PDB_Disordered.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_DSSP.py
Standardize on 'import numpy as np' throughout the codebase
2024-06-27 16:13:14 +09:00
test_PDB_Exposure.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_FragmentMapper.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_internal_coords.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_KDTree.py
remove unused variable (#4934)
2025-02-13 12:11:31 +09:00
test_PDB_MMCIF2Dict.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_MMCIFIO.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_MMCIFParser.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_NACCESS.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_parse_pdb_header.py
Standardize on 'import numpy as np' throughout the codebase
2024-06-27 16:13:14 +09:00
test_PDB_PDBIO.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_PDBList.py
improve coverage of tests
2025-05-29 10:00:50 +01:00
test_PDB_PDBMLParser.py
Tweak black settings as dropped Python 3.8
2024-06-26 15:11:06 +09:00
test_PDB_PDBParser.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_Polypeptide.py
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2024-06-26 15:31:39 +09:00
test_PDB_PSEA.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_QCPSuperimposer.py
Fix QCPSuperimposer bug (#5005)
2025-06-09 14:19:55 -07:00
test_PDB_ResidueDepth.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_SASA.py
Native implementation of Shrake-Rupley algorithm for atomic solvent accessible surface areas. (#3274)
2020-09-17 16:42:42 -07:00
test_PDB_Selection.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_PDB_SMCRA.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_StructureAlignment.py
Add automatic alignment generation to StructureAlignment
2025-07-03 09:33:06 -07:00
test_PDB_Superimposer.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_PDB_vectors.py
Fixing black formatting
2024-09-03 12:30:49 +01:00
test_Phd.py
str
2020-11-27 23:16:07 +00:00
test_phenotype_fit.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_phenotype.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_Phylo_CDAO.py
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2024-06-26 15:31:39 +09:00
test_Phylo_igraph.py
Tweak f-string to avoid flake8 E226
2025-01-10 14:54:05 +00:00
test_Phylo_matplotlib.py
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2024-06-26 15:31:39 +09:00
test_Phylo_networkx.py
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2024-06-26 15:31:39 +09:00
test_Phylo_NeXML.py
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2024-06-26 15:31:39 +09:00
test_Phylo.py
bug fix handle NoneType when writing to newick with branch_length_only=True
2025-01-03 21:12:25 +00:00
test_PhyloXML.py
Preserve root branch length in Phylo.TreeMixin.prune
2024-10-02 13:47:27 +01:00
test_PopGen_GenePop_nodepend.py
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2024-06-26 15:31:39 +09:00
test_PQR.py
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2024-06-26 15:31:39 +09:00
test_prodoc.py
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2024-06-26 15:31:39 +09:00
test_prosite.py
remove old Jython hacks (#3312)
2020-10-18 10:30:05 +09:00
test_ProtParam.py
Deprecate ProteinAnalysis.get_amino_acids_percent() and create ProteinAnalysis.amino_acids_percent (#4783)
2024-07-31 14:48:47 +09:00
test_RCSBFormats.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_Restriction.py
fix test
2025-02-19 21:49:09 +00:00
test_SCOP_Astral.py
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2024-06-26 15:31:39 +09:00
test_SCOP_Cla.py
Apply black style to test_SCOP* files, version 19.10b0.
2020-02-17 09:23:06 +00:00
test_SCOP_Des.py
Apply black style to test_SCOP* files, version 19.10b0.
2020-02-17 09:23:06 +00:00
test_SCOP_Dom.py
use with in SCOP tests (#2705)
2020-02-13 11:01:35 +09:00
test_SCOP_Hie.py
Apply black style to test_SCOP* files, version 19.10b0.
2020-02-17 09:23:06 +00:00
test_SCOP_Raf.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SCOP_Residues.py
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2024-06-26 15:31:39 +09:00
test_SCOP_Scop.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_blast_tab_index.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_blast_tab.py
Automatically remove redundant commas
2021-08-27 13:42:55 +01:00
test_SearchIO_blast_xml_index.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_blast_xml.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_blat_psl_index.py
black v23.9.1
2023-10-05 08:47:54 +01:00
test_SearchIO_blat_psl.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SearchIO_exonerate_text_index.py
black v23.9.1
2023-10-05 08:47:54 +01:00
test_SearchIO_exonerate_vulgar_index.py
black v23.9.1
2023-10-05 08:47:54 +01:00
test_SearchIO_exonerate.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SearchIO_fasta_m10_index.py
black v23.9.1
2023-10-05 08:47:54 +01:00
test_SearchIO_fasta_m10.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hhsuite2_text.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer2_text_index.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer2_text.py
Fix assertAlmostEqual calls in tests, when checking for very small numbers in scientific notation. (#4770)
2024-07-20 08:48:52 +09:00
test_SearchIO_hmmer3_domtab_index.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer3_domtab.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer3_tab_index.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer3_tab.py
Added Infernal tabular format parser and tests
2025-03-22 06:59:36 +01:00
test_SearchIO_hmmer3_text_index.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SearchIO_hmmer3_text.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SearchIO_infernal_tab_index.py
Removed support for user-provided --fmt
2025-03-22 06:59:36 +01:00
test_SearchIO_infernal_tab.py
Removed support for user-provided --fmt
2025-03-22 06:59:36 +01:00
test_SearchIO_infernal_text_index.py
Fixed issues in text format testing
2025-03-22 06:59:36 +01:00
test_SearchIO_infernal_text.py
Fixed docstring
2025-03-22 06:59:36 +01:00
test_SearchIO_interproscan_xml.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_model.py
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2024-06-26 15:31:39 +09:00
test_SearchIO_write.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_Seq_objs.py
Don't allow comments at the beginning of Fasta files (#4780)
2024-09-06 02:44:40 +09:00
test_seq.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_SeqFeature.py
test: add test to check if Location.fromstring is static
2025-03-28 14:47:27 +00:00
test_SeqIO_AbiIO.py
avoid yield in SeqIO AbiIO iterator (#4804)
2024-08-27 08:50:53 +02:00
test_SeqIO_FastaIO.py
Don't allow comments at the beginning of Fasta files (#4780)
2024-09-06 02:44:40 +09:00
test_SeqIO_features.py
Locale independent date serialization (#4977)
2025-03-21 15:39:57 +00:00
test_SeqIO_Gck.py
avoid using yield in Bio.SeqIO GckIO (#4805)
2024-08-28 20:27:29 +09:00
test_SeqIO_Gfa.py
Ran black v24.2.0
2024-03-14 11:05:43 +00:00
test_SeqIO_index.py
use SequenceIterator & binary mode for Bio.SeqIO Uniprot XML (#4833)
2024-09-17 11:24:04 +01:00
test_SeqIO_Insdc.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO_NibIO.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO_online.py
ruff format v0.3.1, black v24.2.0
2024-03-14 11:05:43 +00:00
test_SeqIO_PdbIO.py
Standardizing on import numpy as np
2024-09-03 12:30:49 +01:00
test_SeqIO_QualityIO.py
Bio.SeqIO QualityIO subclass (#4838)
2024-09-17 11:28:13 +01:00
test_SeqIO_SeqXML.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO_SffIO.py
Avoid yield in Bio.SeqIO SffIO (#4813)
2024-09-05 16:40:55 +01:00
test_SeqIO_SnapGene.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO_TwoBitIO.py
Ran black v24.2.0
2024-03-14 11:05:43 +00:00
test_SeqIO_UniprotIO.py
Uniprotxml parse ligand tag (#5001)
2025-05-31 00:09:26 +01:00
test_SeqIO_write.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO_Xdna.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SeqIO.py
Changed several parsers avoid using next.
2025-02-24 14:16:22 +00:00
test_SeqRecord.py
Retain letter_annotation as None in upper and lower methods (#4966)
2025-03-10 14:01:25 +00:00
test_SeqUtils.py
update (#4964)
2025-03-02 09:19:37 +09:00
test_SVDSuperimposer.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_SwissProt.py
ruff format v0.3.1, black v24.2.0
2024-03-14 11:05:43 +00:00
test_TogoWS.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_translate.py
ruff format v0.3.1, black v24.2.0
2024-03-14 11:05:43 +00:00
test_TreeConstruction.py
Fix calculating height of clades when building UPGMA tree version 2 (#3951)
2024-10-16 21:07:35 -07:00
test_Tutorial.py
Always use ELLIPSIS option in test_Tutorial.py
2025-02-28 07:51:11 +00:00
test_UniGene.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00
test_UniProt_GOA.py
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2024-06-26 15:31:39 +09:00
test_UniProt.py
Apply isort (forcing single lines, not sorting by type) via ruff
2024-06-26 15:31:39 +09:00