[med-svn] [Git][med-team/python-biopython][upstream] New upstream version 1.86+dfsg

Wed Oct 29 20:02:54 GMT 2025

Étienne Mollier pushed to branch upstream at Debian Med / python-biopython

Commits:
e7f679d0 by Étienne Mollier at 2025-10-29T19:58:34+01:00
New upstream version 1.86+dfsg
- - - - -

266 changed files:

- .appveyor.yml
- .circleci/config.yml
- .circleci/requirements-sphinx.txt
- .github/workflows/ci.yml
- .gitignore
- .pre-commit-config.yaml
- Bio/Align/AlignInfo.py
- − Bio/Align/Applications/_ClustalOmega.py
- − Bio/Align/Applications/_Clustalw.py
- − Bio/Align/Applications/_Dialign.py
- − Bio/Align/Applications/_MSAProbs.py
- − Bio/Align/Applications/_Mafft.py
- − Bio/Align/Applications/_Muscle.py
- − Bio/Align/Applications/_Prank.py
- − Bio/Align/Applications/_Probcons.py
- − Bio/Align/Applications/_TCoffee.py
- − Bio/Align/Applications/__init__.py
- Bio/Align/__init__.py
- Bio/Align/_aligncore.c
- + Bio/Align/_alignmentcounts.c
- Bio/Align/_codonaligner.c
- Bio/Align/_pairwisealigner.c
- + Bio/Align/_pairwisealigner.h
- Bio/Align/bed.py
- Bio/Align/bigbed.py
- Bio/Align/bigmaf.py
- Bio/Align/bigpsl.py
- Bio/Align/chain.py
- Bio/Align/clustal.py
- Bio/Align/emboss.py
- Bio/Align/exonerate.py
- Bio/Align/hhr.py
- Bio/Align/interfaces.py
- Bio/Align/maf.py
- Bio/Align/msf.py
- Bio/Align/nexus.py
- Bio/Align/phylip.py
- Bio/Align/psl.py
- Bio/Align/sam.py
- Bio/Align/substitution_matrices/__init__.py
- + Bio/Align/substitution_matrices/_arraycore.c
- + Bio/Align/substitution_matrices/_arraycore.h
- Bio/Align/substitution_matrices/data/BLASTN
- Bio/Align/substitution_matrices/data/BLASTP
- Bio/Align/tabular.py
- Bio/AlignIO/MafIO.py
- Bio/AlignIO/NexusIO.py
- − Bio/Application/__init__.py
- − Bio/Blast/Applications.py
- Bio/Blast/_parser.py
- Bio/Cluster/clustermodule.c
- Bio/Data/CodonTable.py
- − Bio/Emboss/Applications.py
- Bio/GenBank/__init__.py
- Bio/Graphics/BasicChromosome.py
- Bio/Graphics/ColorSpiral.py
- − Bio/HMM/DynamicProgramming.py
- − Bio/HMM/MarkovModel.py
- − Bio/HMM/Trainer.py
- − Bio/HMM/Utilities.py
- − Bio/LogisticRegression.py
- − Bio/MarkovModel.py
- − Bio/MaxEntropy.py
- − Bio/NaiveBayes.py
- Bio/Nexus/Nexus.py
- Bio/Nexus/Nodes.py
- Bio/Nexus/Trees.py
- Bio/PDB/Atom.py
- Bio/PDB/Chain.py
- Bio/PDB/Entity.py
- Bio/PDB/PDBExceptions.py
- Bio/PDB/PDBIO.py
- Bio/PDB/PDBList.py
- Bio/PDB/PDBMLParser.py
- Bio/PDB/PICIO.py
- Bio/PDB/SCADIO.py
- Bio/PDB/StructureAlignment.py
- Bio/PDB/StructureBuilder.py
- Bio/PDB/alphafold_db.py
- Bio/PDB/bcifhelpermodule.c
- Bio/PDB/binary_cif.py
- Bio/PDB/ccealignmodule.c
- Bio/PDB/ic_rebuild.py
- Bio/PDB/internal_coords.py
- Bio/PDB/kdtrees.c
- Bio/PDB/qcprot.py
- Bio/PDB/vectors.py
- − Bio/Phylo/Applications/_Fasttree.py
- − Bio/Phylo/Applications/_Phyml.py
- − Bio/Phylo/Applications/_Raxml.py
- − Bio/Phylo/Applications/__init__.py
- Bio/Phylo/Consensus.py
- Bio/Phylo/PAML/_paml.py
- Bio/Phylo/PAML/baseml.py
- Bio/Phylo/PAML/codeml.py
- Bio/Phylo/PAML/yn00.py
- − Bio/PopGen/GenePop/Controller.py
- − Bio/PopGen/GenePop/EasyController.py
- Bio/Restriction/Restriction.py
- Bio/SCOP/__init__.py
- Bio/SearchIO/ExonerateIO/_base.py
- + Bio/SearchIO/InfernalIO/__init__.py
- + Bio/SearchIO/InfernalIO/_base.py
- + Bio/SearchIO/InfernalIO/infernal_tab.py
- + Bio/SearchIO/InfernalIO/infernal_text.py
- Bio/SearchIO/__init__.py
- Bio/SearchIO/_model/_base.py
- Bio/Seq.py
- Bio/SeqFeature.py
- Bio/SeqIO/FastaIO.py
- Bio/SeqIO/InsdcIO.py
- Bio/SeqIO/Interfaces.py
- Bio/SeqIO/PirIO.py
- Bio/SeqIO/QualityIO.py
- Bio/SeqIO/SnapGeneIO.py
- Bio/SeqIO/TabIO.py
- Bio/SeqIO/UniprotIO.py
- Bio/SeqIO/__init__.py
- Bio/SeqRecord.py
- Bio/SeqUtils/ProtParam.py
- − Bio/Sequencing/Applications/_Novoalign.py
- − Bio/Sequencing/Applications/__init__.py
- − Bio/Sequencing/Applications/_bwa.py
- − Bio/Sequencing/Applications/_samtools.py
- Bio/TogoWS/__init__.py
- Bio/UniProt/__init__.py
- Bio/__init__.py
- Bio/_utils.py
- − Bio/kNN.py
- Bio/motifs/__init__.py
- − Bio/motifs/applications/__init__.py
- − Bio/motifs/applications/_xxmotif.py
- Bio/motifs/clusterbuster.py
- Bio/motifs/matrix.py
- BioSQL/BioSeqDatabase.py
- CONTRIB.rst
- DEPRECATED.rst
- Doc/README.rst
- Doc/Tutorial/chapter_align.rst
- Doc/Tutorial/chapter_bibliography.rst
- Doc/Tutorial/chapter_blast.rst
- Doc/Tutorial/chapter_cookbook.rst
- Doc/Tutorial/chapter_msa.rst
- Doc/Tutorial/chapter_pairwise.rst
- Doc/Tutorial/chapter_pairwise2.rst
- Doc/Tutorial/chapter_pdb.rst
- Doc/Tutorial/chapter_phylo.rst
- Doc/Tutorial/chapter_seq_objects.rst
- Doc/Tutorial/chapter_seqio.rst
- Doc/conf.py
- Doc/doc.rst
- + Doc/images/phylo-color-iplotx.png
- NEWS.rst
- README.rst
- − Tests/BWA/HNSCC1_1_truncated.fastq
- − Tests/BWA/HNSCC1_2_truncated.fastq
- − Tests/BWA/human_g1k_v37_truncated.fasta
- + Tests/Infernal/cmscan_115_IRES_5S_U2_Yeast.tbl
- + Tests/Infernal/cmscan_115_IRES_5S_U2_Yeast.txt
- + Tests/Infernal/cmscan_115_IRES_5S_U2_Yeast_fmt_2.tbl
- + Tests/Infernal/cmscan_115_IRES_5S_U2_Yeast_fmt_3.tbl
- + Tests/Infernal/cmscan_115_SSU_clan-fmt_2.tbl
- + Tests/Infernal/cmsearch_114_5S_Yeast.tbl
- + Tests/Infernal/cmsearch_114_5S_Yeast.txt
- + Tests/Infernal/cmsearch_114_5S_Yeast_noali.txt
- + Tests/Infernal/cmsearch_114_IRES_5S_U2_Yeast.txt
- + Tests/Infernal/cmsearch_114_IRES_Yeast.tbl
- + Tests/Infernal/cmsearch_114_IRES_Yeast.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast.tbl
- + Tests/Infernal/cmsearch_114_U2_Yeast.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_full.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_full_noali.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_full_shuffled.tbl
- + Tests/Infernal/cmsearch_114_U2_Yeast_full_shuffled.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_hmmonly.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_noali.txt
- + Tests/Infernal/cmsearch_114_U2_Yeast_notextw.txt
- + Tests/SnapGene/sample-hybridization-params.dna
- + Tests/SwissProt/P62330.xml
- + Tests/SwissProt/multiligand.xml
- Tests/common_BioSQL.py
- Tests/common_BioSQL_online.py
- Tests/run_tests.py
- Tests/seq_tests_common.py
- Tests/test_AlignIO.py
- − Tests/test_AlignInfo.py
- Tests/test_Align_Alignment.py
- Tests/test_Align_a2m.py
- Tests/test_Align_bed.py
- Tests/test_Align_bigbed.py
- Tests/test_Align_bigmaf.py
- Tests/test_Align_bigpsl.py
- Tests/test_Align_chain.py
- Tests/test_Align_clustal.py
- Tests/test_Align_emboss.py
- Tests/test_Align_exonerate.py
- Tests/test_Align_fasta.py
- + Tests/test_Align_format_matrix.py
- Tests/test_Align_hhr.py
- Tests/test_Align_maf.py
- Tests/test_Align_mauve.py
- Tests/test_Align_msf.py
- Tests/test_Align_nexus.py
- Tests/test_Align_phylip.py
- Tests/test_Align_psl.py
- Tests/test_Align_sam.py
- Tests/test_Align_stockholm.py
- Tests/test_Align_tabular.py
- − Tests/test_Application.py
- − Tests/test_BWA_tool.py
- Tests/test_Blast_parser.py
- − Tests/test_ClustalOmega_tool.py
- − Tests/test_Clustalw_tool.py
- − Tests/test_Dialign_tool.py
- − Tests/test_Emboss.py
- − Tests/test_EmbossPhylipNew.py
- Tests/test_Entrez_parser.py
- − Tests/test_Fasttree_tool.py
- Tests/test_GenBank.py
- − Tests/test_HMMCasino.py
- − Tests/test_HMMGeneral.py
- − Tests/test_LogisticRegression.py
- − Tests/test_MSAProbs_tool.py
- − Tests/test_Mafft_tool.py
- − Tests/test_MarkovModel.py
- − Tests/test_Muscle_tool.py
- − Tests/test_NCBI_BLAST_tools.py
- − Tests/test_NaiveBayes.py
- Tests/test_PDB_CEAligner.py
- Tests/test_PDB_KDTree.py
- Tests/test_PDB_PDBIO.py
- Tests/test_PDB_PDBList.py
- Tests/test_PDB_QCPSuperimposer.py
- Tests/test_PDB_SMCRA.py
- Tests/test_PDB_StructureAlignment.py
- − Tests/test_PopGen_GenePop.py
- − Tests/test_PopGen_GenePop_EasyController.py
- − Tests/test_Prank_tool.py
- − Tests/test_Probcons_tool.py
- Tests/test_Restriction.py
- Tests/test_SearchIO_hmmer3_tab.py
- + Tests/test_SearchIO_infernal_tab.py
- + Tests/test_SearchIO_infernal_tab_index.py
- + Tests/test_SearchIO_infernal_text.py
- + Tests/test_SearchIO_infernal_text_index.py
- Tests/test_SeqFeature.py
- Tests/test_SeqIO.py
- Tests/test_SeqIO_SnapGene.py
- Tests/test_SeqIO_UniprotIO.py
- Tests/test_SeqIO_features.py
- Tests/test_SeqRecord.py
- Tests/test_SeqUtils.py
- − Tests/test_TCoffee_tool.py
- Tests/test_Tutorial.py
- − Tests/test_XXmotif_tool.py
- Tests/test_align.py
- Tests/test_codonalign.py
- − Tests/test_kNN.py
- Tests/test_motifs.py
- Tests/test_pairwise_aligner.py
- Tests/test_pairwise_alignment_map.py
- − Tests/test_phyml_tool.py
- − Tests/test_raxml_tool.py
- − Tests/test_samtools_tool.py
- + hht2+-1000.dna
- setup.py

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/e7f679d0ed417224df595c6c9dec0906e32707d9

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