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 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/e7f679d0ed417224df595c6c9dec0906e32707d9 You're receiving this email because of your account on salsa.debian.org.
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