67a37865e5
Retain letter_annotation as None in upper and lower methods ( #4966 )
...
* gitignore .python-version
* added name & email
* fix so that _per_letter_annotations is not set by calling upper or lower methods
* added test for initiation of SeqRecord checking the __dict__ and a test for the __dict__ created by upper
2025-03-10 14:01:25 +00:00
2ae12c78f5
Ignore Biopython_doc.pdf replacing Tutorial.pdf
...
TODO: Tweak the latexpdf build in the makefile to control
placing the generated PDF as Doc/Biopython_doc.pdf
2024-06-28 04:46:43 +01:00
82f23ad847
Tell git to ignore emacs #*.rst# etc too
...
[ci skip]
2023-06-22 02:13:42 +01:00
c313639693
Improve local testing documentation ( #4020 )
...
* doc(CONTRIBUTING): improve local testing section
* Refer to tutorial chapter on testing
Co-authored-by: Julian Maurin <julian.maurin.perso@pm.me >
Co-authored-by: JulianMaurin <julian.maurin.dev@pm.me >
Co-authored-by: Peter Cock <p.j.a.cock@googlemail.com >
2022-10-07 09:35:42 +09:00
06a96c0311
ignore more virtual environment folders ( #3939 )
2022-08-09 11:18:45 +01:00
a8d2647a88
Move self-tests for Bio.PDB.PSEA to unit tests ( #3980 )
...
Authored-by: Valentin Vareskic <valentin.vareskic@gmail.com >
2022-07-26 12:08:32 -04:00
2c132e7087
Deploy API documentation using CircleCI ( #3787 )
...
Based on how we did this with TravisCI, but updated to work on CircleCI
2021-11-12 13:49:17 +00:00
fb567423d0
Add ignore rule for Windows-only pyd files ( #3211 )
2020-08-13 17:56:11 -07:00
181c85d377
Pass version as parameter to Tutorial.tex ( #3030 )
...
* issue #2904 version as parameter to Tutorial.tex
* dynamically extract current version number for Tutorial build
* inserts version number or dev into Tutorial depending on release status
* added today macro to Tutorial.tex
2020-07-21 18:05:47 +01:00
c493dda2eb
Add pygments python file to .gitignore
2020-01-26 19:52:53 +00:00
6bb7a24faa
Add Tests/out.bam to .gitignore. Created by Tests/test_BWA_tool.py
2019-11-19 10:45:26 +00:00
7a925b5d63
Remove *.py{} from .gitignore as it is unneeded
...
It also confuses programs interpreting .gitignore as normal globs (e.g. ripgrep)
2019-11-19 10:45:26 +00:00
9626d6ffc8
Fix keys in DNA_TMM1 ( #2283 )
...
- two keys in Bio.SeqUtils.MeltingTemp.py had spaces that
prevented their lookup during nearest neighbor tm calculation:
"CC/GC" and "GG/CA" (closes #2280 )
- added a ".mypy_cache" ignore to .gitignore
which is autogenerated for devs running mypy (related to #2236 )
- fixed a small mispelling of directory in .gitignore
2019-09-26 20:53:37 +02:00
b0405a2908
.gitignore output from building the docs
...
Without this, my `git status` output gets rather noisy:
markamery@Marks-MacBook-Pro-3 biopython$ git status
On branch fix-entrez-docstring
Your branch is up-to-date with 'origin/fix-entrez-docstring'.
Untracked files:
(use "git add <file>..." to include in what will be committed)
Doc/api/Bio.Affy.CelFile.rst
Doc/api/Bio.Affy.rst
Doc/api/Bio.Align.AlignInfo.rst
Doc/api/Bio.Align.Applications.rst
Doc/api/Bio.Align.rst
Doc/api/Bio.AlignIO.ClustalIO.rst
Doc/api/Bio.AlignIO.EmbossIO.rst
Doc/api/Bio.AlignIO.FastaIO.rst
Doc/api/Bio.AlignIO.Interfaces.rst
Doc/api/Bio.AlignIO.MafIO.rst
Doc/api/Bio.AlignIO.MauveIO.rst
Doc/api/Bio.AlignIO.NexusIO.rst
Doc/api/Bio.AlignIO.PhylipIO.rst
Doc/api/Bio.AlignIO.StockholmIO.rst
Doc/api/Bio.AlignIO.rst
Doc/api/Bio.Alphabet.IUPAC.rst
Doc/api/Bio.Alphabet.Reduced.rst
Doc/api/Bio.Alphabet.rst
Doc/api/Bio.Application.rst
Doc/api/Bio.Blast.Applications.rst
Doc/api/Bio.Blast.NCBIWWW.rst
Doc/api/Bio.Blast.NCBIXML.rst
Doc/api/Bio.Blast.ParseBlastTable.rst
Doc/api/Bio.Blast.Record.rst
Doc/api/Bio.Blast.rst
Doc/api/Bio.CAPS.rst
Doc/api/Bio.Cluster.rst
Doc/api/Bio.Compass.rst
Doc/api/Bio.Crystal.rst
Doc/api/Bio.Data.CodonTable.rst
Doc/api/Bio.Data.IUPACData.rst
Doc/api/Bio.Data.SCOPData.rst
Doc/api/Bio.Data.rst
Doc/api/Bio.Emboss.Applications.rst
Doc/api/Bio.Emboss.Primer3.rst
Doc/api/Bio.Emboss.PrimerSearch.rst
Doc/api/Bio.Emboss.rst
Doc/api/Bio.Entrez.Parser.rst
Doc/api/Bio.Entrez.rst
Doc/api/Bio.ExPASy.Enzyme.rst
Doc/api/Bio.ExPASy.Prodoc.rst
Doc/api/Bio.ExPASy.Prosite.rst
Doc/api/Bio.ExPASy.ScanProsite.rst
Doc/api/Bio.ExPASy.cellosaurus.rst
Doc/api/Bio.ExPASy.rst
Doc/api/Bio.FSSP.FSSPTools.rst
Doc/api/Bio.FSSP.fssp_rec.rst
Doc/api/Bio.FSSP.rst
Doc/api/Bio.File.rst
Doc/api/Bio.GenBank.Record.rst
Doc/api/Bio.GenBank.Scanner.rst
Doc/api/Bio.GenBank.rst
Doc/api/Bio.GenBank.utils.rst
Doc/api/Bio.Geo.Record.rst
Doc/api/Bio.Geo.rst
Doc/api/Bio.Graphics.BasicChromosome.rst
Doc/api/Bio.Graphics.ColorSpiral.rst
Doc/api/Bio.Graphics.Comparative.rst
Doc/api/Bio.Graphics.DisplayRepresentation.rst
Doc/api/Bio.Graphics.Distribution.rst
Doc/api/Bio.Graphics.GenomeDiagram.rst
Doc/api/Bio.Graphics.KGML_vis.rst
Doc/api/Bio.Graphics.rst
Doc/api/Bio.HMM.DynamicProgramming.rst
Doc/api/Bio.HMM.MarkovModel.rst
Doc/api/Bio.HMM.Trainer.rst
Doc/api/Bio.HMM.Utilities.rst
Doc/api/Bio.HMM.rst
Doc/api/Bio.Index.rst
Doc/api/Bio.KDTree.KDTree.rst
Doc/api/Bio.KDTree.rst
Doc/api/Bio.KEGG.Compound.rst
Doc/api/Bio.KEGG.Enzyme.rst
Doc/api/Bio.KEGG.Gene.rst
Doc/api/Bio.KEGG.KGML.KGML_parser.rst
Doc/api/Bio.KEGG.KGML.KGML_pathway.rst
Doc/api/Bio.KEGG.KGML.rst
Doc/api/Bio.KEGG.Map.rst
Doc/api/Bio.KEGG.REST.rst
Doc/api/Bio.KEGG.rst
Doc/api/Bio.LogisticRegression.rst
Doc/api/Bio.MarkovModel.rst
Doc/api/Bio.MaxEntropy.rst
Doc/api/Bio.Medline.rst
Doc/api/Bio.NMR.NOEtools.rst
Doc/api/Bio.NMR.rst
Doc/api/Bio.NMR.xpktools.rst
Doc/api/Bio.NaiveBayes.rst
Doc/api/Bio.Nexus.Nexus.rst
Doc/api/Bio.Nexus.Nodes.rst
Doc/api/Bio.Nexus.StandardData.rst
Doc/api/Bio.Nexus.Trees.rst
Doc/api/Bio.Nexus.rst
Doc/api/Bio.PDB.AbstractPropertyMap.rst
Doc/api/Bio.PDB.Atom.rst
Doc/api/Bio.PDB.Chain.rst
Doc/api/Bio.PDB.DSSP.rst
Doc/api/Bio.PDB.Dice.rst
Doc/api/Bio.PDB.Entity.rst
Doc/api/Bio.PDB.FragmentMapper.rst
Doc/api/Bio.PDB.HSExposure.rst
Doc/api/Bio.PDB.MMCIF2Dict.rst
Doc/api/Bio.PDB.MMCIFParser.rst
Doc/api/Bio.PDB.Model.rst
Doc/api/Bio.PDB.NACCESS.rst
Doc/api/Bio.PDB.NeighborSearch.rst
Doc/api/Bio.PDB.PDBExceptions.rst
Doc/api/Bio.PDB.PDBIO.rst
Doc/api/Bio.PDB.PDBList.rst
Doc/api/Bio.PDB.PDBParser.rst
Doc/api/Bio.PDB.PSEA.rst
Doc/api/Bio.PDB.Polypeptide.rst
Doc/api/Bio.PDB.QCPSuperimposer.rst
Doc/api/Bio.PDB.Residue.rst
Doc/api/Bio.PDB.ResidueDepth.rst
Doc/api/Bio.PDB.Selection.rst
Doc/api/Bio.PDB.Structure.rst
Doc/api/Bio.PDB.StructureAlignment.rst
Doc/api/Bio.PDB.StructureBuilder.rst
Doc/api/Bio.PDB.Superimposer.rst
Doc/api/Bio.PDB.mmcifio.rst
Doc/api/Bio.PDB.mmtf.DefaultParser.rst
Doc/api/Bio.PDB.mmtf.mmtfio.rst
Doc/api/Bio.PDB.mmtf.rst
Doc/api/Bio.PDB.parse_pdb_header.rst
Doc/api/Bio.PDB.rst
Doc/api/Bio.PDB.vectors.rst
Doc/api/Bio.Pathway.Rep.Graph.rst
Doc/api/Bio.Pathway.Rep.MultiGraph.rst
Doc/api/Bio.Pathway.Rep.rst
Doc/api/Bio.Pathway.rst
Doc/api/Bio.Phylo.Applications.rst
Doc/api/Bio.Phylo.BaseTree.rst
Doc/api/Bio.Phylo.CDAO.rst
Doc/api/Bio.Phylo.CDAOIO.rst
Doc/api/Bio.Phylo.Consensus.rst
Doc/api/Bio.Phylo.NeXML.rst
Doc/api/Bio.Phylo.NeXMLIO.rst
Doc/api/Bio.Phylo.Newick.rst
Doc/api/Bio.Phylo.NewickIO.rst
Doc/api/Bio.Phylo.NexusIO.rst
Doc/api/Bio.Phylo.PAML.baseml.rst
Doc/api/Bio.Phylo.PAML.chi2.rst
Doc/api/Bio.Phylo.PAML.codeml.rst
Doc/api/Bio.Phylo.PAML.rst
Doc/api/Bio.Phylo.PAML.yn00.rst
Doc/api/Bio.Phylo.PhyloXML.rst
Doc/api/Bio.Phylo.PhyloXMLIO.rst
Doc/api/Bio.Phylo.TreeConstruction.rst
Doc/api/Bio.Phylo.rst
Doc/api/Bio.PopGen.GenePop.Controller.rst
Doc/api/Bio.PopGen.GenePop.EasyController.rst
Doc/api/Bio.PopGen.GenePop.FileParser.rst
Doc/api/Bio.PopGen.GenePop.LargeFileParser.rst
Doc/api/Bio.PopGen.GenePop.Utils.rst
Doc/api/Bio.PopGen.GenePop.rst
Doc/api/Bio.PopGen.rst
Doc/api/Bio.Restriction.PrintFormat.rst
Doc/api/Bio.Restriction.Restriction.rst
Doc/api/Bio.Restriction.Restriction_Dictionary.rst
Doc/api/Bio.Restriction.rst
Doc/api/Bio.SCOP.Cla.rst
Doc/api/Bio.SCOP.Des.rst
Doc/api/Bio.SCOP.Dom.rst
Doc/api/Bio.SCOP.Hie.rst
Doc/api/Bio.SCOP.Raf.rst
Doc/api/Bio.SCOP.Residues.rst
Doc/api/Bio.SCOP.rst
Doc/api/Bio.SVDSuperimposer.rst
Doc/api/Bio.SearchIO.BlastIO.blast_tab.rst
Doc/api/Bio.SearchIO.BlastIO.blast_text.rst
Doc/api/Bio.SearchIO.BlastIO.blast_xml.rst
Doc/api/Bio.SearchIO.BlastIO.rst
Doc/api/Bio.SearchIO.BlatIO.rst
Doc/api/Bio.SearchIO.ExonerateIO.exonerate_cigar.rst
Doc/api/Bio.SearchIO.ExonerateIO.exonerate_text.rst
Doc/api/Bio.SearchIO.ExonerateIO.exonerate_vulgar.rst
Doc/api/Bio.SearchIO.ExonerateIO.rst
Doc/api/Bio.SearchIO.FastaIO.rst
Doc/api/Bio.SearchIO.HHsuiteIO.hhsuite2_text.rst
Doc/api/Bio.SearchIO.HHsuiteIO.rst
Doc/api/Bio.SearchIO.HmmerIO.hmmer2_text.rst
Doc/api/Bio.SearchIO.HmmerIO.hmmer3_domtab.rst
Doc/api/Bio.SearchIO.HmmerIO.hmmer3_tab.rst
Doc/api/Bio.SearchIO.HmmerIO.hmmer3_text.rst
Doc/api/Bio.SearchIO.HmmerIO.rst
Doc/api/Bio.SearchIO.InterproscanIO.interproscan_xml.rst
Doc/api/Bio.SearchIO.InterproscanIO.rst
Doc/api/Bio.SearchIO.rst
Doc/api/Bio.Seq.rst
Doc/api/Bio.SeqFeature.rst
Doc/api/Bio.SeqIO.AbiIO.rst
Doc/api/Bio.SeqIO.AceIO.rst
Doc/api/Bio.SeqIO.FastaIO.rst
Doc/api/Bio.SeqIO.GckIO.rst
Doc/api/Bio.SeqIO.IgIO.rst
Doc/api/Bio.SeqIO.InsdcIO.rst
Doc/api/Bio.SeqIO.Interfaces.rst
Doc/api/Bio.SeqIO.NibIO.rst
Doc/api/Bio.SeqIO.PdbIO.rst
Doc/api/Bio.SeqIO.PhdIO.rst
Doc/api/Bio.SeqIO.PirIO.rst
Doc/api/Bio.SeqIO.QualityIO.rst
Doc/api/Bio.SeqIO.SeqXmlIO.rst
Doc/api/Bio.SeqIO.SffIO.rst
Doc/api/Bio.SeqIO.SnapGeneIO.rst
Doc/api/Bio.SeqIO.SwissIO.rst
Doc/api/Bio.SeqIO.TabIO.rst
Doc/api/Bio.SeqIO.UniprotIO.rst
Doc/api/Bio.SeqIO.XdnaIO.rst
Doc/api/Bio.SeqIO.rst
Doc/api/Bio.SeqRecord.rst
Doc/api/Bio.SeqUtils.CheckSum.rst
Doc/api/Bio.SeqUtils.CodonUsage.rst
Doc/api/Bio.SeqUtils.CodonUsageIndices.rst
Doc/api/Bio.SeqUtils.IsoelectricPoint.rst
Doc/api/Bio.SeqUtils.MeltingTemp.rst
Doc/api/Bio.SeqUtils.ProtParam.rst
Doc/api/Bio.SeqUtils.ProtParamData.rst
Doc/api/Bio.SeqUtils.lcc.rst
Doc/api/Bio.SeqUtils.rst
Doc/api/Bio.Sequencing.Ace.rst
Doc/api/Bio.Sequencing.Applications.rst
Doc/api/Bio.Sequencing.Phd.rst
Doc/api/Bio.Sequencing.rst
Doc/api/Bio.Statistics.lowess.rst
Doc/api/Bio.Statistics.rst
Doc/api/Bio.SubsMat.FreqTable.rst
Doc/api/Bio.SubsMat.MatrixInfo.rst
Doc/api/Bio.SubsMat.rst
Doc/api/Bio.SwissProt.KeyWList.rst
Doc/api/Bio.SwissProt.rst
Doc/api/Bio.TogoWS.rst
Doc/api/Bio.UniGene.rst
Doc/api/Bio.UniProt.GOA.rst
Doc/api/Bio.UniProt.rst
Doc/api/Bio.Wise.dnal.rst
Doc/api/Bio.Wise.psw.rst
Doc/api/Bio.Wise.rst
Doc/api/Bio.bgzf.rst
Doc/api/Bio.codonalign.chisq.rst
Doc/api/Bio.codonalign.codonalignment.rst
Doc/api/Bio.codonalign.codonalphabet.rst
Doc/api/Bio.codonalign.codonseq.rst
Doc/api/Bio.codonalign.rst
Doc/api/Bio.kNN.rst
Doc/api/Bio.motifs.alignace.rst
Doc/api/Bio.motifs.applications.rst
Doc/api/Bio.motifs.clusterbuster.rst
Doc/api/Bio.motifs.jaspar.db.rst
Doc/api/Bio.motifs.jaspar.rst
Doc/api/Bio.motifs.mast.rst
Doc/api/Bio.motifs.matrix.rst
Doc/api/Bio.motifs.meme.rst
Doc/api/Bio.motifs.minimal.rst
Doc/api/Bio.motifs.pfm.rst
Doc/api/Bio.motifs.rst
Doc/api/Bio.motifs.thresholds.rst
Doc/api/Bio.motifs.transfac.rst
Doc/api/Bio.motifs.xms.rst
Doc/api/Bio.pairwise2.rst
Doc/api/Bio.phenotype.phen_micro.rst
Doc/api/Bio.phenotype.pm_fitting.rst
Doc/api/Bio.phenotype.rst
Doc/api/Bio.rst
Doc/api/Bio.triefind.rst
Doc/api/BioSQL.BioSeq.rst
Doc/api/BioSQL.BioSeqDatabase.rst
Doc/api/BioSQL.DBUtils.rst
Doc/api/BioSQL.Loader.rst
Doc/api/BioSQL.rst
Doc/api/_build/
nothing added to commit but untracked files present (use "git add" to track)
2019-09-25 09:53:21 +01:00
8da81f889d
Automatically download the Gck test files.
...
Let the Gck test module automatically download the archive from
the Drosophila Gateway Vector Collection before the tests are run.
2019-08-21 16:46:22 +01:00
430874eb97
Add _minted-Tutorial/ to .gitignore
...
Generated when pdflatex calls Pygments via the minted package
for syntax coloring.
2019-06-06 11:59:54 +01:00
87f18655c0
Emphasise mmCIF over PDB format in the tutorial ( #2102 )
...
* update pdb chapter
* add name to contributor's list
Should close #1102 .
2019-06-06 08:27:20 +01:00
75e2ce3dd3
Explicitly ignore *.so files
2019-05-08 11:52:15 +01:00
0e67a85230
test_Tutorial.py now removes test files it creates ( #1747 )
...
* removes file created during running test_Tutorial.py
* added comments to the .tex docs where files are deleted after the run of test_Tutorial.py
* added files to .gitignore
2018-08-15 13:53:47 +01:00
4877464dc9
tell git to ignore emacs temp files
2018-04-02 14:23:38 +01:00
880e658f82
Ignore unittest cache dirctory
2017-12-27 23:53:47 +00:00
b56f70db6b
Tell git to ignore .tox/ directory
2017-03-03 17:16:35 +00:00
2b0f33fd4b
Avoid accidentally checking in Doc/examples/other_trees.nwk
2016-11-29 09:57:08 +00:00
083e745976
Ignore local BioSQL settings in git
2016-05-20 08:04:38 +01:00
4c7c629394
Ignore *.py{} and *.py-e files (from PyPy?)
2014-08-30 10:51:40 +09:00
0b80de4c1a
Add biopython.egg-info to git ignore list
2013-04-04 11:34:15 +01:00
b2ba0f8d3a
Tell git to ignore the generated MANIFEST file
2012-06-25 11:18:31 +01:00
e9c668afc7
Add Doc/biopdb_faq.pdf to the .gitignore list
2011-08-18 17:20:34 +01:00
eb3c20289f
Tell git to ignore IntelliJ IDEA directory and project files
2011-05-24 10:01:51 +01:00
1d99fd80a3
Ignore *.rej files from patch command
2010-09-21 14:49:08 +01:00
08b16ca66c
Add *.bak to the .gitignore file
2010-07-16 18:07:35 +01:00
7139d723f0
Ignore Doc/Tutorial.txt for git tracking
2010-07-11 10:36:13 +01:00
a477c0114f
Tell git to ignore hevea temp files from documentation
2010-04-18 17:01:31 +01:00
278b28a4c9
Update .gitignore to ignore patch files
2010-04-02 13:25:57 +01:00
c1e409d7fb
Tell git to ignore Tests/BioSQL/temp_sqlite.db-journal
2010-03-04 21:43:27 +00:00
401fe04d3d
Tell git to ignore temp_sqlite.db (we should really ensure the BioSQL unit tests remove it)
2010-03-04 19:05:23 +00:00
80ca97066a
Get git to ignore more LaTeX related files which should not be tracked
2009-11-13 14:27:32 +00:00
e55899c8dc
Tell git to ignore assorted LaTeX temp files from building the documentation
2009-10-30 11:24:39 +00:00
b72d7aae3d
Update to git ignore file from David W for hidden files from Dolphin window manager
2009-09-20 10:43:48 +00:00
fec1989dc7
Tell git and CVS to ignore the dist directory, and tell git to ignore any Jython class files
2009-08-11 09:52:28 +00:00
f63942a7f3
Tweaks to the .gitignore file from Cymon Cox
2009-05-05 08:49:59 +00:00
a3893b4a18
Ignore .DS_Store files from Mac OS X
2009-04-21 17:35:33 +00:00
ac4738fc66
Adding a .gitignore file to make testing our CVS mirror on github a little smoother.
2009-03-20 16:10:39 +00:00
