CVS log for pkgsrc/biology/bioperl/distinfo

Up to [cvs.NetBSD.org] / pkgsrc / biology / bioperl

Request diff between arbitrary revisions

Keyword substitution: kv
Default branch: MAIN

biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

biology: Remove SHA1 hashes for distfiles

bioperl: update to 1.7.7.

1.7.7     2019-12-07 13:41:36-06:00 America/Chicago

    * The program bp_chaos_plot has been removed.

    * GD is now no longer a dependency, suggestion or requirement.

    * #321 - GenBank format fix for un-quoted features, text wrapping

    * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
      and a 'private' _sleep() function that mirror those from
      Bio::DB::WebDBSeqI, primarily for compliance with potential website
      restrictions for the number and frequency of queries (e.g. NCBI eUtils).

    * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
      in last release.

1.7.6     2019-08-28 12:37:01+01:00 Europe/London

    * The program bp_classify_hits_kingdom has been removed and is
      now part of the examples documentation instead.

    * GD is now listed as a suggestion instead of a requirement.  The
      bp_chaos_plot program will now work with the GD module.

    * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
      to compute Transfer Bootstrap Expectation (TBE) for internal
      nodes based on the methods outlined in Lemoine et al, Nature,
      2018.

    * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
      sequence in the stream faster but not perfect.


1.7.5     2019-02-11 14:57:45+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution with
      independent development:

          Bio::Symbol::*

    * The Bio::Seq::SeqWithQuality module, which was deprecated since
      2001, was finally removed.

    * The deprecated() method has been deprecated.  It is recommended
      to use Carp::carp to warn.

    * The following methods have been deprecated for a long while and
      have now been removed:

          Bio::Align::AlignI->no_residues
          Bio::Align::AlignI->no_sequences
          Bio::LocatableSeq->no_gap
          Bio::LocatableSeq->no_sequences
          Bio::SeqFeature::Generic->slurp_gff_file
          Bio::SimpleAlign->no_residues
          Bio::SimpleAlign->no_sequences


1.7.4     2019-02-05 16:23:53+00:00 Europe/London

    * Fix Bio::Root::Test, and the testuite, to properly check for
      internet connection and the NO_NETWORK_TESTING environment
      variable.  Previously, tests that required internet connection
      were not being skipped, causing tests to fail.


1.7.3     2019-01-30 13:30:34+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution.  They have
      been integrated into other module distributions for independent
      development:

          Bio::Align::Graphics
          Bio::AlignIO::nexml
          Bio::AlignIO::stockholm
          Bio::Assembly::*
          Bio::Cluster::*
          Bio::ClusterI::*
          Bio::ClusterIO::*
          Bio::DB::Ace
          Bio::DB::BioFetch
          Bio::DB::CUTG
          Bio::DB::EMBL
          Bio::DB::EntrezGene
          Bio::DB::Expression::*
          Bio::DB::GFF
          Bio::DB::GFF::Adaptor::*
          Bio::DB::GFF::Aggregator::*
          Bio::DB::GFF::Featname
          Bio::DB::GFF::Feature
          Bio::DB::GFF::Homol
          Bio::DB::GFF::RelSegment
          Bio::DB::GFF::Segment
          Bio::DB::GFF::Typename
          Bio::DB::GenBank
          Bio::DB::GenPept
          Bio::DB::HIV::*
          Bio::DB::MeSH
          Bio::DB::NCBIHelper
          Bio::DB::Query::GenBank
          Bio::DB::Query::HIVQuery
          Bio::DB::RefSeq
          Bio::DB::SeqFeature::*
          Bio::DB::SeqVersion::*
          Bio::DB::SwissProt
          Bio::DB::TFBS::*
          Bio::DB::Taxonomy::entrez
          Bio::DB::Taxonomy::sqlite
          Bio::DB::Universal
          Bio::Draw::Pictogram
          Bio::Factory::MapFactoryI
          Bio::Index::Hmmer
          Bio::Index::Stockholm
          Bio::LiveSeq::*
          Bio::Map::*
          Bio::MapIO::*
          Bio::MolEvol::CodonModel
          Bio::Nexml::Factory
          Bio::NexmlIO
          Bio::Perl
          Bio::Phenotype::*
          Bio::PhyloNetwork::*
          Bio::PopGen::*
          Bio::Restriction::*
          Bio::Root::Build
          Bio::Search::HSP::HMMERHSP
          Bio::Search::HSP::HmmpfamHSP
          Bio::Search::Hit::HMMERHit
          Bio::Search::Hit::HmmpfamHit
          Bio::Search::Hit::hmmer3Hit
          Bio::Search::Result::HMMERResult
          Bio::Search::Result::HmmpfamResult
          Bio::Search::Result::hmmer3Result
          Bio::SearchDist
          Bio::SearchIO::hmmer
          Bio::SearchIO::hmmer2
          Bio::SearchIO::hmmer3
          Bio::SearchIO::hmmer_pull
          Bio::SeqEvolution::*
          Bio::SeqFeature::SiRNA::*
          Bio::SeqIO::abi
          Bio::SeqIO::agave
          Bio::SeqIO::alf
          Bio::SeqIO::chadoxml
          Bio::SeqIO::chaos
          Bio::SeqIO::chaosxml
          Bio::SeqIO::ctf
          Bio::SeqIO::entrezgene
          Bio::SeqIO::excel
          Bio::SeqIO::exp
          Bio::SeqIO::flybase_chadoxml
          Bio::SeqIO::lasergene
          Bio::SeqIO::nexml
          Bio::SeqIO::pln
          Bio::SeqIO::strider
          Bio::SeqIO::ztr
          Bio::Structure::*
          Bio::Taxonomy::*
          Bio::Tools::AlignFactory
          Bio::Tools::Analysis::* (except SimpleAnalysisBase)
          Bio::Tools::Gel
          Bio::Tools::HMMER::*
          Bio::Tools::Hmmpfam
          Bio::Tools::Phylo::Gumby
          Bio::Tools::Protparam
          Bio::Tools::Run::RemoteBlast
          Bio::Tools::SiRNA::*
          Bio::Tools::dpAlign
          Bio::Tools::pSW
          Bio::Tree::AlleleNode
          Bio::Tree::Draw::Cladogram
          Bio::TreeIO::nexml
          Bio::TreeIO::svggraph
          Bio::Variation::*

    * The following modules are new in the BioPerl distribution.  They
      have been previously released in the BioPerl-Run distribution.
      This will enable smaller distributions that provide a
      Bio::Tool::Run interface, to be only dependent on the BioPerl
      distribution instead of the whole (very large) BioPerl-Run:

          Bio::Tools::Run::Analysis
          Bio::Tools::Run::AnalysisFactory
          Bio::Tools::Run::Phylo::PhyloBase
          Bio::Tools::Run::WrapperBase
          Bio::Tools::Run::WrapperBase::CommandExts

    * The following programs have been removed:

          bp_biofetch_genbank_proxy
          bp_blast2tree
          bp_bulk_load_gff
          bp_composite_LD
          bp_das_server
          bp_download_query_genbank
          bp_fast_load_gff
          bp_flanks
          bp_genbank2gff
          bp_generate_histogram
          bp_heterogeneity_test
          bp_hivq
          bp_hmmer_to_table
          bp_load_gff
          bp_meta_gff
          bp_netinstall
          bp_parse_hmmsearch
          bp_process_wormbase
          bp_query_entrez_taxa
          bp_remote_blast
          bp_seqfeature_delete
          bp_seqfeature_gff3
          bp_seqfeature_load

    * Because of the move of so many modules and programs into
      separate distributions, the following modules are no longer
      prerequisites:

          Ace
          Ace::Sequence::Homol
          Algorithm::Munkres
          Apache::DBI
          Archive::Tar
          Array::Compare
          Bio::ASN1::EntrezGene
          Bio::Expression::Contact
          Bio::Expression::DataSet
          Bio::Expression::Platform
          Bio::Expression::Sample
          Bio::Ext::Align
          Bio::GMOD::CMap::Utils
          Bio::Phylo::Factory
          Bio::Phylo::Forest::Tree
          Bio::Phylo::IO
          Bio::Phylo::Matrices
          Bio::Phylo::Matrices::Datum
          Bio::Phylo::Matrices::Matrix
          Bio::SeqFeature::Annotated
          Bio::SeqIO::staden::read
          Bio::Tools::Run::Alignment::Clustalw
          Bio::Tools::Run::Ensembl
          Bio::Tools::Run::Phylo::Molphy::ProtML
          Bio::Tools::Run::Phylo::Phylip::Neighbor
          Bio::Tools::Run::Phylo::Phylip::ProtDist
          Bio::Tools::Run::Phylo::Phylip::ProtPars
          Bio::Tools::Run::Samtools
          CGI
          CPAN
          Cache::FileCache
          Config
          Convert::Binary::C
          DBD::Pg
          DBD::SQLite
          Data::Stag::XMLWriter
          Encode
          English
          ExtUtils::Install
          ExtUtils::Manifest
          File::Glob
          GD::Simple
          Getopt::Std
          Graph::Undirected
          GraphViz
          HTML::HeadParser
          HTML::TableExtract
          LWP
          LWP::Simple
          MIME::Base64
          Memoize
          PostScript::TextBlock
          SVG
          SVG::Graph
          SVG::Graph::Data
          SVG::Graph::Data::Node
          SVG::Graph::Data::Tree
          Sort::Naturally
          Spreadsheet::ParseExcel
          Term::ReadLine
          Text::NSP::Measures::2D::Fisher2::twotailed
          Text::ParseWords
          Time::Local
          Tree::DAG_Node
          URI::Escape
          WWW::Mechanize
          XML::Simple

    * The following is a new prerequisite:

          Test::RequiresInternet

    * The deobfuscator has been removed.

    * The emacs bioperl minor mode is no longer distributed as part of the
      perl module distributions.  See
      https://github.com/bioperl/emacs-bioperl-mode

bioperl: update to 1.007002.

Add p5-Text-Diff as test dependency.

1.7.2 - "Entebbe"

    [Bugs]

    * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
    * #245 - Code coverage fixes [zmughal,cjfields]
    * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
    * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
    * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
    * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
    * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
    * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
    * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
    * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
    * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
    * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]

    [Code changes]

    * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]

Update to 1.007001

Upstream changes:
1.7.1 - "Election"

    [Bugs]

    * Minor release to incorporate fix for CPAN indexing, which
      prevented proper updates [cjfields]
    * Fix problem in managing Target attribute for gff3 [Jukes34]
    * Minor bug fixes related to NCBI HTTPS support [cjfields]

1.7.0 - "Disney"

    [New site]

    * We have migrated to Github Pages. This was actually planned, but the
      recent OBF server compromise forced our hand.

      Brian Osborne [bosborne] took this under his wing to move docs and has
      done a tremendous amount of work formatting the site and working out some
      of the idiosyncracies with the new Jekyll-based design.  Mark Jensen, Paul
      Cantalupo and Franscison Ossandon also helped.  Kudos!!

    * Similarly, the official issue tracker is now Github Issues.  This has
      been updated in the relevant documentation bits (we hope!)

    [Code changes]

    * Previously deprecated modules removed
      * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
    * Bio::DB::SeqHound has been removed due to the service no longer being
      available
    * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
      reasons due to the server no longer having a valid cert
    * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
    * Bio::Coordinate, Bio::SearchIO::blastxml,
      Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
      added on CPAN

    [New features]

    * Docker instances of tagged releases are available! [hlapp]
    * NCBI HTTPS support [mjohnson and others]
    * Bio::SearchIO::infernal
      - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
    * Bio::Search::HSP::ModelHSP
      - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
        reports [pcantalupo]
    * Bio::Search::Result::INFERNALResult
      - Added new module to represent features of Infernal reports [pcantalupo]
    * Bio::DB::Taxonomy SQLite option [cjfields]
    * WrapperBase quoted option values [majensen]
    * Various documentation fixes and updates [bosborne]

   [Bug Fixes]

    * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
    * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
    * NeXML parser fixes [fjossandon]
    * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
    * RT 103272 : SeqFeature database deletion skipped features with a decimal -
      Joshua Fortriede (Xenbase)
    * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
    * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
    * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
    * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
    * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
    * Issue #84: EMBL format wrapping problem [nyamned]
    * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
    * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
      or compiled C code (when Inline::C is installed) [rocky]
    * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
    * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
    * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
    * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
      to be consistent with "$hit->bits" behaviour [fjossandon]
    * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
      aminoacids made "next_seq" confused and broke the parser [fjossandon]
    * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
      Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
      to "complement(join(A..B,C..D))" [fjossandon]
    * For the many many many fixes that weren't mentioned - blame the release guy!

Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

Update to 1.6.924

Upstream changes:
1.6.924

    [Significant changes]

    * Bug/feature issue tracking has moved to GitHub Issues:
          https://github.com/bioperl/bioperl-live/issues
    * DB_File has been demoted from "required" to "recommended",
      which should make easier for Windows users to install BioPerl
      if they don't need that module.

    [New features]

    * Bio::Search::HSP::GenericHSP
        - Bug #3370, added a "posterior_string" method to retrieve the
          posterior probability lines (PP) from HMMER3 reports [fjossandon]
        - Added a "consensus_string" method to retrieve the consensus
          structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
    * Bio::SearchIO::hmmer2
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Query Length and Hit Length are reported when the alignment
          runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
    * Bio::SearchIO::hmmer3
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Hit Length is reported when the alignment runs until the end
          of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
        - Implemented the capture of the posterior probability lines [fjossandon]
        - Completed the development of NHMMER parsing, including alignments [fjossandon]
    * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
        - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
          "min_score", "min_bits, and "hit_filter" methods from
          'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
          This means that the Bio::SearchIO->new() parameters '-signif', '-score',
          '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
          besides Blast, instead of being ignored. Added tests for all moved methods
          using HMMER outputs and run the full test suite and everything pass [fjossandon]
    * Bio::SeqIO::MultiFile
        - Autodetection of file format [fangly]
    * Bio::Tools::GuessSeqFormat:
        - Format detection from non-seekable filehandles such as STDIN [fangly]

    [Bug fixes]

    * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
    * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
    * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
    * Abstract: Fixed ActivePerl incapability of removing temporary files
      because of problems closing tied filehandles [fjossandon]
    * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
      because ActivePerl were producing a ".index.pag" and ".index.dir"
      files instead of a single ".index" file (like Strawberry Perl).
      Now those temporary files are correctly considered and deleted. [fjossandon]
    * Test files: Added missing module requirements (DB_File and Data::Stag)
      to several tests files that were failing because those modules were
      not present. Now those test files are correctly skipped instead. [fjossandon]
    * Blast: Added support to changes in bl2seq from BLAST+ output, which
      now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
    * Phylip: Return undef in "next_aln" at file end to avoid
      an infinite loop [yschensandiego]
    * HMMER3: When a hit description is too long, it is truncated in
      the Scores table. In those cases, the more complete description from
      the Annotation line (>>) will be used [fjossandon]
    * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
      since it is now used by HMMER3 format in alignments [fjossandon]
    * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
      to return undef if the query/hit length is unknown (like in some
      HMMER outputs), to avoid division by 0 crashes. Also "query_length"
      now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
    * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
      added support to multi-query reports, reduced code redundancy,
      and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
    * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
    * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
    * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
    * Fixed some Bio::Root::Utilities subroutines [fjossandon]
    * Double-quotes on paths are needed in some places [fjossandon]
    * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
    * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
    * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
      with the latest changes made in their own repositories [fjossandon]
    * General synching of files with the master branch [fjossandon]
    * Fixed tests failing in Windows because of using Linux commands [fjossandon]
    * Closed many open filehandles that prevented temporary files deletion [fjossandon]
    * Fixed broken MeSH parser [fjossandon]
    * Fixed missing detection of format in SeqIO when given a -string [fangly]

Update biology/bioperl to 1.6.923.

Way too many changes (0.7.0 was released in 2001!).

See changelog at:

https://github.com/bioperl/bioperl-live/blob/master/Changes

Fixed one unit test.

Add RMD160 digests in addition to the SHA1 ones.

Move to sha1 digests, and add distfile sizes.

+ move the distfile digest/checksum value from files/md5 to distinfo
+ move the patch digest/checksum values from files/patch-sum to distinfo