BioPerl 1.7.0 "Disney"

@hlapp hlapp released this Sep 25, 2016 · 18 commits to master since this release

Philosophy for 1.7.x:

In order to reduce the number of dependencies, we are actively encouraging
developers wanting to submit new code with additional dependencies to release
code in a separate repository and release it on CPAN. We can help assist in this
process and can also place this under the 'bioperl' Github organization (and
similarly under the bioperl umbrella account in CPAN), though this is not
required.

We will also be moving additonal code to other repositories and will release
them separately on CPAN. Modules considered obsolute (relies on a dead web
service or utilizes strict dependencies that are also considered obsolete) will
be removed.

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!

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