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Commits on Aug 23, 2016
  1. @cjfields

    Merge pull request #193 from dk/master

    refs #190: understand unquoted multiline FT entries
    cjfields committed on GitHub Aug 23, 2016
  2. @cjfields

    Merge pull request #192 from lairdm/master

    Ambiguous codons being returned as stop codons
    cjfields committed on GitHub Aug 23, 2016
Commits on Aug 14, 2016
  1. @lairdm
Commits on Aug 12, 2016
  1. refs #190: understand unquoted multiline FT entries

    Dmitry Karasik committed Aug 12, 2016
Commits on Aug 10, 2016
  1. @lairdm

    - is_ter_codon was incorrectly returning ambiguous codons as stop cod…

    …ons (ie. NNN was being returned true), any failure in the list of unambiguous codons should return false, the opposite was occuring
    
    - U was not being remapped to T, it's needed for UAG and such
    - Added tests for better coverage of corner cases
    lairdm committed Aug 10, 2016
Commits on Aug 3, 2016
  1. @bosborne

    Merge pull request #191 from bioperl/fix-spellings

    Fix spellings
    bosborne committed on GitHub Aug 3, 2016
  2. @bosborne

    Fix spellings

    bosborne committed Aug 3, 2016
Commits on Aug 2, 2016
  1. @cjfields

    possible fix for #187

    cjfields committed Aug 2, 2016
Commits on Aug 1, 2016
  1. @cjfields

    Merge pull request #188 from RoyChaudhuri/master

    SeqIO documentation update to clarify that piped commands should be o…
    cjfields committed on GitHub Aug 1, 2016
  2. @RoyChaudhuri
Commits on Jul 20, 2016
  1. @cjfields

    Merge pull request #186 from bioperl/docker-install

    Adds instructions for installing BioPerl as a Docker image.
    cjfields committed on GitHub Jul 20, 2016
Commits on Jul 18, 2016
  1. @hlapp

    Adds instructions for installing BioPerl as a Docker image.

    This required some minor restructuring to fit it into the current
    documentation, mainly decrementing the level of the headings for
    installing locally.
    hlapp committed Jul 18, 2016
  2. @cjfields

    Merge pull request #185 from elucify/ncbi-https

    Updated http URLs to https
    cjfields committed on GitHub Jul 18, 2016
  3. @cjfields

    Merge pull request #181 from bioperl/limit-dockerhub-trigger

    Limit Docker Hub trigger
    cjfields committed on GitHub Jul 18, 2016
  4. @elucify

    missed one url

    elucify committed Jul 18, 2016
  5. @elucify

    Updated http URLs to https

    elucify committed Jul 18, 2016
Commits on Jul 16, 2016
  1. @cjfields

    bump RC

    cjfields committed Jul 16, 2016
  2. @cjfields
  3. @cjfields

    update Changes (first of a few)

    cjfields committed Jul 16, 2016
Commits on Jul 12, 2016
  1. @hlapp
  2. @hlapp
  3. @cjfields

    Merge pull request #179 from christiam/master

    Change BLAST URL to https
    cjfields committed on GitHub Jul 12, 2016
  4. @christiam

    Change BLAST URL to https

    christiam committed Jul 12, 2016
Commits on Jul 11, 2016
  1. @cjfields
  2. @cjfields

    Incorporate recommended fix for RT98374; notably tests actually got t…

    …his wrong, so fixing those as well
    cjfields committed Jul 11, 2016
  3. @cjfields
Commits on Jul 9, 2016
  1. @cjfields
  2. @cjfields
Commits on Jul 8, 2016
  1. @fjossandon
  2. @heikkil

    Bio::DB::Mesh: removed backend Bio::Root::HTTPget

    - Docs updated
    - Needs better code coverage in tests
    - Manually tested both remaining backends
    - Automatic testing would need a way to set the backend
    heikkil committed Jul 8, 2016
  3. @heikkil

    Merge pull request #177 from bioperl/topic/mesh_webagent

    Topic/mesh webagent
    heikkil committed on GitHub Jul 8, 2016
  4. @cjfields

    Merge branch 'master' of github.com:bioperl/bioperl-live

    Resolve small collision with .travis.yml stuff
    cjfields committed Jul 8, 2016
  5. @cjfields

    add 5.24

    cjfields committed Jul 8, 2016
Commits on Jul 7, 2016
  1. @fjossandon

    MeSH: Moved the cgi webpage check from '_cgi_url' into '_init'.

    The webpage check was being done for every request, so moved the
    webpage check and URL setting to the moment of object creation.
    Now $self->url will set either $URL for WWW::Mechanize or the cgi url
    for the other webagents.
    fjossandon committed Jul 7, 2016
  2. @fjossandon

    MeSH: Now '_cgi_url()' function retrieves current-year webpage

    instead of 2003 version. Also fixed test result.
    fjossandon committed Jul 7, 2016