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Commits on Feb 25, 2015
  1. Peter Cock
  2. Eric Rasche Peter Cock

    Reflow long lines to make flake happy

    erasche authored peterjc committed
  3. Eric Rasche Peter Cock

    Refactor into separate instantiations to fix jython failure

    erasche authored peterjc committed
Commits on Feb 24, 2015
  1. Peter Cock
Commits on Feb 17, 2015
  1. Peter Cock
  2. Eric Rasche Peter Cock

    Correct repeated initialisation of keys

    erasche authored peterjc committed
    Thanks to @bow for the suggestion, the _INSTRUMENT_SPECIFIC_TAGS dict
    was being initialised repeatedly.
  3. Eric Rasche Peter Cock
  4. Eric Rasche Peter Cock

    Remove duplicate key

    erasche authored peterjc committed
  5. Eric Rasche Peter Cock

    Implement rest of ABIF spec

    erasche authored peterjc committed
  6. Fix for issue #461 to handle the change in output format in meme

    Michiel de Hoon authored
Commits on Feb 12, 2015
  1. Peter Cock

    Thank Gleb Kuznetsov for GenBank work

    peterjc authored
    See pull request #472
Commits on Feb 10, 2015
  1. Gleb Kuznetsov
Commits on Feb 4, 2015
  1. Peter Cock
  2. Peter Cock
Commits on Jan 30, 2015
  1. Peter Cock
Commits on Jan 26, 2015
  1. Eric Talevich
Commits on Jan 25, 2015
  1. Peter Cock

    Don't install T-COFFEE under TravisCI

    peterjc authored
    Recently the TravisCI builds have been stalling during
    test_TCoffee_tool.py which suggests a recent update to
    T-COFFEE is cause a problem somehow. This change will
    allow us to confirm if T-COFFEE is invovled.
Commits on Jan 22, 2015
  1. Peter Cock
Commits on Jan 20, 2015
  1. Peter Cock

    Fix typo in dependency check

    peterjc authored
  2. Peter Cock

    HexColor with alpha transparency broken on ReportLab 2.6

    peterjc authored
    We could cope with the argument name change from alpha to hasAlpha
    between ReportLab 2.6 and 2.7, but Under ReportLab 2.6, both
    HexColor('#8080F780') and HexColor('#8080F780', alpha=True)
    fail with:
    
        Traceback (most recent call last):
          File ".../site-packages/reportlab/lib/colors.py", line 365, in HexColor
            return Color((val>>24)&0xFF/255.0,((val>>16)&0xFF)/255.0,((val>>8)&0xFF)/255.0,(val&0xFF)/255.0)
        TypeError: unsupported operand type(s) for &: 'int' and 'float'
    
    Essentially we seem to need at least ReportLab 2.7 for transparency.
    
    See discussion on GitHub #458 and #463.
Commits on Jan 18, 2015
  1. Peter Cock

    Clearer error message; update failing test.

    peterjc authored
    One of the orchid examples now returns different enough
    results that the test was failing. The new error message
    makes it much easier to pick another positive example to
    add to the the white-list.
Commits on Jan 17, 2015
  1. Peter Cock
Commits on Jan 16, 2015
  1. Leighton Pritchard

    KGML_vis.py: Catch argument error for HexColor hasAlpha/alpha

    widdowquinn authored
    Implemented bugfix suggested by Peter Cock.
Commits on Jan 14, 2015
  1. Tiago Antao

    Bug on parsing loci name

    tiagoantao authored
Commits on Jan 11, 2015
  1. Tiago Antao

    type

    tiagoantao authored
Commits on Jan 9, 2015
  1. Peter Cock
  2. Brandon Invergo Peter Cock

    fix more assertions for Python 2.6

    brandoninvergo authored peterjc committed
  3. Brandon Invergo Peter Cock

    fix assertions for Python 2.6

    brandoninvergo authored peterjc committed
  4. Brandon Invergo Peter Cock

    add test cases for bad codeml tree parsing

    brandoninvergo authored peterjc committed
  5. Brandon Invergo Peter Cock

    fix #453: codeml (Bio.Phylo.PAML) tree regexp

    brandoninvergo authored peterjc committed
Commits on Jan 8, 2015
  1. Leighton Pritchard

    KGML_vis.py: Added handling of alpha-channel transparency.

    widdowquinn authored
    bgcolor and fgcolor attributes of KGML elements now render with transparency
    if an alpha channel is specified either as a 4-element tuple, 4-value hex
    string, or Reportlab Color object.
    
    The test_KGML_graphics.py tests are modified to test transparency of
    stroke (fgcolor) and fill (bgcolor).
  2. Leighton Pritchard
Commits on Jan 7, 2015
  1. Peter Cock

    Use new-style classes consistently.

    peterjc authored
    Quick of python history that unless you subclass object
    then on Python 2 you get an 'old-style' class which as
    some subtle differences from a 'new-style' class.
  2. Peter Cock

    PEP8 whitespace; W293 and E231

    peterjc authored
    Part of tackling GitHub issue #406
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