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Commits on Jun 15, 2012

• removing blank spaces

  cathoderay

  committed
  1419727

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Commits on Jun 12, 2012

• test_raxml_tool: read RAxML_result.* instead of RAxML_bestTree.*

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  etal

  committed
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• Phylo.Applications: Correct the homepage URL for RAxML

  etal

  committed
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Commits on Jun 11, 2012

• Address more potential handle leaks under PyPy or Jython

  peterjc

  committed
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• Stricter about closing handles in test (PyPy can still run out)

  peterjc

  committed
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• Stricter about closing handles in test (seen PyPy run out again)

  peterjc

  committed
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• Conditional testing of Bio.Phylo.Applications wrappers

  peterjc

  committed
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• Basic PhyML detection in unit test (except Windows)

  peterjc

  committed
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• Should have removed this when added test_phyml_tool.py & test_raxml_tool.py

  peterjc

  committed
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• revert name changes of public variables

  

  mattfenwick

  authored and

  peterjc

  committed
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• Refactor CodonUsage style according to Pep 0008, including:

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  mattfenwick

  authored and

  peterjc

  committed
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• Use doctest for RAXML (like Bio.Align.Applications doctests)

  peterjc

  committed
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• Correct RAXML example output

  peterjc

  committed
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• Use one unit test file per external tool (for skipping tests)

  peterjc

  committed
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Commits on Jun 10, 2012

• Added unit tests for Phylo applications: PhyML, RAxML

  etal

  committed
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Commits on Jun 9, 2012

• NEWS: summarized recent changes in the Phylo module

  etal

  committed
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• Phylo.Applications: Added a wrapper for RAxML (Feature #3218)

  etal

  committed
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Commits on Jun 8, 2012

• Explicitly close database connection in test (needed with SQLite+PyPy+Windows)

  peterjc

  committed
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• Hack to get test to pass on PyPy 1.9 under Windows (handle issue)

  peterjc

  committed
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Commits on Jun 6, 2012

• Thank Matt in NEWS file for README changes

  peterjc

  committed
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• Use numbered list for bug report info (also suggested by Matt Fenwick)

  peterjc

  committed
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• Backticks for markdown (also suggested by Matt Fenwick)

  peterjc

  committed
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• Symlinked readme.md file to make it display nicely on github

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  peterjc

  committed
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• Try and mark the README file look nicer on GitHub

  peterjc

  committed
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Commits on Jun 5, 2012

• test_Phylo: 'places' is a keyword-only argument to assertAlmostEqual in Py3.1

  etal

  committed
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Commits on Jun 1, 2012

• test_Phylo: replace 'delta' kwarg w/ positions

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  etal

  committed
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Commits on May 31, 2012

• speed up root_at_midpoint algorithm

  brandoninvergo

  committed
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• Phylo: added Tree method root_at_midpoint

  etal

  committed
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Commits on May 30, 2012

• PHYLIP variants missing from AlignIO docstring

  peterjc

  committed
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Commits on May 24, 2012

• PDB: copy the .xtra dictionary in Atom (Bug #3358)

  etal

  committed
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Commits on May 23, 2012

• fix ignored exception in test_PAML_tools by removing unnecessary cleanup code

  brandoninvergo

  committed
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• add PAML codeml test case for single NSsite cases

  brandoninvergo

  committed
  7dfb9e5

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• fix new bug in PAML parsing of models with >1 NSsites

  brandoninvergo

  committed
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Commits on May 22, 2012

• fix bug in PAML codeml parsing of site-class model names

  

  brandoninvergo

  authored and

  peterjc

  committed
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• Brandon has contributed to the current release (PAML mult-genes)

  peterjc

  committed
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