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Feature/morphology2#32

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wrightaprilm wants to merge 65 commits intobrettc:paul_developbrettc/partitionfinder:paul_developfrom wrightaprilm:feature/morphology2wrightaprilm/partitionfinder:feature/morphology2Copy head branch name to clipboard

+25,479-215

Commits

Commits on Jun 24, 2013

• morphology works in principle

  Show description for 3fbecd6
  roblanf

  committed
  3fbecd6

Commits on Jul 1, 2013

• added dummy morphology models for phyml

  roblanf

  committed
  e0d9e80

Commits on Sep 30, 2013

• Include support for LG4M and LG4X models

  Show description for 6010c94
  roblanf

  committed
  6010c94

• exclude LG4X models from all predefined model lists

  Show description for dc55bf6
  roblanf

  committed
  dc55bf6

• edit raxml parser to parse output from LG4* models

  roblanf

  committed
  6119350

Commits on Oct 14, 2013

• Include support for LG4M and LG4X models

  Show description for d298d0a
  

  roblanf

  authored and

  brettc

  committed
  d298d0a

• exclude LG4X models from all predefined model lists

  Show description for 8cacdb5
  

  roblanf

  authored and

  brettc

  committed
  8cacdb5

• edit raxml parser to parse output from LG4* models

  

  roblanf

  authored and

  brettc

  committed
  b940dcc

• Merge branch 'feature_LG4M' of https://github.com/brettc/partitionfinder into feature_LG4M

  brettc

  committed
  5f84f5d

Commits on Oct 16, 2013

• update download stats

  roblanf

  committed
  2079378

• update download plot script

  Show description for 4a8a58b
  roblanf

  committed
  4a8a58b

• change plot size for download plots

  roblanf

  committed
  fbd9b9a

Commits on Oct 31, 2013

• Now using python "shelve" to store subsets.

  Show description for 44a5e62
  brettc

  committed
  44a5e62

• Reformatting.

  brettc

  committed
  18ed427

• Get rid of all phylofiles for now.

  brettc

  committed
  1fdcee4

• Merge branch 'feature/simple-database' into develop

  brettc

  committed
  ca287bd

Commits on Nov 20, 2013

• update download and citation stats and plots

  roblanf

  committed
  ba091ac

Commits on Nov 21, 2013

• Merge branch 'feature/morphology' into feature/morphology2

  Show description for a2187be
  roblanf

  committed
  a2187be

• resolve conflict in parser.py

  roblanf

  committed
  3e33ac5

• resolve conflict in raxml_models.py

  roblanf

  committed
  58d84aa

• add comment back to raxml_models.py

  roblanf

  committed
  0a85bff

• resolve conflict in reporter.py

  roblanf

  committed
  d011a79

• resolve paser.py conflict

  roblanf

  committed
  b9ee57a

• resovle subset.py conflice

  roblanf

  committed
  f730ace

• add morphology test

  roblanf

  committed
  2325c31

• clean up model list checking

  Show description for dcc88c3
  roblanf

  committed
  dcc88c3

Commits on Jan 20, 2014

• added switch for deafulting to raxml if morph

  wrightaprilm

  committed
  1f8174d

Commits on Jan 22, 2014

• rescaling algo

  wrightaprilm

  committed
  911565c

• added rescaling as randint.py

  wrightaprilm

  committed
  92561b7

Commits on Jan 23, 2014

• changed around recaling metric

  wrightaprilm

  committed
  4960bb9

• modified scaling a little bit to be more inclusive to older builds of numpy

  wrightaprilm

  committed
  abf7037

Commits on Jan 26, 2014

• added matrix test

  wrightaprilm

  committed
  3f569f3

• tested rescaling unctions and times them. see comments for time info.

  wrightaprilm

  committed
  b0c8e36

Commits on Feb 4, 2014

• added comprehension to replace NaNs with ?

  wrightaprilm

  committed
  e50dda8

• added comments on timeit testing

  wrightaprilm

  committed
  cedb014

• revamped some of the unit tests, started to fix another.

  wrightaprilm

  committed
  7800da6

Commits on Feb 6, 2014

• updated tests. will integrate tests with the testing suite l8r.

  wrightaprilm

  committed
  c0dd145

Commits on Feb 8, 2014

• Have integrated (loosely) my tests, html file full of code coverage results

  wrightaprilm

  committed
  f3f9587

Commits on Feb 18, 2014

• added testing datawq

  wrightaprilm

  committed
  2649855

• demystified test names

  wrightaprilm

  committed
  500646e

• demystified names

  wrightaprilm

  committed
  ab8c4bd

Commits on Feb 19, 2014

• tabs-> spaces

  wrightaprilm

  committed
  7d5f0e2

Commits on Feb 24, 2014

• de-specified tests to run in general paths

  wrightaprilm

  committed
  df84901

• removed spare files

  wrightaprilm

  committed
  e216765

Commits on Mar 10, 2014

• fixed abspath

  wrightaprilm

  committed
  9e3de7b

Commits on Dec 12, 2014

• modifying models and parsing for morphology

  wrightaprilm

  committed
  0c2dd1b

Commits on Dec 19, 2014

• fixed param bug

  wrightaprilm

  committed
  5b3f9ae

Commits on Dec 20, 2014

• trying to remove shelf.

  wrightaprilm

  committed
  a20f237

• fixed pickle bug. reverted to pickle from shelf

  wrightaprilm

  committed
  5f0669d

Commits on Jan 9, 2015

• mostly clean-up

  wrightaprilm

  committed
  4c1ee54

• Merging paul's changes

  wrightaprilm

  committed
  5469766

Commits on Jan 13, 2015

• pre-merge commit of small typo fixes

  wrightaprilm

  committed
  07ee2b1

• Merge branch 'paul_develop' of https://github.com/brettc/partitionfinder into paul_merge

  Show description for 3d4940e
  wrightaprilm

  committed
  3d4940e

• new tiger exec

  wrightaprilm

  committed
  ed88d6d

Commits on Jan 15, 2015

• caught a few morph-specific bugs

  wrightaprilm

  committed
  287ee4e

• putting in a second commit due to binaries; added new binaries for RAXML and Fast_tiger

  wrightaprilm

  committed
  12f1086

Commits on Jan 16, 2015

• added a 0-index, which fixes the indexing prob

  wrightaprilm

  committed
  924035c

Commits on Jan 17, 2015

• added paul's patches

  wrightaprilm

  committed
  00de58d

Commits on Jan 18, 2015

• added to readme, removed extra function

  wrightaprilm

  committed
  4955394

• added phylip converter and more readme

  wrightaprilm

  committed
  ccbe53f

• Update README.md

  wrightaprilm

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  c5f6d24

Commits on Jan 21, 2015

• Update README.md

  wrightaprilm

  committed
  500449f

• Update README.md

  wrightaprilm

  committed
  849d148

Commits on Jan 31, 2015

• untracked extra stuff for pull request to Paul

  wrightaprilm

  committed
  9bddfe6

• remove unnecessary call to shelve.

  wrightaprilm

  committed
  e75c23f