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Refactor code.#177

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sdhutchins wants to merge 78 commits intodev-refactoreddatasnakes/OrthoEvolution:dev-refactoredfrom refactor-phylodatasnakes/OrthoEvolution:refactor-phyloCopy head branch name to clipboard

+1,102-887

Commits

Commits on Jul 31, 2019

• Renamed orthophyl.py to phyml.py

  

  sdhutchins

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  dc1529c

• Renamed orthophylip.py to phylip.py

  

  sdhutchins

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  68be622

• Updated import of phylip.py

  

  sdhutchins

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  6ff9dcd

• Updated import of phyml.py

  

  sdhutchins

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  3c9edcc

Commits on Aug 1, 2019

• Added docstrings for the init of the PhyML class.

  

  sdhutchins

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  68608e5

• Refactored init in ETE3PAMl to create better API.

  

  sdhutchins

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  7bf7740

• Fixed logging issue.

  

  sdhutchins

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  0d6b792

Commits on Aug 8, 2019

• Added check_exe function.

  

  sdhutchins

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  4b267b3

• Added new examples to README.

  

  sdhutchins

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  dfaf2f3

• Added ApplicationError to try/except in run method.

  

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  c7d08cc

• Added a test for phyml

  

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  7c420b9

• Added test data for phyml test.

  

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  01b458c

• Added phyml installation to travis script.

  

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  f4edaf7

• Added ability for user to choose number of processors.

  

  sdhutchins

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  7ee4e7b

• Updated README for new api.

  

  sdhutchins

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  a2214ea

• Removed deprecated csvtolist

  

  sdhutchins

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  73261f2

• Added logging to ETE3PAML

  

  sdhutchins

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  215a24d

• Added _import_alignment method

  

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  2734fc7

Commits on Aug 12, 2019

• Added a README for the PHYLIP class.

  

  sdhutchins

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  2feab29

• Added try/except/else/finally for phylip methods

  

  sdhutchins

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  5e75f38

• Removed phylip test from Phylip folder.

  

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  1d47901

Commits on Aug 19, 2019

• Added docstrings to ETE3PAML class.

  

  sdhutchins

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  a584164

• Fixed errors in README.

  

  sdhutchins

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  eb5914d

• Added TODO in codeml.py

  

  sdhutchins

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  32676ae

• Changed data in test.

  

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  f86847a

• Added missing doctrings.

  

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  2a718e3

• Updated example in README.

  

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  8a27d3b

• Refactored TreeViz api.

  

  sdhutchins

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  a764257

• Refactored ncbi-download script

  

  sdhutchins

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  9cbfc28

Commits on Aug 21, 2019

• Added validation function. Extended run api.

  

  Shaurita D. Hutchins

  committed
  073f272

• Updated PhyML test data.

  

  Shaurita D. Hutchins

  committed
  c0084ac

Commits on Aug 22, 2019

• Added ability to capture output for Phylip

  

  sdhutchins

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  a61a05d

• Fixed validate format issue.

  

  sdhutchins

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  0e697f1

• Fixed PhyML arg.

  

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  03ed667

Commits on Aug 23, 2019

• Renamed PhyloTree module to TreeViz

  

  sdhutchins

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  d1589a9

Commits on Aug 27, 2019

• Added a treeviz test.

  

  sdhutchins

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  732e120

• Removed sciluigi. Added matplotlib.

  

  sdhutchins

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  ccc8230

• Removed matplotlib from travis CI pip install line

  

  sdhutchins

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  1d6341a

• Added updated example to readme.

  

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  eec0b1f

• Added docstrings.

  

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  e3a1464

• Removed version of matplotlib

  

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  10c9261

• Corrected path to tree file in test.

  

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  35dd071

• Updated Flask to latest version and removed other flask libraries.

  

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  c96b91c

• Corrected paths in tests.

  

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  b40adb6

• Additional fix to current directory for tests.

  

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  1b7fe33

• Changed paths of test output.

  

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  e8d8638

• Fixed Phyml tests

  

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  007efd5

Commits on Dec 16, 2022

• Merge branch 'dev-refactored' into refactor-phylo

  sdhutchins

  authored
  e4d860f

Commits on Dec 18, 2022

• Merge branch 'dev-refactored' into refactor-phylo

  sdhutchins

  authored
  fbbc7f8

Commits on Dec 25, 2022

• Fix extra lines in code.

  sdhutchins

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  a5805f2

Commits on Jan 2, 2023

• Fix psutil requirement.

  sdhutchins

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  ff5662c

• Remove cookiecutter version.

  sdhutchins

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  e167cab

• Remove Flask version requirements.

  Show description for 813215b
  sdhutchins

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  813215b

• Drop support for Python < 3.7.

  sdhutchins

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  124fdf5

• Fix name for log level to format color.

  sdhutchins

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  75dee6c

• Remove version for setuptools.

  sdhutchins

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  50d5621

• Merge branch 'dev-refactored' into refactor-phylo

  sdhutchins

  authored
  a4dfd41

• Remove incorrect character from travis script.

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  1219a2e

• Add commands to PyBasher.

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  b41dd60

• Refactor blastpipeline.

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  59f33f2

• Remove Flask-User.

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  6cd21c5

• Set _COLORS for logging.

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  82b2827

• Deprecate airflow.

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  9a59d64

Commits on Jan 3, 2023

• Comment out phyml test.

  sdhutchins

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  33aec9c

• Add more test infrastructure.

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  963ab83

• Remove luigi version.

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  7ba045b

• Fix cookies test.

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  7b32f0a

Commits on Jan 6, 2024

• Test.

  sdhutchins

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  5caa2b8

• Test.

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  5bcaffd

• Add github action for ci.

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  1389ee9

• Fix test.

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  ed7783d

• Fix texts for Oven and CookBook.

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  e2ae3ca

• Updated utils tests.

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  7b7a8c5

• Remove PackageVersion test.

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  54a72f8

• Fix Cookies tests.

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  38f9b58

• Remove github action.

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  39788c0

Commits on Jan 8, 2024

• Add ci back. Remove blast tests.

  sdhutchins

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  3ca103a

• Change timeout.

  sdhutchins

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  ab2ef59