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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

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Commits

Commits on Jul 31, 2019

• Renamed orthophyl.py to phyml.py

  

  sdhutchins

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• Renamed orthophylip.py to phylip.py

  

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• Updated import of phylip.py

  

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• Updated import of phyml.py

  

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Commits on Aug 1, 2019

• Added docstrings for the init of the PhyML class.

  

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• Refactored init in ETE3PAMl to create better API.

  

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• Fixed logging issue.

  

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Commits on Aug 8, 2019

• Added check_exe function.

  

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• Added new examples to README.

  

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• Added ApplicationError to try/except in run method.

  

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• Added a test for phyml

  

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• Added test data for phyml test.

  

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• Added phyml installation to travis script.

  

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• Added ability for user to choose number of processors.

  

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• Updated README for new api.

  

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• Removed deprecated csvtolist

  

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• Added logging to ETE3PAML

  

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• Added _import_alignment method

  

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Commits on Aug 12, 2019

• Added a README for the PHYLIP class.

  

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

  

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• Removed phylip test from Phylip folder.

  

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Commits on Aug 19, 2019

• Added docstrings to ETE3PAML class.

  

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• Fixed errors in README.

  

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• Added TODO in codeml.py

  

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• Changed data in test.

  

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• Added missing doctrings.

  

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• Updated example in README.

  

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• Refactored TreeViz api.

  

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• Refactored ncbi-download script

  

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Commits on Aug 21, 2019

• Added validation function. Extended run api.

  

  Shaurita D. Hutchins

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• Updated PhyML test data.

  

  Shaurita D. Hutchins

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Commits on Aug 22, 2019

• Added ability to capture output for Phylip

  

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• Fixed validate format issue.

  

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• Fixed PhyML arg.

  

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Commits on Aug 23, 2019

• Renamed PhyloTree module to TreeViz

  

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Commits on Aug 27, 2019

• Added a treeviz test.

  

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• Removed sciluigi. Added matplotlib.

  

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• Removed matplotlib from travis CI pip install line

  

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• Added updated example to readme.

  

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• Added docstrings.

  

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• Removed version of matplotlib

  

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• Corrected path to tree file in test.

  

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

  

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• Corrected paths in tests.

  

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• Additional fix to current directory for tests.

  

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• Changed paths of test output.

  

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• Fixed Phyml tests

  

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Commits on Dec 16, 2022

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

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Commits on Dec 18, 2022

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

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Commits on Dec 25, 2022

• Fix extra lines in code.

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Commits on Jan 2, 2023

• Fix psutil requirement.

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• Remove cookiecutter version.

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• Remove Flask version requirements.

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• Drop support for Python < 3.7.

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• Fix name for log level to format color.

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• Remove version for setuptools.

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

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• Remove incorrect character from travis script.

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• Add commands to PyBasher.

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• Refactor blastpipeline.

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• Remove Flask-User.

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• Set _COLORS for logging.

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• Deprecate airflow.

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Commits on Jan 3, 2023

• Comment out phyml test.

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• Add more test infrastructure.

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• Remove luigi version.

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• Fix cookies test.

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Commits on Jan 6, 2024

• Test.

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• Test.

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• Add github action for ci.

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  1389ee9

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• Fix test.

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• Fix texts for Oven and CookBook.

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  e2ae3ca

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• Updated utils tests.

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• Remove PackageVersion test.

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• Fix Cookies tests.

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• Remove github action.

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Commits on Jan 8, 2024

• Add ci back. Remove blast tests.

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• Change timeout.

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