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[DOC] convertFA2Tree #94

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the-mayer opened this issue Oct 9, 2024 · 2 comments
Open

[DOC] convertFA2Tree #94

the-mayer opened this issue Oct 9, 2024 · 2 comments
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@jananiravi @the-mayer @epbrenner @Klangina
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cleanup Rm deadcode & duplication, streamline documentation Improvements or additions to documentation, incl. R docstring/roxygen2 outreachy for outreachy interns

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@the-mayer
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the-mayer commented Oct 9, 2024 •
edited by jananiravi
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MolEvolvR contains functions with very similar/duplicate functionality:

Previous Name Current Name
convert_fa2tre convertFA2Tree
generate_fa2tre convertFA2Tree

These functions should be disambiguated, or refactored so that they can be combined with a parameter switching between the different functionality.

Originally posted by @teddyCodex in #54 (comment)
@the-mayer the-mayer added the documentation Improvements or additions to documentation, incl. R docstring/roxygen2 label Oct 9, 2024
@Klangina
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I'd like to work on this, may I be assigned this issue?

@jananiravi
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sure, go for it!

Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 22, 2024
@Klangina
Fixes Issue JRaviLab#94-
4124b68 
 - Refactored  and merged R/tree.R CreateFA2Tree and ConvertFA2Tree.
- Parametrized every hardcoded value and path in ConvertFA2Tree
- Refactored convertAlignment2Trees to support running both modes.
- Backward compatible
- Updated all documentation for R/tree.R
@jananiravi jananiravi added the outreachy for outreachy interns label Oct 26, 2024
@jananiravi jananiravi changed the title convertFA2Tree [DOC] convertFA2Tree Oct 26, 2024
@jananiravi jananiravi added the cleanup Rm deadcode & duplication, streamline label Oct 26, 2024
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@jananiravi jananiravi

@the-mayer the-mayer

@epbrenner epbrenner

@Klangina Klangina

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cleanup Rm deadcode & duplication, streamline documentation Improvements or additions to documentation, incl. R docstring/roxygen2 outreachy for outreachy interns
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@jananiravi @the-mayer @epbrenner @Klangina