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Allow export of trees #88

Merged
merged 20 commits into from
Dec 19, 2023
Merged

Allow export of trees #88

merged 20 commits into from
Dec 19, 2023

Commits on Dec 12, 2023

  1. getconnections() allows branch(es) to be excluded

    @richardreeve
    richardreeve committed Dec 12, 2023
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  2. Rewrite show() commands for trees

    @richardreeve
    richardreeve committed Dec 12, 2023
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  3. Allow export of newick trees with outputtree!()

    @richardreeve
    richardreeve committed Dec 12, 2023
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Commits on Dec 14, 2023

  1. Add Phylo.write() to output a tree.

    @richardreeve
    richardreeve committed Dec 14, 2023
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Commits on Dec 18, 2023

  1. Newick output can map names

    @richardreeve
    richardreeve committed Dec 18, 2023
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  2. Fix newick export and export Newick, Nexus types

    @richardreeve
    richardreeve committed Dec 18, 2023
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  3. Add tests for tree export

    @richardreeve
    richardreeve committed Dec 18, 2023
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Commits on Dec 19, 2023

  1. Fix typos, improve testing for show and outputtree(!)

    @richardreeve
    richardreeve committed Dec 19, 2023
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  2. Testing node and branch outputs

    @richardreeve
    richardreeve committed Dec 19, 2023
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  3. Write nexus files and test

    @richardreeve
    richardreeve committed Dec 19, 2023
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  4. Add in nexus tests

    @richardreeve
    richardreeve committed Dec 19, 2023
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  5. Simplify writing trees to different formats, more testing

    @richardreeve
    richardreeve committed Dec 19, 2023
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  6. Simplify write

    @richardreeve
    richardreeve committed Dec 19, 2023
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  7. Remove pairs from API.jl

    @richardreeve
    richardreeve committed Dec 19, 2023
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  8. Add docs and simplify io for nexus

    @richardreeve
    richardreeve committed Dec 19, 2023
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  9. Fix docs

    @richardreeve
    richardreeve committed Dec 19, 2023
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  10. Fix doc example

    @richardreeve
    richardreeve committed Dec 19, 2023
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  11. Bump version, add NEWS and fix docs

    @richardreeve
    richardreeve committed Dec 19, 2023
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  12. Extend parse for parsing newick/nexus input, and add format keyword t… 

    …o write.
    @richardreeve
    richardreeve committed Dec 19, 2023
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  13. Add and fix docs. Export treesettype().

    @richardreeve
    richardreeve committed Dec 19, 2023
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