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Document CSV export format #257

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gaurav opened this issue Aug 22, 2022 · 1 comment
Open

Document CSV export format #257

gaurav opened this issue Aug 22, 2022 · 1 comment
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documentation priority: low
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Klados v1.0

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@gaurav
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gaurav commented Aug 22, 2022

The CSV export format is designed to mimic the summary table we show the user, but it would be good for downstream applications to have this format documented on the website or docs somewhere.
@gaurav gaurav added this to the Klados v1.0 milestone Aug 22, 2022
@gaurav gaurav mentioned this issue Aug 22, 2022
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gaurav commented May 24, 2023 •
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This should go into the Klados wiki, with a link to it from the application.
This won't be archived. Let's put it into a docs/ folder and then link directly to the Markdown file.

gaurav added a commit that referenced this issue Feb 28, 2024
@gaurav
Added documentation of the CSV export format.
5413f89 
As per #257.
@gaurav gaurav mentioned this issue Feb 28, 2024
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gaurav added a commit that referenced this issue Jun 22, 2024
@gaurav
Merge pull request #321 from phyloref/improve-documentation
fa4a8d8 
- Added note that definition should include qualifiers (closes #168)
- Documented the CSV export format (related to #257, but I won't close that until I like to it from somewhere in the interface) as [a Markdown file](https://github.com/phyloref/klados/blob/bfae34e42e954920191e3e473f31ee2ae49ffdde/docs/ExportFormats.md).
- Fixed a bug in which we were providing all the expected resolutions before all the actual resolution in the CSV file, despite the header saying that they should be interleaved (i.e. `expected 1, actual 1, expected 2, actual 2`).
- The Open Tree of Life lookup code was previously recording the provenance of the phylogeny in the phylogeny description field, but since this field is no longer used, I've moved it into the phylogeny curator notes field (see example below).
- I accidentally turned on "reformat file on save", and so my IDE changed a bunch of file formatting without me noticing. That shouldn't change any functionality and should be easier to read/maintain in the future, but it's still annoying. 

This PR also closes #300 by modifying the summary table to make it clear that the final columns refer to phylogenies and replacing phylogeny descriptions (which are no longer displayed in Klados) with phylogeny curator notes.
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