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export: Clarify behavior of --lat-longs #1715

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Jan 10, 2025
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@victorlin victorlin commented Jan 10, 2025

Description of proposed changes

The previous text mentioned built in mappings but did not specify where to find them or specifics around the overriding behavior.

The link to the GitHub-hosted lat_longs.tsv file associated with the installation's version is not perfect since the local version of lat_longs.tsv can be changed (i.e. in a development environment), but this should work for most users.

Related issue(s)

Closes #1714

Checklist

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  • Checked output locally:

      --lat-longs TSV       Latitudes and longitudes for geography traits. See this file
                            for the format: <https://github.com/nextstrain/augur/blob/27.0.
                            0/augur/data/lat_longs.tsv>. This file provides the default set
                            of latitudes and longitudes. An additional file specified by
                            this option will extend the default set. Duplicates based on
                            the first two columns will be resolved by taking the
                            coordinates from the user-provided file. (default: None)
    

@victorlin victorlin self-assigned this Jan 10, 2025
@victorlin victorlin added the documentation Improvements or additions to documentation label Jan 10, 2025
The previous text mentioned built in mappings but did not specify where
to find them or specifics around the overriding behavior.

The link to the GitHub-hosted lat_longs.tsv file associated with the
installation's version is not perfect since the local version of
lat_longs.tsv can be changed (i.e. in a development environment), but
this should work for most users.
@victorlin victorlin force-pushed the victorlin/clarify-lat-longs branch from 51b78d4 to 314722c Compare January 10, 2025 18:58
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codecov bot commented Jan 10, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.72%. Comparing base (19308f0) to head (314722c).
Report is 3 commits behind head on master.

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1715   +/-   ##
=======================================
  Coverage   72.72%   72.72%           
=======================================
  Files          79       79           
  Lines        8286     8287    +1     
  Branches     1697     1697           
=======================================
+ Hits         6026     6027    +1     
  Misses       1972     1972           
  Partials      288      288           

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@victorlin victorlin merged commit 871a3c2 into master Jan 10, 2025
36 checks passed
@victorlin victorlin deleted the victorlin/clarify-lat-longs branch January 10, 2025 19:50
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export: Clarify behavior of --lat-longs
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