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Add local GBIF archive reading#505

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tpoisot merged 19 commits into
PoisotLab:feat/gbif/localfilefrom
jeetsukumaran:js-develop
Mar 29, 2026
Merged

Add local GBIF archive reading#505
tpoisot merged 19 commits into
PoisotLab:feat/gbif/localfilefrom
jeetsukumaran:js-develop

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In reference to #504

@tpoisot
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tpoisot commented Mar 29, 2026

Hey @jeetsukumaran - I finally took the time to refactor the code a little bit. I am going to add a vignette to the doc, and also make changes to the download function so that it will work with DwC files as well (so, thanks for that!).

Summary of changes:

  • no |> (I love them for code, but not a fan for debugging)
  • I removed the license block, but added you to the package authors in the Project.toml
  • I have dropped the function to return as a DataFrame, but will make some light refactoring to be able to passe a second argument to localarchive
  • I have changed the function names (internals start with _)

Current to-do list on my end before merging:

  • edit CHANGELOG processing to link GitHub usernames
  • vignette
  • change download to use localarchive internally
  • change_materialize to work on arrays
  • add second argument to download (and localarchive) to accept something other than Occurrences

@tpoisot tpoisot changed the base branch from main to feat/gbif/localfile March 29, 2026 19:44
@tpoisot tpoisot merged commit 888e2a0 into PoisotLab:feat/gbif/localfile Mar 29, 2026
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tpoisot commented Mar 29, 2026

Moving this to another branch so we can build the documentation preview.

@jeetsukumaran
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Thanks @tpoisot ! Appreciate the time and effort put into this package very much!

tpoisot added a commit that referenced this pull request Mar 30, 2026
* Add local GBIF archive reading (#505)

* Add local GBIF archive reading

* doc(gbif): CHANGELOG

* semver(gbif): v1.2.0

* chore(gbif): rename file

* chore(gbif): cutting location functions from the archive (already handled by occurrences interface)

* feat(gbif): localarchive for local reading

* doc(gbif): CHANGELOG

* chore(gbif): AUTHORSHIP @jeetsukumaran

* compat(gbif): JSON@1

* feat(gbif): donwload uses the localarchive function internally

* doc(gbif): CHANGELOG

* test(gbif): tests for the reading / conversion

* feat(gbif): localarchive/download integration complete

* bug(gbif): use AbstractDict for internals to support JSON v1

* doc(gbif): vignette

---------

Co-authored-by: Timothée Poisot <timothee.poisot@umontreal.ca>

* doc: fix variable name

* test(gbif): fix import

* doc: clarify simple/dwc

* ci: link github usernames in changelogs

* test(gbif): fix test for equality

* doc: tweak local

* test(gbf): add CSV to test module

* doc: change vignette title

* doc: add DataFrame  to local gbif vignette

* chore: fix github user link in changelog

* chore: username needs space before in CI

---------

Co-authored-by: Jeet Sukumaran <jeetsukumaran@users.noreply.github.com>
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2 participants