Changes for v5 austraits.build #78
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
changes to austraits functions that will be required once v5 is released
|
Zenodo is currently down so some tests will fail... |
|
I am a bit confused with .data$ usage now! Passing locally when I use .data$ throughout functions, but tidyselect throws warnings in GitHub Action R CMD check |
Less confused now after reading this: https://community.rstudio.com/t/use-of-data-in-tidyselect-expressions-is-now-deprecated/150092 |
|
Bah! I can't get this passing with all the tidyselect stuff. Will look on Monday!!! Assistance would be great if someone knows what I am doing wrong |
- As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user
|
@dfalster over to you :D |
|
Sorry for touching this branch! I was trying to get @fontikar When you're back I'm happy to look through tidyselect warnings as I had to remove them for traits.build so might have an idea where they're coming from. |
|
Also my changes were wrong, it was fine as is! |
Changes column names, reflecting recent changes to traits.build output. One thing I haven't yet changed, under taxa, the only "required" columns going forward as `taxon_name`, `taxon_rank` and `aligned_name`, so maybe use an `any_of`? AusTraits will have all columns indicated, but other traits.build databases won't.
add `any_of` to column selection within `as_wide_table` to accommodate other traits.build databases that don't have the same columns in taxon_list.csv
…or update with as_wide_table with removal of variable
|
@dfalster all good to merge this?? |
dfalster
approved these changes
Nov 19, 2023
|
@fontikar The austraits.build tutorial that uses the functions is rendering. But maybe wait 1-2 hours until I've finished going through it line by line? |
|
Sounds good no worries! I reran tests locally and all passing so its should be smooth sailing from here |
fontikar
added a commit
that referenced
this pull request
Nov 22, 2023
* #60 fixed imports for pivot_wider, organised tests, currently not working for new version, waiting for austraits.build update * Minor naming adjustments in test * Change some dependencies to imports Some packages needed to make plots are included in suggests. This means that core functions of package may not work. * Remove helper functions to vignettes * Update deprecated functions * Restructure tests to run faster - reuse outputs from previous function calls to reduce runtime - reduce dataset sizes for slow functions (summarise_trait_means, trait_pivot_wider, plot_locations) - silence some outputs closes #62 * Change GH actions triggers * ensure consistent ordering of rows * bumped version number * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Pulled files we want to develop from change-v5 * Changes for v5 austraits.build (#78) * changes required for v5 austraits.build * Removed original_name for trait_pivot_wider3 for v5.0.0 * Added trait_pivot_wider for v4.x.x and code for what_version * Making new switches for join and as_wide_table based on new versioning * Sub switch for extract_ and recreated internal data * Sub switches for trait_pivot_longer * Minor fix in join_methods * Added vars a global vars * Removed .data calls when not needed * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Recreated data so extract is passing * Update `treatment_id` with `treatment_context_id` * Revert "Update `treatment_id` with `treatment_context_id`" This reverts commit 3fc6717. * minor column name changes Changes column names, reflecting recent changes to traits.build output. * Update as_wide_table.R add `any_of` to column selection within `as_wide_table` to accommodate other traits.build databases that don't have the same columns in taxon_list.csv * Fixed getting versions and load austraits with zenodo updates and minor update with as_wide_table with removal of variable * Fixed minor bug in get_version_latest --------- Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: yangsophieee <sophie.yang917@gmail.com> * Bumped version number and updated news * Added references to packages * Updated version for GH steps * Updated v number for GHA * Expanding testing suite to all 3 major versions of AusTraits (#86) * Created lites for all main versions of AusTraits * Passing for as_wide_table * Passing for as_wide_table and for extract_ * expanding test suite to all 3 majors, switches for method id adjusted * expanding test suite to all 3 majors for summarise_D * Expanding these for all 3 versions * Added PR trigger for dev branch * Added codecov yml * Setting limit for patch cov --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Working with @ehwenk to update functions so they work across all versions of AusTraits.
R CMD check still gives 1 x NOTE but I want see if I can deal with these later and if GitHub Action will be unhappy with me