traits.build v2.0.0 release #191
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* Add `standard_error` as an allowable `value_type` Closes issues #171 * Fix minor issues causing tests to fail --------- Co-authored-by: Daniel Falster <[email protected]>
Update the traits.build citation on GitHub to also display the traits.build paper in Ecological Informatics
Removal of functions from traits.build to accompany release of austraits 3.0
* util_df_to_list and util_list_to_df are now sourced from austraits (as convert_df_to_list and convert_list_to_df)
* build_combine is now replaced by austraits::bind_databases
* plot_trait_distribution_beeswarm, trait_pivot_longer and trait_pivot_wider had been in both packages and have now been removed from traits.build
* the function flatten_database is a replacement for database_create_combined_table, which was still on a branch
* at the bottom of utils.R, the functions that have been moved and renamed are also assigned their old names, to ensure that the names included in our Eco Informatics publication are still "valid" and that people using old remake/build.R files are not inconvenienced by these changes
* add deprecation warnings:
- Added lifecycle as dependency, reverted function for util_list_to_df1, added deprecation warning, reexported austraits::convert_list_to_df1
- Enabled md capabailities in rd docs, added lifecycle as a dependency, reexported austraits::convert_list_to_df2
- Deprecated util_list_to_df2 added lifecycle as a dependency, reexported austraits::convert_list_to_df2
- Deprecated convert_df_to_list, reexported austraits::convert_list_to_df
- Deprecated build_combine, reexported austraits::bind_databases
- Calling incorrect function in utils, added suppresswarnings in tests
---------
Co-authored-by: Fonti Kar <[email protected]>
Fixing two small tests errors:
- error is no contexts
- test for unit_in in unit_conversions.csv isn't correct - we don't expect this behaviour always. (Remove check for units in unit_conversions - this isn't expected. The `unit_in` field can also be a data.csv column. Or there can be units that are used, but happen to not be in the unit_conversions because there aren't any instances where they require converting.)
solves issue #150, noted in issue #146
This branch was mistakenly never merged in and is the reason for issue #179 emerging.
Fixes issue #131 * Move custom expect_ functions out of dataset_test, into R/test_functions.R so that R CMD check warnings are removed (otherwise "no visible global function definition" warning comes up) * Rename prefixes to test_expect_ to differentiate between custom testthat functions and built-in testthat functions * I kept using expect_silent() from {testthat} instead of writing a custom function because I'm not sure how to rewrite the function to capture messages on top of errors and warnings --------- Co-authored-by: ehwenk <[email protected]>
* Update traits.build_schema.yml * Update traits.build_schema.yml
* a few bug fixes, identified in part by @hrlai - further mismatches to function names, functions that are now in `austraits` were still listed in `_pkgdown.yml` * another issue uncovered by @hrlai indicated we really needed to run dataset_test on the traits.build example datasets: * added dataset_test for example datasets - includes allowing "output" folders and Readme files in data folders closes issue #183 closes issue #185 closes issue #143
* Add standard deviation to allowed value types Although SE mostly reported today, older manuscripts often document SD instead
Two fixes: - needed to add deprecated/renamed functions to pkgdown.yml since they are still valid function names output by traits.build - missed a pair of brackets in ontology
prepare for release by updating NEWS and DESCRIPTION files
* bump ontology to 1.0.0 for first official release * rebuild traits.build website * preparing for traits.build 2.0.0
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bind_databases<--build_combineconvert_df_to_list<--util_df_to_listconvert_list_to_df1<--util_list_to_df1convert_list_to_df2<--util_list_to_df2plot_trait_distribution_beeswarm,trait_pivot_longerandtrait_pivot_widerhad been in both austraits and traits.build packages and have now been removed from traits.buildflatten_database(had been suggested to bedatabase_create_combined_table)dataset_testdataset_testfunction, so it is checked explicitly by traits.build (run on Example datasets)Issues addressed since last traits.build release:
Issue #150 & Issue #154 (error if no contexts)
Issue #179 (incorrect test written that flagged an error if input/output units identical)
Issue #171 (SE required as a value type)
Issue #131 (remove duplicate functions)
Issue #183 (deprecated function still being used)
Issue #185 (context table columns mis-ordered, dataset test failing)
Issue #143 (add dataset_test tests)