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Update function URLs to fix a number of tests (SRS, ChemSpider) #424

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merged 8 commits into from
Dec 23, 2024

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@stitam stitam commented Dec 22, 2024

Related to issue #422, #423.

Brief description of the PR:

Two functions broke, probably because their webservice URLs changed. This PR updates these URLs so they work again.

srs_query() now uses a new URL and returns a list of tibbles instead of a list of data frames. I switched to tibble because the output contains nested data frames as well which print better with tibble.

is.inchikey(type = "chemspider") used a ChemSpider webservice which did not require an API key. It seems this webservice is no longer working. I implemented another ChemSpider API, but the alternative requires an API key. Because of the API key I also recorded all related tests using vcr.

When I R CMD checked the package I received some notes which were probably related to a new roxygen2 version. To handle these, I 1. tidied get_cid() documentation, 2. created separate R scripts to describe each webchem data set, 3. moved part of the webchem-package.R script to zzz.R, 4. Implemented this "_PACKAGE" thing in webchem-package.R which seems to guide roxygen2 in creating the documentation page behind ?webchem.

I plan to merge this PR first to ensure all checks pass and then rebase other PRs on the new master.

PR task list:

  • Update NEWS
  • Add tests (if appropriate)
  • Update documentation with devtools::document()
  • Check package passed

@stitam stitam merged commit 2e875ec into ropensci:master Dec 23, 2024
7 checks passed
@stitam stitam deleted the issue422 branch December 23, 2024 21:28
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