## Pull request overview

[sedv8808]

Pull request overview

This PR is a broad robustness + maintenance update to the neotoma2 R package, focusing on more resilient API parsing/transport, new convenience APIs (count(), samples(..., chronname=)), more capable filtering (including spatial loc), and making the test suite more stable via httptest fixtures + CI workflow tuning.

Changes:

• Added a new exported count() generic with site/sites methods to tally sites, collection units, or datasets.
• Improved API parsing and request utilities (grouping endpoint responses into a consistent shape, dropping malformed/empty records, Swagger param caching, WKT support for spatial inputs, retry/pagination logic).
• Reworked tests/CI for reliability (offline fixtures via httptest::with_mock_api(), more CI skips for heavy live calls, workflow timeouts/environment guards).

Reviewed changes

Copilot reviewed 119 out of 128 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
vignettes/neotoma2-package.Rmd	Updates vignette to use set_publication() API.
tests/testthat/test_toWide.R	Wraps tests with httptest mock API.
tests/testthat/test_taxa.R	Skips large live test on CI.
tests/testthat/test_summary.R	Adds mocked summary tests + regression for sites with no datasets.
tests/testthat/test_sites.R	Adds mocked tests and new count() test; reduces spatial load.
tests/testthat/test_samples.R	Adds mocked samples test and CI skips for heavy live tests.
tests/testthat/test_plot.R	Avoids interactive device issues by opening a null PDF device.
tests/testthat/test_parseURL.R	New unit tests for pagination/retry/base URL/body helpers and swagger caching.
tests/testthat/test_parse_speleothem.R	New unit tests for partial speleothem records parsing.
tests/testthat/test_parse_site.R	New tests for consistent parsing across endpoints + dataset field retention.
tests/testthat/test_length.R	Wraps tests with httptest mock API.
tests/testthat/test_group_data.R	New tests for endpoint-shape grouping utilities.
tests/testthat/test_getids.R	Wraps tests with httptest mock API.
tests/testthat/test_get_taxa.R	Skips very heavy/flaky live integration test on CI and when API unreachable.
tests/testthat/test_get_sites.R	Makes heavy spatial/all_data tests CI-safe and uses shared fixtures from setup.
tests/testthat/test_get_manual.R	Stubs browser opening in tests and asserts URL.
tests/testthat/test_get_downloads.R	Reduces heaviness (limit instead of all_data) + CI skips for flaky calls.
tests/testthat/test_get_documentation.R	Stubs browser opening in tests and asserts URL.
tests/testthat/test_get_datasets.R	Adds WKT loc coverage + clearer error test; CI skips for spatial flakiness.
tests/testthat/test_filter.R	Major expansion of filter tests (multi-condition, spatial, WKT/GeoJSON parity) + split mocked vs live tests.
tests/testthat/test_doi.R	Wraps DOI tests with httptest mock API.
tests/testthat/test_datasets.R	Wraps datasets accessor tests with httptest mock API and bounds fixture size.
tests/testthat/test_coordinates.R	Wraps coordinates tests with httptest mock API.
tests/testthat/test_collunits.R	Wraps collunits accessor tests with httptest mock API + adds empty-collunits regression.
tests/testthat/test_clean.R	Wraps clean tests with httptest and strengthens duplicate/clean invariants.
tests/testthat/test_cite_data.R	Wraps cite_data tests with httptest mock API.
tests/testthat/test_chronologies.R	Wraps chronology tests with httptest mock API.
tests/testthat/test_chroncontrols.R	Wraps chroncontrols tests with httptest mock API.
tests/testthat/test_c.R	Wraps c() tests with httptest mock API.
tests/testthat/test_add_chronology.R	Skips heavy Bchron-based live test on CI.
tests/testthat/setup.R	Centralizes httptest fixture path + shared Brazil polygon + spatial endpoint probe skip helper.
tests/testthat/fixtures/data_sites24.json	Adds hand-made parser fixture.
tests/testthat/fixtures/data_datasets24.json	Adds hand-made parser fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/5.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/24.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/24,1001,2001.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/24,100.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/101,102.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/1001.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites/1001,2001,15,24.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites-989a41.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites-8d5f39.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites-6700b2.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/sites-01cad7.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/downloads-711600.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/7870.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24,7870-c34357.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24,7870-5b7af1.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24,100.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24,100,101.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24-c34357.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/24-5b7af1.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/101-c34357.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/101-5b7af1.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/1001,2001,15,24.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/100-c34357.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/100-5b7af1.json	Adds recorded API fixture.
tests/testthat/fixtures/api.neotomadb.org/v2.0/data/datasets/1,2,3,4,5,6,7,7857,8,7858,10469,9,7859,10-c34357.json	Adds recorded API fixture.
README.md	Updates release tracking entries and wording.
R/taxon-methods.R	Updates roxygen aliases for subset/subscript methods.
R/subset-methods.R	Makes datasets/chronologies extractors handle empty/NULL slots safely.
R/speleothems.R	Renames speleothem age field usage to rockage.
R/speleothemdetails.R	Renames speleothem age field usage to rockage.
R/speleothem-methods.R	Renames speleothem age field usage to rockage + roxygen alias updates.
R/site-methods.R	Hardens summary() and adds count() methods.
R/set_speleothem.R	Renames argument/slot from relativeage to rockage.
R/samples.R	Adds chronname support and safer handling of empty datasets.
R/samples-methods.R	Updates roxygen aliases for subset/subscript methods.
R/publication-methods.R	Updates roxygen aliases for subset/subscript methods.
R/pick.R	Adds pick() helper to avoid partial matching and handle endpoint spelling differences.
R/parseLocation.R	Adds WKT detection + WKT support path for spatial inputs.
R/parse_speleothem.R	Hardens speleothem parsing for missing fields and drops malformed entries.
R/parse_site.R	Refactors parsing around grouped endpoint shape; drops malformed entries at each level.
R/group_data.R	Replaces endpoint-specific grouping with unified split/group helpers and preserves API order.
R/get_params.R	Adds session-level Swagger caching to avoid repeated downloads.
R/filter.R	Reworks filter condition analysis and adds spatial loc filter support.
R/dataset-methods.R	Updates roxygen aliases for subset/subscript methods.
R/contact-methods.R	Updates roxygen aliases for subset/subscript methods.
R/collunits-methods.R	Makes c(collunits) robust when all inputs are empty/NULL.
R/clean.R	Fixes site de-duplication to operate on site objects directly and handle empty datasets safely.
R/chronology-methods.R	Adds missing roxygen alias for [[ method.
R/build_speleothem.R	Drops malformed speleothems missing entityid; renames rockage.
R/build_specimen.R	Drops malformed specimens missing specimenid.
R/build_site.R	Refactors site builder to map API field names in one place and handle missing geometry safely.
R/build_sample.R	Adds records_to_df() fast-path and drops malformed samples missing sampleid.
R/build_dataset.R	Refactors dataset builder; drops malformed datasets missing datasetid.
R/build_collunit.R	Refactors collunit builder; drops malformed collunits missing collectionunitid; uses pick() for spelling variants.
R/build_chron.R	Refactors chronology builder; drops malformed chronologies and empty chroncontrols.
R/02_genericDefinitions.R	Adds samples(..., chronname=) generic signature and new count() generic.
R/01_classDefinitions.R	Renames speleothem slot relativeage -> rockage.
NEWS.md	Adds 1.1.0 release notes for new features and robustness changes.
NAMESPACE	Exports count() and updates imports for new/refactored code paths.
man/subset.Rd	Regenerates docs for updated S4 subset replacement signatures.
man/sub.Rd	Regenerates docs for updated S4 subset signatures.
man/sub-subset.Rd	Regenerates docs for updated S4 [[<- signatures.
man/sub-sub.Rd	Regenerates docs for updated S4 [[ signatures.
man/set_speleothem.Rd	Regenerates docs for rockage parameter rename.
man/samples.Rd	Documents new chronname argument across samples() methods.
man/samples-sites-method.Rd	Documents new chronname argument for samples,sites.
man/plot.Rd	Updates plot method signatures/aliases.
man/filter.Rd	Documents spatial loc filter support.
man/count.Rd	Adds generated documentation for new count() generic/methods.
inst/CITATION	Updates author metadata formatting and roles.
DESCRIPTION	Bumps version/date and updates Authors@R and Suggests/Imports formatting.
cran-comments.md	Adds 1.1.0 CRAN submission notes.
.Rbuildignore	Excludes additional non-package files and recorded httptest fixtures from CRAN tarball.
.gitignore	Ignores data-raw and vignette build artifacts.
.github/workflows/test-coverage.yml	Adds timeouts and API request bounds for coverage job.
.github/workflows/r-cmd-check.yml	Modernizes workflow and forces CRAN-like skipping of live API tests.

Suppressed comments (2)

R/site-methods.R:575

• count(x, level = "datasets") will error when a site has NULL collunits or when a collunit has a NULL/empty datasets slot (cu@datasets@datasets). Given the PR adds multiple guards for optional slots, this should be made NULL-safe too.
  R/site-methods.R:612
• count() for a single site assumes x@collunits and each cu@datasets slot are always present. This can error on partial objects (e.g. set_site() with no collunits, or collunits with no datasets), even though the rest of the PR treats those slots as optional.

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Originally posted by @Copilot in #67 (review)