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V5.0.0 #283

Merged
merged 6 commits into from
Aug 12, 2024
Merged

V5.0.0 #283

merged 6 commits into from
Aug 12, 2024

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cboettig
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Welcome to rfishbase 5! This is the fourth rewrite of the original rfishbase package described in Boettiger et al. (2012).

Another streamlined re-design following new abilities for data hosting and access.
This release relies on a HuggingFace datasets hosting for data and metadata hosting
in parquet and schema.org.

Data access is simplified to use the simple HuggingFace datasets API instead
of the previous contentid-based resolution. This allows metadata to be defined
with directly alongside the data platform independent of the R package.

A simplified access protocol relies on duckdbfs for direct reads of tables.
Several functions previously used only to manage connections are now deprecated
or removed, along with a significant number of dependencies.

Core use still centers around the same package API using the fb_tbl() function,
with legacy helper functions for common tables like species() are still accessible and
can still optionally filter by species name where appropriate. As before, loading the
full tables and sub-setting manually is still recommended.

Historic helper functions like load_taxa() (combining the taxonomic classification from Species,
Genus, Family and Order tables), validate_names(), and common_to_sci() and
sci_to_common() should be in working order, all using table-based outputs.

@cboettig cboettig merged commit 0fdb957 into master Aug 12, 2024
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