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Load a Pipeline Config Bundle (Manifest)

Source: R/lnk_config.R
lnk_config.Rd

Reads a config bundle manifest (config.yaml) and returns a single list object describing what a pipeline variant does — paths, file declarations, pipeline knobs, provenance — but no parsed data.

Usage

lnk_config(name_or_path)

Arguments

name_or_path

Character. Either a bundled config name ("bcfishpass", "default") or an absolute path to a config directory. Bundled names resolve to system.file("extdata", "configs", name, package = "link").

Value

An lnk_config S3 list with these slots:

  • name — config name from the manifest

  • dir — absolute path to the config directory

  • description — manifest's free-text description (or NULL)

  • rules — absolute path to the rules YAML (consumed by fresh::frs_habitat_classify())

  • dimensions — absolute path to the dimensions CSV (input to lnk_rules_build())

  • species — character vector of species the rules YAML classifies (parsed from rules.yaml top-level keys)

  • files — named list of file declarations. Each entry is a list with path (resolved absolute path) and optionally source (free-text provenance label) and canonical_schema ("<source>/<file_name>" — keys into crate's registry to dispatch ingest via crate::crt_ingest())

  • pipeline — named list of pipeline knobs (apply_habitat_overlay, break_order, cluster, spawn_connected)

  • provenance — named list of per-file provenance metadata, keyed by file path relative to dir. Drift detection against these checksums lives in lnk_config_verify().

  • extends — character or NULL, the parent config name/path this manifest declared (post-resolution; not used by callers beyond audit)

Details

Tabular data (override CSVs, habitat classifications, parameters) is loaded by lnk_load_overrides(), which dispatches each declared file through crate::crt_ingest() for source-registered entries and falls through to local reads otherwise. This split keeps lnk_config() cheap to call (no CSV parsing) and lets provenance-only consumers like lnk_config_verify() and lnk_stamp() work without touching data.

A config bundle is a directory under inst/extdata/configs/<name>/ (for bundled variants) or an arbitrary directory path (for custom variants) containing config.yaml plus the files the manifest references. All file paths in the manifest are resolved relative to the bundle directory.

Configs may declare extends: <parent> to inherit from another config. The parent is resolved (recursively, if it also extends) and merged shallowly: child entries override parent entries with the same key in files:, pipeline:, and provenance:; top-level scalars (description, rules, dimensions) override directly.

Examples

cfg <- lnk_config("bcfishpass")
cfg$name
#> [1] "bcfishpass"
cfg$rules
#> [1] "/home/runner/work/_temp/Library/link/extdata/configs/bcfishpass/rules.yaml"
names(cfg$files)
#>  [1] "parameters_fresh"                    
#>  [2] "user_habitat_classification"         
#>  [3] "observation_exclusions"              
#>  [4] "wsg_species_presence"                
#>  [5] "user_modelled_crossing_fixes"        
#>  [6] "user_pscis_barrier_status"           
#>  [7] "pscis_modelledcrossings_streams_xref"
#>  [8] "user_barriers_definite"              
#>  [9] "user_barriers_definite_control"      
#> [10] "user_crossings_misc"                 
#> [11] "cabd_exclusions"                     
#> [12] "cabd_blkey_xref"                     
#> [13] "cabd_passability_status_updates"     
#> [14] "cabd_additions"                      
cfg$files$user_habitat_classification
#> $source
#> [1] "bcfp"
#> 
#> $path
#> [1] "/home/runner/work/_temp/Library/link/extdata/configs/bcfishpass/overrides/user_habitat_classification.csv"
#> 
#> $canonical_schema
#> [1] "bcfp/user_habitat_classification"
#> 
cfg$pipeline$break_order
#> [1] "observations"      "gradient_minimal"  "falls"            
#> [4] "barriers_definite" "subsurfaceflow"    "habitat_endpoints"
#> [7] "crossings"        

if (FALSE) { # \dontrun{
# Custom config: point at any directory containing config.yaml
my_cfg <- lnk_config("/path/to/my/variant")

# Materialize the data tables declared in the manifest
loaded <- lnk_load_overrides(my_cfg)
loaded$user_habitat_classification
} # }