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v0.12.0: lnk_pipeline_classify call site for fresh 0.22.0#66

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NewGraphEnvironment merged 1 commit intomainfrom
0.12.0-fresh-0.22.0-callsite
Apr 27, 2026
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v0.12.0: lnk_pipeline_classify call site for fresh 0.22.0#66
NewGraphEnvironment merged 1 commit intomainfrom
0.12.0-fresh-0.22.0-callsite

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Summary

Caller-side update for fresh 0.22.0's overlay simplification (fresh#177). Unblocks the broken pipeline.

Diff

R/lnk_pipeline_classify.R:

fresh::frs_habitat_overlay(conn,
  from   = paste0(schema, ".user_habitat_classification"),
  to     = "fresh.streams_habitat",
  bridge = "fresh.streams",
  species = species,
- format = "long",
- long_value_col = "habitat_ind",
+ species_col = "species_code",
+ habitat_types = c("spawning", "rearing"),
  verbose = FALSE)

DESCRIPTION: Suggests: fresh (>= 0.22.0). Version 0.11.20.12.0.

Why

bcfishpass changed user_habitat_classification.csv from long to row-per-(segment × species) shape on 2026-04-26. Auto-sync pulled it. fresh's overlay didn't natively understand the shape; fresh 0.22.0 (just merged) drops the format parameter and accepts only the canonical (post-2026-04-26) shape. This PR is link's three-line caller-side adaptation.

Test plan

  • R CMD INSTALL clean against fresh 0.22.0
  • devtools::test(): 453 PASS, 0 FAIL, 1 pre-existing WARN
  • Manual sanity: re-run tar_make() against the now-updated pipeline (deferred — separate PR for the vignette regen will exercise this)

Coordination

🤖 Generated with Claude Code

Three-line caller-side update consuming fresh's overlay simplification
(fresh#177, fresh 0.22.0):

- Drop format = "long"
- Drop long_value_col = "habitat_ind"
- Add species_col = "species_code"
- Add habitat_types = c("spawning", "rearing")

Matches bcfishpass's authoritative CSV shape (post-2026-04-26): one
row per (segment x species) with per-habitat indicator columns.

DESCRIPTION: Suggests: fresh (>= 0.22.0). Version 0.11.2 -> 0.12.0
(minor — caller-side breaking match for the fresh API).

Pipeline runs again. Vignette stays in dev/ until link#64 + link#65
land.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@NewGraphEnvironment NewGraphEnvironment merged commit 9e89962 into main Apr 27, 2026
1 check passed
@NewGraphEnvironment NewGraphEnvironment deleted the 0.12.0-fresh-0.22.0-callsite branch April 27, 2026 18:55
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