Harden bioenergetic space API + Bioconductor readiness

[vcjdeboer]

Summary

Hardens the bioenergetic space / trajectory feature and the surrounding package to a Bioconductor-shippable standard, so working scientists can install from Bioconductor and run it on their own data. Executed as a planned, task-by-task effort with per-task review plus a whole-branch review.

Design/plan: docs/superpowers/plans/2026-09-05-seahtrue-bioc-space-improvements.md.

What changed

Phase 1 — hygiene (no behavior change), takes R CMD check to Status: OK

• Exclude prototype .qmd files and tooling dirs from the build; ASCII-only R source; remove hidden-file/.git bundling.
• cat() → cli; ggplot2 size= → linewidth= on line geoms.
• Register NSE column names via utils::globalVariables() — clears the "no visible binding" NOTEs (2 → 0).

Phase 2 — space API hardening

• calculate_space() input validation with clear cli::cli_abort messages (bad param_set_* / malformed rate).
• Documented + guarded the canonical injection-name contract: instead of silently returning NA metrics, calculate_space() now warns when it can't produce the columns the plot functions require.
• Extracted the three space functions into R/space_xfplate.R.
• Renamed args OCR_var/ECAR_var → ocr_var/ecar_var (snake_case).

Phase 3 — tests

• Real testthat coverage for revive_xfplate(), calculate_space(), and both plot functions (suite: 20 → 33 checks).

Maintainer-gated decisions (now resolved)

• Gate A — the metabolic-space plot width uses amrot_ecar by design; documented the distinction from the max_ecar (mon_ecar/om_ecar) used by the supply_index/glyco_index_max metrics. (docs-only)
• Gate B — added an optional atp_factors argument to calculate_space() so users can supply custom ATP conversion factors (validated; presets unchanged when omitted).

Release prep

• Version: → 1.7.1 (valid, odd-minor devel; > Bioconductor devel 1.7.0).
• Removed the disallowed Remotes: field (BiocStyle stays in Suggests:). NEWS updated.

Verification

• devtools::test(): FAIL 0 | PASS 33 (47 warnings are pre-existing tidyselect .data deprecations in R/assertions_read.R, unrelated to this branch).
• R CMD check: Status: OK.
• BiocCheck: version-format and Remotes ERRORs cleared. Two remaining ERRORs are environment artifacts only (worktree dir-name mismatch; BiocCheck's own scratch dir) and won't reproduce in a normal seahtrue-named checkout.

Deliberately NOT done here (maintainer follow-ups)

• Bioconductor upstream sync — reconcile with upstream/devel and push to git.bioconductor.org (never automated in this work).
• Merging to devel will trigger webr.yml and update what the book of seahtrue serves — merge deliberately.
• Non-blocking BiocCheck NOTEs left for a future pass: 18 functions > 50 lines (e.g. get_xf_assayinfo()), 3× suppressWarnings(), line-length/indent style, and the pre-existing tidyselect deprecation warnings.

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