cellpy 2.1 (Stage 4) — tracking issue

[jepegit]

Status (2026-07-28): tag-ready. Every Stage-4 sub-issue is closed except #164 (live/incremental c.update()), which was deferred to v.2.2. #345 (batch custom-JSON + file search) was split out to the v.2.1.2 patch milestone so it does not block the tag. This umbrella closes when v2.1.0 is tagged.

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Stage 4 = the cellpy 2.1 release. 2.0 finalized everything that could not be shimmed (frame schemas, header API, loader contract, on-disk v9 format, metadata, packaging) and deferred the rest behind warn_once shims. 2.1 spends those shims: it lands the batch/collectors redesigns their facades were holding a place for, surfaces engine features that already exist, rebuilds live/incremental on core, and removes every deprecation registered for removal: 2.1.

Single release (patch-release distribution was considered and rejected — Epic E is breaking, so a semver-clean 2.1 carries all of Stage 4).

Plan: architecture-plan/stage4-github-issues.md · coordinating: architecture-plan/cellpy2-architecture-plan.md §Stage 4.

Epic A — Batch v3 (cellpy/batch/)

• A1: batch v3 — Phase 0 characterization net #697 A1 — Phase 0 characterization net
• A2: batch v3 — journal.py + layout.py (folds #345) #698 A2 — journal.py + layout.py (folds batch - read custom json #345)
• A3: batch v3 — policy.py + resolve_specs() #699 A3 — policy.py + resolve_specs()
• A4: batch v3 — runner + result + store (fixes lstrip bug) #700 A4 — runner + result + store (fixes lstrip bug)
• A5: batch v3 — aggregate + qc + outputs #701 A5 — aggregate + qc + outputs
• A6: batch v3 — facade + golden parity #702 A6 — facade + golden parity
• A7: batch v3 — utils.batch shims + docs migration #703 A7 — utils.batch shims + docs migration
• A8: batch v3 — process-pool executor + handover #704 A8 — process-pool executor + handover

Epic B — Collectors (cellpy/collect/)

• B1: collectors — Phase 0 characterization + cross-cell bug xfail #705 B1 — Phase 0 + cross-cell bug xfail
• B2: collectors — options + pipeline (fixes cross-cell bug) #706 B2 — options + pipeline (fixes cross-cell bug)
• B3: collectors — class re-based, no constructor I/O #707 B3 — class re-based, no constructor I/O
• B4: collectors — plotting handover #708 B4 — plotting handover

Epic C — Utils waves 3–4

• C1: utils wave 3 — ocv_rlx port/refactor #709 C1 — ocv_rlx port/refactor
• Allow for c.update() #164 C2 — live/incremental rebuilt on core (c.update()) — deferred to v.2.2

Epic D — F6 feature menu

• D1: F6 — exclude_step_types on make_summary #710 D1 — exclude_step_types on make_summary
• D2: F6 — test-level summaries in batch reports #711 D2 — test-level summaries in batch reports
• D3: F6 — native-only report columns #712 D3 — native-only report columns

Epic E — Shim removals (BREAKING)

• E1: remove plotting shims (interactive=, xlim/ylim, seaborn, bokeh, summary_plot_legacy) #713 E1 — plotting shims
• E2: remove ICA shims (Converter, dqdv kwargs, dqdv_cycle/np, dq column) #714 E2 — ICA shims
• E3: remove headers_* attribute access + make_new_cell #715 E3 — headers_* access + make_new_cell
• E4: delete batch_tools/ + collectors elevated-kwarg shims #716 E4 — delete batch_tools/ + elevated kwargs (needs A7: batch v3 — utils.batch shims + docs migration #703 + B3: collectors — class re-based, no constructor I/O #707)
• E5: remove prms shim + DEPRECATIONS.md audit (keep c.mass facade) #717 E5 — remove prms shim + DEPRECATIONS audit (keep c.mass facade)

Epic G / H — Docs + housekeeping

• G1: regenerate hosted example data as v9 #718 G1 — regenerate example data as v9
• G2: docstring-driven API-reference cleanup #719 G2 — API-reference cleanup
• G3: migration guide 2.0->2.1 + release notes (write last) #720 G3 — migration guide + release notes (write last)
• H1: cellpy-core doc-sync pass (F7) #721 H1 — cellpy-core doc-sync (F7)
• Test data gaps: missing fixtures for thorough / batch / loader / error coverage #655 H2 — test-fixture coverage carry-over (Phase 1; Phase 2 dataset curation → Custom loader silently omits a declared-but-absent column #761)

Linked (other milestones): #668 (batch bugs, v1-follow-up) closed-verified by A1/A8/E4; #73 GITT/PITT → v.2.2. Split out: #345 batch custom-JSON → v.2.1.2; #164 live/incremental → v.2.2.

Sequencing

#701 → #706 (collectors need batch.aggregate); #703 + #707 → #716 (can't remove what has no replacement); #705 → #706 (cross-cell bug xfail→fix); #717 early; #720 last. Startable immediately: #713, #714, #715, #709, #164, #710, #721, #718.

Decisions locked (2026-07-26)

bokeh+seaborn dropped (plotly+matplotlib remain) · iterate_batches/process_batch → docs recipes · cellpy.batch + cellpy.collect packages · prms shim removed, c.mass facade kept past 2.1 · SPEED-30 headers parked → 2.2 · #73 GITT/PITT → 2.2.