v0.5.0

What's Changed

• [after-v0.4.0-tag] Roadmap: explicit projection step (P1) and experiment schema (P2) by @guijacquemet in #174
• I/O minors: same_file export, OME-Zarr time unit, open errors, 1-D refusal by @guijacquemet in #177
• Per-channel group statistics and explicit refusal of cyclic mask hierarchies by @guijacquemet in #178
• Bind masks to their fingerprints for the whole run and the relationship scan by @guijacquemet in #180
• Index MaskInventory by image once (for_image O(1)) by @guijacquemet in #181
• Doc cleanup: archive plan milestones and status log, refresh v0.4.0 status by @guijacquemet in #182
• Vendor the Spec conformance fixtures at a pinned commit (Stage 1, PR 1 of 3) by @guijacquemet in #183
• Strict description reader, phases 1-3 (Stage 1, PR 2 of 3) by @guijacquemet in #184
• Strict description reader, phases 4-5 and warnings (Stage 1, PR 3 of 3) by @guijacquemet in #185
• Re-pin the vendored Spec to 745259b; condition single rule (Stage 1, PR A) by @guijacquemet in #186
• Description model, canonical writer and section digests (Stage 1, PR 4) by @guijacquemet in #187
• Description publication: lock, base SHA, symlink refusal, transitions, records (Stage 1, PR 5) by @guijacquemet in #188
• Turn content hashing of the sources on by default by @guijacquemet in #189
• Discovery and header additions for the experiment description (Stage 1, PR 6) by @guijacquemet in #190
• Reconciliation of the published description with the folder (Stage 1, PR 9) by @guijacquemet in #193
• Physical R_* checks of an experiment description (Stage 1, PR 8) by @guijacquemet in #192
• Safe display of planes: reduced reads, channel strip, mask overlay (Stage 1, PR 13) by @guijacquemet in #194
• Draft description, proposed IDs and legacy design migration (Stage 1, PR 7) by @guijacquemet in #191
• Re-pin the vendored Spec to 7dbae0c (byte rules, goldens, t13, records encoding) by @guijacquemet in #195
• Say a time step cannot be stated in calibration.csv by @guijacquemet in #201
• Derived experiment_design.csv and cross-version parity suite (Stage 1, PR 10) by @guijacquemet in #196
• Detect mask hierarchy cycles before reducing direct edges by @guijacquemet in #200
• Re-check every mask fingerprint right before the manifest replacement by @guijacquemet in #202
• Hold module-level skips and missing modules in the Spec test gate by @guijacquemet in #205
• Make the records append rollback-safe and validate record shapes by @guijacquemet in #207
• Re-pin the vendored Spec to b197ac1; reserved names apply to used_ids.channels by @guijacquemet in #208
• Run integration of the published experiment description (Stage 1, PR 11) by @guijacquemet in #209
• Semantic RunInputs from a published description (Stage 1, PR 12) by @guijacquemet in #210
• Notebook bootstrap: show the Git identity of a local checkout and refuse a non-release one by @guijacquemet in #214
• Z projection 1/6: the pure arithmetic (part of #176) by @guijacquemet in #211
• Z projection 2/6: conversion record version 3 (part of #176) by @guijacquemet in #212
• Spec conformance P26: per-unit header channel-name checks for described runs by @guijacquemet in #218
• Description reader: own rule vocabulary; pin path and value of five refusals by @guijacquemet in #219
• CLI describe, docs and conformance run (Stage 1, PR 17) by @guijacquemet in #220
• Draft file and draft-to-description (Stage 1) by @guijacquemet in #221
• Z projection 3/6: plan and write projected copies (part of #176) by @guijacquemet in #213
• Z projection 4/6: convert --project on the command line (part of #176) by @guijacquemet in #215
• Publication writes the removed and image_count_changed records (RR2, RR1) by @guijacquemet in #216
• Refuse a draft written under another Spec commit at resume and save by @guijacquemet in #224
• List images without header channel names in a described run by @guijacquemet in #226
• Stage 2: described runs write manifest version "4" by @guijacquemet in #227
• Stage 2: make_clean_run(description=...) builds a described run for tests by @guijacquemet in #228
• Stage 2: A_* error classes and RunInputs.section_digests() by @guijacquemet in #229
• Z projection 5/6: the run side (part of #176) by @guijacquemet in #217
• Re-pin the vendored Spec to c8f6852 by @guijacquemet in #230
• Notebook Step 1 cards: IDs, names, pairing, references (Stage 1, PR 14) by @guijacquemet in #231
• Document the window after the final mask check by @guijacquemet in #232
• Notebook: your channels (labels first, then tag per unit) (Stage 1, PR 15) by @guijacquemet in #233
• Fixes #234: make_described_run spreads image_count over technical repeats by @guijacquemet in #236
• Notebook: your masks (Stage 1, PR 16a) by @guijacquemet in #237
• Notebook: check and save, reopen (Stage 1, PR 16b) by @guijacquemet in #238
• Run page: channel and replicate IDs, no-problems icon, plan card, mask kinds by @guijacquemet in #241
• Re-pin Spec 1bed024; read_records follows §4.6 (R_RECORDS_FILE_INVALID) by @guijacquemet in #242
• Described runs: pixel-type and dimension checks per unit (#239, narrowed) by @guijacquemet in #243
• Notebook: one step at a time, in the decided order (PR 17a) by @guijacquemet in #244
• Report the layout refusal first in described runs with several layouts by @guijacquemet in #246
• Notebook: tags per header block, colour pictures, one-click axes (PR 17b-1) by @guijacquemet in #247
• Notebook: fold unchanged rows on reopen (PR 17b-2) by @guijacquemet in #248
• Notebook: Stains is not applicable when every folder is colour (RGB) by @guijacquemet in #249
• Notebook: folder pictures with a 1:1 crop, tag like the saved group, colour mask evidence (PR 17c) by @guijacquemet in #250
• Audit batches 33, 34a, 34b: publish only what was answered, of the image checked by @guijacquemet in #254
• Batch 34b: preview-gated one-click axes, header evidence on reopen, NaN crop by @guijacquemet in #255
• Pre-release follow-ups to #254 and #255 by @guijacquemet in #257
• Release candidate v0.5.0: Gate G1 record, version 0.5.0, notebook installs v0.5.0 by @guijacquemet in #253

Full Changelog: v0.4.0...v0.5.0