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Docs: human test protocol rewritten for the alpha test set, one install page (docs only) - #132
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…tall page; true apps, hosts and pins - HUMAN_TEST_PROTOCOL.md rewritten: test-set record sheet (Tools tag, template, host tags, app releases, links, OS, tester, date), install rules (no space in the path, Linux -u only after a finished install, tagged installs, latest only), discovery matrix as the rule to be, W1 as a refusal test, QuPath as a host, Fiji jar/script zip and its limits, Napari with PyQt6. - Per-app case files in docs/human_tests/ (NucleiSky, Playground, GuessTheCondition, VLab4Mic, CellTracksColab); CellTracksColab is no longer expected in any host and its bridge fixtures are gone. - New docs/INSTALL.md (apps and the three hosts); linked from README and the protocol. - TESTING.md, REPOSITORIES.md, OPERATIONS.md (pin table), HOST_FEATURES.md, README.md updated; CellTracksColab link fixed. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
…bers, placeholders Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
guijacquemet
marked this pull request as ready for review
October 14, 2026 06:18
…-alpha1 Resolve docs/REPOSITORIES.md keeping the discovery table and rule line from the branch and the binding hosts: rule from main; bring TESTING.md, HOST_FEATURES.md, HUMAN_TEST_PROTOCOL.md and README.md in line with the merged rule and sandbox. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
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Docs only. Not merged, no tag, nothing published. Based on main 535450d.
What changed
docs/HUMAN_TEST_PROTOCOL.mdrewritten (404 lines) + per-app case files indocs/human_tests/(nucleisky, playground, guessthecondition, vlab4mic, celltrackscolab; all < 250 lines).<fill in>stop the round.Destination Folder contains 1 space), Linux-uonly after a finished install (else delete<prefix>/pkgs), tagged installs only (no main.zip), testers run only the latest.discovery rule: see PROTOCOL.md section <TBD by the discovery PR>. PROTOCOL.md/MANIFEST.md untouched.napari[pyqt6](not pyqt5), Python 3.11+; Fiji jar intoFiji.app/plugins, script+lib zip alternative, pixel-size limit, no "use the image's calibration" button, CAL-T9; QuPath jar, Script Editor needs the singleLabConstrictorTools-all.groovy.bridge-testfixtures dependency is gone. Images N14 and F9 (CellTracksColab in a host) removed.docs/INSTALL.md(one install page), linked from README, protocol, REPOSITORIES, OPERATIONS, HOST_FEATURES.TESTING.md: smoke defaults, what the sandbox covers per app/host, PyQt6, Linux-urule, napari_ref finding.REPOSITORIES.md,HOST_FEATURES.md,README.md,TESTING_PROMPT.mdupdated.OPERATIONS.md: install section and pin table.Evidence for the non-obvious claims
v0.2.0-rc.1:post_install.sh:83/.bat:232(Playground),:73/:223(NucleiSky, VLab4Mic, GuessTheCondition, template) on eachmain. Pin PRs Spec: Wave 1 manifest (sliders/radio, copy as command, ShapesOut, RegionOf) #27, Round-trip test matrix, fuzzing, sabotage, coverage gate, nightly mutation, regression ledger #38, Protocol: Intel Macs are not supported #17, Protocol: F12 as a hand-typed macro, notes for fixed items removed #14 and template Docs: Wave 1 is live in all three hosts #33 exist as drafts (GitHub PR lists).smoke_migrationdefaultclaude/merge-bridge-test: branch exists in NucleiSky (GitHub branch list, 14 Oct) but is a leftover (nucleisky_lc_toolsis on NucleiSky main);.github/workflows/smoke_migration.ymllines 31, 67.smoke_installdefaultbridge-testexists in CellTracksColab.release_sandbox.yml:237builds.../archive/refs/heads/${napari_ref}.zip, sonapari_refcannot be a tag (documented as such; not changed). Same file:napari[pyqt6]; W1 lines 116-146 (refusal, exit code, regexpDestination Folder contains).release.ymllines 59-64, 266. QuPath README (9e64c6d) lines 8-16 andrelease.ymllines 58-71, 106. Napari README line 83 (Qt6, PyQt5 not tested), lines 75-76 (main.zip, no tag).src/nucleisky_lc_tools/__init__.py(Optional,PixelSizeOf, "Required"),lc_tests/cases.jsoncases 20-22. Numbers (12.0 +/- 1, 700.06 +/- 4, 429/9) fromcases.json.src/*_lc_toolsandlc_tests/cases.json..tools/docs/install.mdon the (unmerged) branch of template Docs: Wave 1 is live in all three hosts #33; plan section 22.Checks run
black, ruff,
scripts/check_annotations.py: pass. Relative links and anchors of README and docs/*.md: 0 broken (own script). Doc-reading tests (versions, run-record, features, reserved inputs, conformance, compat): pass excepttest_installed_metadata_matches_the_sourceandtest_the_built_wheel_contains_..., which fail identically on clean main in this sandbox (environment).Not verified (written as such in the docs)
See the report in the session: CellTracksColab_LabConstrictor link (replaced by CellTracksColab; old repo unreachable), Linux/macOS path with a space, hosts' behaviour before the discovery rule, helper tools in tool lists, QuPath steps by a person, Fiji/QuPath release assets (none published), Napari tag, release numbers, templates carried by the app releases.
🤖 Generated with Claude Code
https://claude.ai/code/session_01Y2SN8SuEakTdiWy3F2WUqN
Generated by Claude Code