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Docs: state of 6 Nov 2026; smoke workflows default to the apps' main - #154

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Nov 6, 2026
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Several pages still described the situation of 14 Oct 2026. This PR updates them to 6 Nov 2026, and fixes two workflow defaults that pointed at deleted branches.

What changed in the docs

Said Now true (checked 6 Nov 2026) Where
template 0.1.18 "not merged / not released yet" template PR #33 merged 14 Oct; all five apps are on template 0.1.19 or 0.1.20, so every current app release passes hosts: README, HOST_FEATURES, REPOSITORIES, TESTING, HUMAN_TEST_PROTOCOL (D3)
hosts and the Napari plugin have "no tag or release"; <NAPARI_TAG> placeholder alpha pre-releases: napari and Fiji v0.1.0-alpha.4, QuPath v0.1.0-alpha.5 HOST_FEATURES (Releases row), REPOSITORIES, OPERATIONS
pin table: apps pin v0.2.0-rc.1, pin PRs are drafts, next releases "decided" every app pins v0.3.0-alpha.1 on main and in its latest release; pin PRs merged; current line numbers and latest releases (Playground 0.0.5, NucleiSky 0.1.4, VLab4Mic 0.1.7, Guess the Condition 0.0.1, CellTracksColab 1.1.5) OPERATIONS (pinning section)
CellTracksColab: "no tools on main", "1.1.2 held, latest 1.1.1" the bridge (celltracks_lc_tools, 1 tool, hosts: [notebook]) is on main and in 1.1.5 OPERATIONS, REPOSITORIES, INSTALL, human_tests/celltrackscolab.md
app table column "Tag of the next release (decided)" "Latest release", with the tool counts recounted from each main (unchanged: 2, 6, 17, 2, plus 1 for CellTracksColab) REPOSITORIES

Still open and left as is: VLab4Mic's README line 57 installs the napari plugin from refs/heads/main.zip. This is now stated in the pin table. The dated history paragraph at the end of HUMAN_TEST_PROTOCOL ("updated for the tagged alpha.4 set") is also unchanged.

Workflow defaults

smoke_install and smoke_migration defaulted app_ref to bridge-test (CellTracksColab) and claude/merge-bridge-test (NucleiSky). Both branches no longer exist, so a run started without inputs would fail at checkout. Both now default to main, where each app's tools module lives:

  • celltracks_lc_tools and the lc_tests/fixtures/tracks.csv that the smoke args use;
  • nucleisky_lc_tools.

TESTING.md's table of defaults says the same. Both workflows only run when started by hand, and neither was run for this PR.

Checks

🤖 Generated with Claude Code

Several pages still described 14 Oct 2026: template 0.1.18 "not
merged", the hosts and the Napari plugin "without a tag", apps "pinned
to v0.2.0-rc.1" with "decided" next releases, and CellTracksColab
"1.1.2 held, no tools on main". Template 0.1.18 merged on 14 Oct, every
current app release is built with it and pins v0.3.0-alpha.1, the hosts
have alpha releases, and CellTracksColab's bridge is on main and in
1.1.5. The pin table (OPERATIONS) and the app table (REPOSITORIES) now
give the state of 6 Nov 2026, read from each repository.

smoke_install and smoke_migration defaulted app_ref to the branches
bridge-test (CellTracksColab) and claude/merge-bridge-test (NucleiSky),
which no longer exist, so a run without inputs would fail at checkout.
Both now default to main, where each app's tools module lives.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@IvanHCenalmor
IvanHCenalmor merged commit 5a28949 into main Nov 6, 2026
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@IvanHCenalmor
IvanHCenalmor deleted the docs-outdated-status branch November 6, 2026 22:51
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