wormscore 0.10.0

wormscore 0.10.0

Two optional features for checking your own scoring. Both are off unless you turn them on in
config.json before building the blind set; with them off, wormscore codes, measures and reports
exactly as 0.9.1 did.

Hidden repeat images (scorer consistency)

• Set "reliability": {"repeat_fraction": 0.1} and Build blind set codes about 10% of each genotype's
  images a second time under new codes, mixed in with the rest and placed well away from the original
  in the scoring list. A repeat looks exactly like any other image.
• Which codes are repeats is recorded only in the key. Repeats are never counted in any result.
• At unblinding, reliability.csv reports percent agreement and Cohen's kappa between each repeat and
  its original: usable, animal affected, each neuron's call (weighted kappa), cells seen and each
  per-neuron question outcome. The draft Methods text describes the repeats and the agreement.

A measured cutoff for checking calls

• Set "unblinding": {"dim_cutoff_sd": 3} to record, before scoring, a cutoff based on the background
  noise around each measured cell (robust SD of the background ring in the sharpest plane).
• At unblinding, dim_check.csv lists, per settings group and call, how many measured neurons fall
  below the cutoff. Calls are never changed by numbers. The cutoff is part of the analysis plan, so it
  is locked once scoring starts.

Update before you build a blind set, or after you unblind, never in the middle of scoring.

wormscore 0.9.1

Windows open full size, and removing a project from the list asks first. Codes, measurements, scoring and results are the same as 0.9.0.

• The first time, the wormscore window and the scoring window open maximized.
• After that, each window opens the way you left it: maximized, or at the size you gave it.
• The X next to a project now asks first, and says plainly that only the list changes: the folder and every file in it stay on your computer.

wormscore 0.9.0

wormscore now has its own windows on Windows. Codes, measurements, scoring and results are the same as 0.8.3.

• The app window is wormscore's own (drawn by WebView2, the web engine built into Windows 10 and 11), not an Edge window. It behaves like any other app: one taskbar button from the first moment, on your pinned icon.
• wormscore ends the moment you close its last window, and it can no longer lose its window: no "Failed to fetch", no "not running", and closing the lid or losing Wi-Fi does not affect it.
• Closing the last window while a step is running (for example Build blind set) asks first instead of stopping it.
• A second click on wormscore, or on Continue scoring, brings the open window forward instead of opening another.
• Updates close the window, swap the version and reopen it. If you update from 0.8, the old window says that wormscore now opens in its own window; close it.
• If a computer has no WebView2, wormscore uses an Edge window as before.

wormscore 0.8.3

Fixes for closing the laptop lid, a clearer message when wormscore is not running, and one taskbar button. Codes, measurements and results are the same as 0.8.2.

• Closing the lid (sleep) no longer stops wormscore. After waking, 0.8.2 could think its window had closed and quit. Now it always looks for its windows before quitting, and allows extra time after the computer wakes.
• When the connection drops, the window first shows a small "Reconnecting to wormscore..." and tries again every 2 seconds, and at once when the computer wakes or you click into the window.
• If wormscore really is not running, the window says so plainly, says your work is safe, and has a Start wormscore button (your browser asks before opening it). The window then reconnects by itself.
• The pinned taskbar icon and the wormscore windows now share one button. wormscore gives its Start menu and desktop shortcuts the same taskbar identity as its windows. If you pinned wormscore before, unpin it and pin it again once.
• wormscore keeps a short log (app.log, next to its settings) of when it started and why it closed.

wormscore 0.8.2

The app window no longer goes dead, and unsaved answers survive a crash. Codes, measurements and results are the same as 0.8.1.

• wormscore keeps running as long as any of its windows is open, even minimized or behind other windows. Before, it could quit after 3 quiet minutes and leave a window that only said "Failed to fetch". When every wormscore window is closed, it quits by itself after about a minute.
• A window that lost its connection reconnects by itself as soon as wormscore runs again. Opening wormscore while it is already running brings its window to the front instead of opening a second one.
• Scoring: answers you have not saved yet are kept as a draft on every change. After a crash or a restart, open the image again: your answers are filled back in, then click Save. Drafts are never counted as scores.
• A scoring window left open from another project can never save into the one you are scoring.

wormscore 0.8.1

Fixes for the app window. Scoring, codes, measurements and results are the same as 0.8.0.

• The X next to a project now removes it from the list. It did nothing when the saved path used forward slashes (C:/...).
• When wormscore has closed itself after a few quiet minutes, its window now says so ("wormscore has closed, open it again") instead of showing "Failed to fetch".

wormscore 0.8.0

In-app updates. Scoring, codes, measurements and results are the same as 0.7.2.

• When the app opens and a newer version exists, it asks whether to update, with what's new. Update and restart, Not now, or Skip this version. After Not now, a small "available" button next to the version number brings it back.
• Update downloads the zip for your computer (Windows or Mac), checks it against the SHA-256 checksum GitHub lists for it, runs the new copy once to confirm its version, and swaps it in after the app closes. If anything fails, the old copy stays.
• The previous version is kept. Settings (the gear at the top) has "Go back to ..." to swap it back.
• If a project has a blind set built but is not unblinded yet, the app warns that updating would put two wormscore versions in that project's Methods, and Not now is the default.
• The check sends nothing about you or your projects (one request to GitHub's latest-release page). Turn it off in Settings.
• Copies installed with pip are told to run: pip install -U wormscore
• Command line: wormscore update, wormscore update --install, wormscore update --rollback
• The Guide button now brings the browser window to the front instead of opening it behind the app.
• New ROADMAP.md lists planned features.

This version still has to be downloaded by hand once. From 0.8.0 on, the app offers new versions itself.

wormscore 0.7.2

Sharp taskbar icon. Nothing else changes: scoring, codes, measurements and results are the same as 0.7.1.

• The wormscore window now shows a sharp icon on the taskbar, also on high-resolution and scaled screens. Before, Windows stretched a small copy of the icon, which looked blurry.
• wormscore windows (home and scoring) share one "wormscore" taskbar button instead of being grouped under Edge, and pinning that button starts wormscore.

Windows: download wormscore-windows.zip, unzip, run wormscore.exe. Mac: wormscore-mac.zip (see README.txt inside). Python: pip install wormscore

wormscore 0.7.1

Faster and lighter. Results are unchanged: on a 141-image project, every blind image, measurement and key entry was compared against 0.7.0 and is identical.

• Build blind set uses a third of the memory: peak 1.97 GB down to 0.65 GB on large images, and about 12% faster (861 s to 754 s). It no longer keeps every image in memory until the end.
• Scan data is faster: file checksums run on several threads (28 s to 22 s on 15 GB).
• Less memory at start: about 1 GB less reserved per wormscore window on many-core computers (numpy's math library no longer reserves a buffer per core; wormscore does no matrix math).
• Sharp app icon in Windows search, the Start menu and the taskbar, and for the Mac app.
• Guide opens in your default browser.
• Mac: wormscore-mac.zip (Apple silicon) is attached to every release, built automatically.

Windows: download wormscore-windows.zip, unzip, run wormscore.exe. Mac: wormscore-mac.zip (see README.txt inside). Python: pip install wormscore

wormscore 0.7.0

A new app window. Codes, blinding, the scoring page, measurements and statistics are unchanged, so projects already being scored can upgrade.

• Home screen: wormscore.exe opens a window in the same design as the scoring page. Your recent projects are on the left. The four steps (Scan data, Build blind set, Score, Unblind) are a guided list showing what is done, running or next, with counts such as "Scored 12 of 138".
• Progress: a progress bar with time left while a step runs, and the full log when you want it.
• Same safety questions: rebuilding, adding images, and unblinding ask the same questions as before, now as clear dialogs. Unblinding still needs "I have finished scoring".
• Folder picker that starts in your user folder, not OneDrive. Sharp text on high-resolution screens. Light and dark mode.
• The app closes itself shortly after its windows are closed, never while a step is running.
• The older window is still available for this version: wormscore.exe --classic.
• With Python on macOS or Linux, wormscore-launcher opens the same screen in your browser.

Windows: download wormscore-windows.zip, unzip, run wormscore.exe. Python: pip install wormscore