Tapqir

Enhancement
* cosmos model with Markov dependency by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/336

Bug fixes
* Fix nonspecific toggle bug by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/334
* Fix crosstalk model by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/337
* Bug fix. Remove `channels` option from the fit gui by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/338


**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.1.0...v1.1.1

Breaking
* instead of specifying channel number to be analyzed now all color channels in the data are analyzed using multi-color cosmos models (see below)
* to analyze only a single color channel create a new folder and extract AOIs only for that particular color channel and then perform the analysis
* `channels-xxx` suffix was dropped from model and parameter files names
* model file and parameter file contents are not backward compatible

New
* cosmos model now supports multiple color channel analysis by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/333
* EXPERIMENTAL: multi-color cosmos model with crosstalk between channels by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/275


**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.0.5...v1.1.0

Breaking change
* New configuration file (`.tapqir/config.yaml`) is incompatible with previous versions of Tapqir

Enhancements
* Extend image distribution (KSMOGN) to support multi-dye multi-color data by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/323
* Add a GUI element for the offset histogram bin size by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/329
* Add GUI for prior inputs by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/330
* Add GUI for offset parameter inputs by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/331
* update docs to reflect new changes by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/332

Internal
* Fix ksmogn dist by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/325
* Lowercase Cosmos model name by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/326
* Move concatenation logic into handler by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/327
* Convert ndarray stats to list before saving summary by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/328

**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.0.4...v1.0.5

New features & GUI
* Field of View images are now also displayed in the Results GUI by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/318
* AOIs can be manually excluded from analysis by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/319
* Hide frame range instead of disabling by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/321

Internal & Fixes
* inputBox by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/317
* Update cosmos model reference by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/320
* Update docs by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/322


**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.0.3...v1.0.4

GUI & usability
* Make loading messages appear more responsive by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/301
* Reset offtarget path on toggle of `use offtarget` by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/304
* Validate paths in CLI application by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/305
* Handle errors and exceptions by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/307
* Add `View logs` tab by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/311
* Show summary table in results tab by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/315
* Disable load results button after the first click (reloading doesn't work) by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/316
* Update instructions accordingly by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/314

Bug fixes
* fix small bugs & clean up by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/312

Optimization & Internal
* Refactor SNR computation to avoid memory overflow by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/313
* Optimize `Cosmos.compute_probs` by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/302
* Add & use StatsMessenger to compute credible intervals by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/303
* Refactor load gui defaults by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/306
* Publish latest branch to TestPyPi by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/308
* Publish Python 🐍 distributions 📦 to PyPI by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/309
* Update python-app.yml by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/310

**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.0.2...v1.0.3

What's Changed
* Fix google colab installation by ordabayevy in https://github.com/gelles-brandeis/tapqir/pull/300
* Constrain to `click<=8.0.4` due to `ImporError` (https://github.com/tiangolo/typer/issues/377)

Breaking
* Now to install Tapqir on desktop computers (Linux, WSL2) run `pip install tapqir[desktop]`

**Full Changelog**: https://github.com/gelles-brandeis/tapqir/compare/v1.0.1...v1.0.2