Waveorder

PTI documentation and example scripts release in preparation for PTI paper.

What's Changed
* PTI example jupyter notebook to script and .pdf by talonchandler in https://github.com/mehta-lab/waveorder/pull/160


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.0.0...2.1.0

Overview

This major release of `waveorder` is a well-tested and stable version of phase, birefringence, and fluorescence simulation and reconstruction algorithms, **now running in `torch`, with each reconstruction factored into an precalculation and an (typically less-expensive) reconstruction**.

**Key changes:**
- phase, birefringence, and fluorescence reconstruction use `torch`
- these reconstructions are factored into an expensive precalculation and an inexpensive reconstruction
- Key PTI reconstruction code paths are conserved through the refactor, with automated example scripts on synthetic data and one data-based jupyter notebook

What's Changed
* Remove `__init__` imports by talonchandler in https://github.com/mehta-lab/waveorder/pull/134
* Add optional parameters `plot_path` and `threshold_FWHM` to `focus_from_transverse_band` by talonchandler in https://github.com/mehta-lab/waveorder/pull/132
* Fix threshold-free focus-finding edge case by talonchandler in https://github.com/mehta-lab/waveorder/pull/135
* close figure after saving by ieivanov in https://github.com/mehta-lab/waveorder/pull/136
* **Major changes:** `alg-dev` branch merge to `main` by talonchandler in https://github.com/mehta-lab/waveorder/pull/121
* Specify meshgrid indexing order by talonchandler in https://github.com/mehta-lab/waveorder/pull/138
* Fix readme figure by talonchandler in https://github.com/mehta-lab/waveorder/pull/141
* Simplify dependencies by talonchandler in https://github.com/mehta-lab/waveorder/pull/147
* Add rotate and flip orientation options to `waveorder` options by talonchandler in https://github.com/mehta-lab/waveorder/pull/148
* `waveorder` handles all rotational quantities (including retardance) in radians by talonchandler in https://github.com/mehta-lab/waveorder/pull/149
* Device agnostic compute for polarization by ziw-liu in https://github.com/mehta-lab/waveorder/pull/150
* Document order-dependent scripts by talonchandler in https://github.com/mehta-lab/waveorder/pull/155
* M1 installation documentation by talonchandler in https://github.com/mehta-lab/waveorder/pull/156
* Prepare README for 2.0.0 by talonchandler in https://github.com/mehta-lab/waveorder/pull/157
* Link BIA data next to examples by talonchandler in https://github.com/mehta-lab/waveorder/pull/158
* Update a single PTI example notebook by talonchandler in https://github.com/mehta-lab/waveorder/pull/159


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/1.0.0...2.0.0

Overview

Ths first major release of `waveorder` is a well-tested and stable version of phase, birefringence, and fluorescence simulation and reconstruction algorithms.

**Key changes**
Since `waveorder==1.0.0rc0`, we have:
- moved all I/O functionality to `iohub`.
- curated and updated the `/examples/` folder, and added the most important example scripts to CI/CD testing for maintenance through the upcoming refactoring.
- added focus finding algorithms
- dropped support for 3.7 and bumped to 3.8-3.10

What's Changed
* Bump version to 1.0.0rc0 by ieivanov in https://github.com/mehta-lab/waveorder/pull/82
* BSD 3-clause by talonchandler in https://github.com/mehta-lab/waveorder/pull/84
* Don't delete test data by talonchandler in https://github.com/mehta-lab/waveorder/pull/83
* improve readability of waveOrder by mattersoflight in https://github.com/mehta-lab/waveorder/pull/85
* Drop 3.7 and add 3.8, 3.9, 3.10 by talonchandler in https://github.com/mehta-lab/waveorder/pull/99
* Find focus by optimizing a transverse spatial frequency band by talonchandler in https://github.com/mehta-lab/waveorder/pull/92
* Improve README.md by talonchandler in https://github.com/mehta-lab/waveorder/pull/101
* uPTI -> PTI; black formatting; improved comments by talonchandler in https://github.com/mehta-lab/waveorder/pull/104
* README copy edits by talonchandler in https://github.com/mehta-lab/waveorder/pull/105
* Replace OpenCV with pillow by ziw-liu in https://github.com/mehta-lab/waveorder/pull/108
* Add .git-blame-ignore-revs by talonchandler in https://github.com/mehta-lab/waveorder/pull/109
* Prepare for `waveorder==1.0.0` release by talonchandler in https://github.com/mehta-lab/waveorder/pull/114
* Fix link to example by talonchandler in https://github.com/mehta-lab/waveorder/pull/115
* Pin README links by talonchandler in https://github.com/mehta-lab/waveorder/pull/116

New Contributors
* ziw-liu made their first contribution in https://github.com/mehta-lab/waveorder/pull/108

**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/1.0.0rc0...1.0.0