Myofinder

This release brings only minor changes to `myofinder` as a Python module, but a number of important changes to the deployment and automated test environment around it.

The changes related to the Python module are:
* Rename classes to make them PEP8-compliant (not exposed to the user)
* Add a `--test` command-line argument to the module (useful for automated testing only)
* Add an `--app-folder` command line argument for choosing where to store and read the application files
* Switch from a `setup.py` metadata file to a `pyproject.toml` file (concerns only users installing MyoFInDer from source)
* Fix a bug making MyoFInDer crash on macOS
* Update the help hyperlink in the user interface

The changes related to the automated testing are:
* Various minor improvements to the test workflows
* Tests are now ran against a locally built version of MyoFInDer
* Switch to `macos-13` runner for automated testing on macOS, instead of `macos-latest`
* Automatically push the latest built MSI file after a modification on the `main` branch

The changes related to the Windows Installer file are:
* Switch from the Advanced Installer application to WiX for building the MSI file
* Create a custom user interface for the Windows installation process
* Switch from a `start_myofinder.bat` file to a proper `myofinder.exe` file for starting MyoFInDer on Windows

Merged pull requests
* Automate Windows installer build by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/27
* Various minor improvements by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/28
* Add a `--test` command line option by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/29
* Improve the test workflows by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/30
* Update the Windows installer config file by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/31
* Move metadata from `setup.py` to `pyproject.toml` by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/32
* Fixes in `pyproject.toml` by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/34
* Automatically push the Windows installer to the main branch by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/35
* Replace `start_myofinder.bat` with `myofinder.exe` by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/37
* Handling exceptions when saving project by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/38
* Switch `.msi` build backend from Advanced Installer to WiX by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/40
* Remove `Gemfile.lock` by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/41
* Bug on macOS when running MyoFInDer by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/42
* Read application folder from registry by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/43
* Switch to a custom WiX UI by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/44
* Bug when rolling back installation and venv wasn't created by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/45
* macos-latest runner now only supports Python 3.12 and 3.13 by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/48
* Add warning for installing Python from Microsoft Store by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/46
* Update help hyperlink in application by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/47
* Update version from 1.0.7 to 1.0.8 by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/49

**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.7...v1.0.8

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.8/)

This release brings major adjustments to the available settings.

It renames:

* `Nuclei Threshold` to `Minimum nucleus intensity`
* `Fiber Threshold` to `Minimum fiber intensity`

The range of `Fiber Threshold` is also changed from 0-160 to 0-100.

It adds:

* `Maximum fiber intensity`, similar to `Minimum fiber intensity` but setting a maximum threshold
* `Maximum nucleus intensity`, similar to `Minimum nucleus intensity` but setting a maximum threshold

It replaces:

* `Small Objects threshold` with `Minimum nucleus diameter (px)`. Instead of driving directly the minimum area a detected nucleus must possess, it drives the minimum "average" diameter it must have, in pixels. This change was brought in response to 16.

In addition, the documentation about the available settings was also updated, and other minor documentation improvements were brought.

Finally, the `settings.pickle` files storing the last used setting values are now forward- and backward compatible starting from this version.

Merged pull requests
* Improve the available settings by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/23
* Add automated workflows by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/24
* Documentation improvement by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/25
* Release version 1.0.7 of MyoFInDer by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/26


**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.6...v1.0.7

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.7/)

What's Changed
* Re-enable and fix the nuclei_threshold setting by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/15
* Minor documentation update in 64373e1c

**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.5...v1.0.6

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.6/)

What's Changed
* Improvement of segmentation performance by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/13


**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.4...v1.0.5

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.5/)

What's Changed
* 11 obvious nuclei not being detected by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/12


**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.3...v1.0.4

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.4/)

What's Changed
* fix: fix authentication error on recent releases of DeepCell by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/8
* 9 microsoft visual c++ error during install by WeisLeDocto in https://github.com/TissueEngineeringLab/MyoFInDer/pull/10


**Full Changelog**: https://github.com/TissueEngineeringLab/MyoFInDer/compare/v1.0.2...v1.0.3

The tarball and the wheel are available [on PyPI](https://pypi.org/project/myofinder/1.0.3/)