Cnapy

This is a hotfix regarding issue 528 and, if you use the installer, an occassional "numpy.bool" error".
While this hotfix mitigates the Gurobi error in the former, **the newest Gurobi version (starting from version 12) are currently unsupported** until this issue in CNApy's dependency is fixed.

Installation Options

There are 4 alternative ways to install CNApy:

1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see [Using CNApy installer](https://github.com/cnapy-org/CNApy#using-cnapy-installer) for more.
2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through pip install cnapy in your console. Afterwards, you can start CNApy's GUI by running either cnapy or, if this doesn't work, python -m cnapy where "python" must call your Python 3.10 installation.
3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named cnapy-1.2.2 as follows: 1) Run conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge, 2) run conda activate cnapy-1.2.2, 3) run pip install cnapy. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either cnapy or, if this doesn't work, python -m cnapy. Note that the [cnapy conda package](https://anaconda.org/cnapy/cnapy) is currently *not* being updated due to licensing uncertainties.
4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).

What's Changed
* Gurobi hotfix by Paulocracy in https://github.com/cnapy-org/CNApy/pull/529


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.2.2...v1.2.3

This release contains two major changes for CNApy:

1. The **much-improved installation process** is introduced, now with an **automatic installer for Windows, Linux and MacOS**. For more details, see the 1st point in the "Installation Options" below.
2. Due to licensing issues, **we suspend providing new conda packages for CNAPy**. Instead, **CNApy can now be installed using pip** as it is now available as a PyPI package, see the 2nd point in the "Installation Options" below. For instructions on still using CNApy in a conda/mamba environment, see the 3rd point in the "Installation Options" below.


Installation Options

There are 4 alternative ways to install CNApy:

1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see [Using CNApy installer](https://github.com/cnapy-org/CNApy#using-cnapy-installer) for more.
2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through pip install cnapy in your console. Afterwards, you can start CNApy's GUI by running either cnapy or, if this doesn't work, python -m cnapy where "python" must call your Python 3.10 installation.
3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named cnapy-1.2.2 as follows: 1) Run conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge, 2) run conda activate cnapy-1.2.2, 3) run pip install cnapy. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either cnapy or, if this doesn't work, python -m cnapy. Note that the [cnapy conda package](https://anaconda.org/cnapy/cnapy) is currently *not* being updated due to licensing uncertainties.
4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).

What's Changed
* Pypi by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/525
* Version 122 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/526

**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.2.1...v1.2.2

*Important note for those who are using the cnapy-dev Anaconda environment: Since CNApy's Anaconda environment requirements are changed with this release, it is recommended to create CNApy's Anaconda enviroment again, e.g. by deleting the old environment and creating a new one.*

Major changes

This release bumps CNApy's Python requirement from Python 3.8 to Python 3.10. While this makes CNApy a bit more performant and easier to delevop, this also means that external solver versions that do not support Python 3.10 will not work with CNApy anymore.
Furthermore, this release includes a multitude of important bug fixes (see below) as well as a much better Escher map integration and small quality-of-life enhancements.

Installation Options

There are 4 alternative ways to install CNApy:

1. If you use Windows, the easiest way is to use our Windows installer, see section [Using the Windows installer](https://github.com/cnapy-org/CNApy#using-the-windows-installer).
2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](https://github.com/cnapy-org/CNApy#assisted-installation-under-linux-and-macos-x).
3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](https://github.com/cnapy-org/CNApy#install-cnapy-as-conda-package).
4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).


Changes in this release

What's Changed
* File management by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/510
* Fix annoying OptMDFpathway bugs by Paulocracy in https://github.com/cnapy-org/CNApy/pull/511
* Scenario in clipboard by Paulocracy in https://github.com/cnapy-org/CNApy/pull/512
* Push to Python 3.10 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/514
* fix 515 and ensure that a changed objective is always set by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/518
* improved Escher integration by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/513
* Per default use system font size by sthiele in https://github.com/cnapy-org/CNApy/pull/517
* Store EFMs as JSON by Paulocracy in https://github.com/cnapy-org/CNApy/pull/522
* possible fix for 520 by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/521
* unified strain design by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/519
* Bump to 1.2.1 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/523


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.11...v1.2.1

Main changes

This update provides a multitude of bug fixes, including the solution for a crash during plotting when it was installed using the Windows installer. Furthermore, one can now easily take a map screenshot under the respective options in the "Map" menu, EFMs can now be easily normalized and scenario-dependent annotations were added (e.g., for scenario-dependent variances or thermodynamic parameter values).

Installation Options

There are 4 alternative ways to install CNApy:

1. If you use Windows, the easiest way is to use our Windows installer, see section [Using the Windows installer](https://github.com/cnapy-org/CNApy#using-the-windows-installer).
2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](https://github.com/cnapy-org/CNApy#assisted-installation-under-linux-and-macos-x).
3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](https://github.com/cnapy-org/CNApy#install-cnapy-as-conda-package).
4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).


**If you have questions or suggestions regarding CNApy, you can use either of the [CNApy GitHub issues](https://github.com/cnapy-org/CNApy/issues), the [CNApy GitHub discussions](https://github.com/cnapy-org/CNApy/discussions) or the [CNApy Gitter chat room](https://gitter.im/cnapy-org/community).**

What's Changed
* Fix SDS loading by Paulocracy in https://github.com/cnapy-org/CNApy/pull/500
* Addressing 489 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/502
* Add screenshot capability for CNApy maps by Paulocracy in https://github.com/cnapy-org/CNApy/pull/501
* Add EFM normalization button (503) by Paulocracy in https://github.com/cnapy-org/CNApy/pull/504
* Add Scenario annotations by Paulocracy in https://github.com/cnapy-org/CNApy/pull/506
* explicitaly show unchanged IDs as such by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/507
* Improved installation guide by Paulocracy in https://github.com/cnapy-org/CNApy/pull/508


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.10...v1.1.11

*Important note for those who are using the cnapy-dev Anaconda environment: Since CNApy's Anaconda environment requirements are changed with this release, it is recommended to create CNApy's Anaconda enviroment again, e.g. by deleting the old environment and creating a new one.*

Main changes

This update provides a multitude of bug fixes and several small enhancements such as an improved Compute MCS dialog with a reaction auto-completion and the ability to use the "-" sign.

Installation Options

There are 4 alternative ways to install CNApy:

1. If you use Windows, the easiest way is to use our Windows installer, see section [Using the Windows installer](https://github.com/cnapy-org/CNApy#using-the-windows-installer).
2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](https://github.com/cnapy-org/CNApy#assisted-installation-under-linux-and-macos-x).
3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](https://github.com/cnapy-org/CNApy#install-cnapy-as-conda-package).
4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).


**If you have questions or suggestions regarding CNApy, you can use either of the [CNApy GitHub issues](https://github.com/cnapy-org/CNApy/issues), the [CNApy GitHub discussions](https://github.com/cnapy-org/CNApy/discussions) or the [CNApy Gitter chat room](https://gitter.im/cnapy-org/community).**

What's Changed
* Fix several bugs by Paulocracy in https://github.com/cnapy-org/CNApy/pull/492
* small improvements by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/493
* sequential editing of scenario values using up/down arrow keys in sce… by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/497
* Multiple MCS dialog improvements by Paulocracy in https://github.com/cnapy-org/CNApy/pull/496
* Version 1.1.10 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/494


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.9...v1.1.10

Main changes

This update provides a multitude of bug fixes and several small enhancements such as the new "Apply" button for calculated MCS (which directly sets them as a scenario) and the new ability to export an XLSX spreadsheet file with extensive in/out flux data for all metabolites of a model.

Installation Options

There are 4 alternative ways to install CNApy:

1. If you use Windows, the easiest way is to use our Windows installer, see section [Using the Windows installer](https://github.com/cnapy-org/CNApy#using-the-windows-installer).
2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](https://github.com/cnapy-org/CNApy#assisted-installation-under-linux-and-macos-x).
3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](https://github.com/cnapy-org/CNApy#install-cnapy-as-conda-package).
4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).


**If you have questions or suggestions regarding CNApy, you can use either of the [CNApy GitHub issues](https://github.com/cnapy-org/CNApy/issues), the [CNApy GitHub discussions](https://github.com/cnapy-org/CNApy/discussions) or the [CNApy Gitter chat room](https://gitter.im/cnapy-org/community).**

What's Changed
* Unify scenario_file_name label and load scenario_button by sthiele in https://github.com/cnapy-org/CNApy/pull/476
* Schedule old MapViews for deletion by sthiele in https://github.com/cnapy-org/CNApy/pull/477
* Escher profile by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/479
* if a loaded scenario is modified mark the displayed filename as changed by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/482
* Apply button by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/483
* Misc by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/485
* Small fixes by Paulocracy in https://github.com/cnapy-org/CNApy/pull/484
* Bump to version 1.1.9 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/486


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.8...v1.1.9