Cnapy

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

*Important note if you're 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 updates provides an improved GUI experience including a history of viewed model items, a multitude of bug fixes and now officially supports the new easier way to install CNApy on Windows.

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 434 and other minor enhancements by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/458
* Fix small bugs and expanded search features by Paulocracy in https://github.com/cnapy-org/CNApy/pull/457
* Enhanced readme by Paulocracy in https://github.com/cnapy-org/CNApy/pull/459
* some bug fixes by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/460
* Add default concentration ranges in thermodynamic dialog by Paulocracy in https://github.com/cnapy-org/CNApy/pull/461
* popup list with recently viewed model items, various small GUI improvemets by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/464
* Add new installation instructions by Paulocracy in https://github.com/cnapy-org/CNApy/pull/465
* Misc updates by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/469
* replace deprecated add_reaction with add_reactions by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/474
* Bump to 1.1.8 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/475

**Full Changelogs**:
* https://github.com/cnapy-org/CNApy/compare/v1.1.6...v1.1.7 (version 1.1.7 is skipped due to blocking errors fixed in 1.1.8)
* https://github.com/cnapy-org/CNApy/compare/v1.1.7...v1.1.8

*Important note if you're 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 updates provides an improved GUI experience including a history of viewed model items, a multitude of bug fixes and now officially supports the new easier way to install CNApy on Windows.

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 434 and other minor enhancements by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/458
* Fix small bugs and expanded search features by Paulocracy in https://github.com/cnapy-org/CNApy/pull/457
* Enhanced readme by Paulocracy in https://github.com/cnapy-org/CNApy/pull/459
* some bug fixes by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/460
* Add default concentration ranges in thermodynamic dialog by Paulocracy in https://github.com/cnapy-org/CNApy/pull/461
* popup list with recently viewed model items, various small GUI improvemets by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/464
* Add new installation instructions by Paulocracy in https://github.com/cnapy-org/CNApy/pull/465
* Misc updates by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/469
* Version 1.1.7 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/471


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.6...v1.1.7

*Important note if you're 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.*

This is a **major new release** containing many new and novel features, as well as many important bug fixes:

New features

* You can now set *free linear constraints in scenarios and scenario-specific reactions* in CNApy under the "Scenario" tab (445). E.g., aside from many other new possibilities, you can now set linear constraints such that a minimal yield is reached or add import/export reactions for a specific scenario.
* The thermodynamics-based method *OptMDFpathway and a derived thermodynamic FBA as well as bottleneck reaction analysis are now integrated into CNApy* (441). You can find the functionality under the "Analysis" menu entry. To use OptMDFpathway, you have to provide dG'° values and metabolite concentration ranges, which can be manually added as annotations or loaded from a respective Excel XLSX or JSON file.
* You can now perform the flux feasibility analysis with customizable biomass reaction modifications (450).
* You can now copy the content of the reaction (438) and metabolite (446) lists in an Excel or text file by right-clicking on the respective heading and copying it to the clipboard. For the reactions list, this is directly possible (as JSON or Excel XLSX) through the "Clipboard" menu tab (449).
* Added ability to set exact box positions in the interactive maps (433).

Bug fixes

* Circumvent "numpy.float is not defined" error (442)
* Fix parsing of annotation values which are Python list strings (436)
* Fix error message when multiple empty annotations are created (440)

Installation Options

There are three ways to install CNApy:

1. As the easiest way only under Windows, you can use the .exe installer attached to the assets at the bottom of [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).
2. Under any operating system, you can 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).
3. If you want to clone and/or develop CNApy, follow the instruction 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 432 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/433
* set Qt version to 5.15 (LTS) by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/431
* parse lists of annotation values as lists by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/436
* Copy reaction table to UI clipboard by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/438
* Scenario constraints by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/445
* Visual OptMDFpathway by Paulocracy in https://github.com/cnapy-org/CNApy/pull/441
* Fix 439 (error with multiple empty annotations) by Paulocracy in https://github.com/cnapy-org/CNApy/pull/440
* Add automatic blank background with reaction addition by Paulocracy in https://github.com/cnapy-org/CNApy/pull/447
* Add free linear constraints to OptMDFpathway and thermodynamic bottleneck analysis by Paulocracy in https://github.com/cnapy-org/CNApy/pull/446
* Scenario tab updates by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/448
* Add menu entry for storing reaction list content by Paulocracy in https://github.com/cnapy-org/CNApy/pull/449
* Move website data to master branch by sthiele in https://github.com/cnapy-org/CNApy/pull/444
* In out fluxes additions by Paulocracy in https://github.com/cnapy-org/CNApy/pull/451
* Flux feasibility with biomass modification by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/450
* Bump to 1.1.5 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/452
* Fix concentration setting by Paulocracy in https://github.com/cnapy-org/CNApy/pull/453

**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.4...v1.1.5
and
**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.5...v1.1.6

*Important note if you're 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.*

This is a **major new release** containing many new and novel features, as well as many important bug fixes:

New features

* You can now set *free linear constraints in scenarios and scenario-specific reactions* in CNApy under the "Scenario" tab (445). E.g., aside from many other new possibilities, you can now set linear constraints such that a minimal yield is reached or add import/export reactions for a specific scenario.
* The thermodynamics-based method *OptMDFpathway is now integrated into CNApy* (441). You can find the functionality under the "Analysis" menu entry. To use OptMDFpathway, you have to provide dG'° values and metabolite concentration ranges, which can be manually added as annotations or loaded from a respective Excel XLSX or JSON file.
* You can now perform the flux feasibility analysis with customizable biomass reaction modifications (450).
* You can now copy the content of the reaction (438) and metabolite (446) lists in an Excel or text file by right-clicking on the respective heading and copying it to the clipboard. For the reactions list, this is directly possible (as JSON or Excel XLSX) throuch the "Clipboard" menu tab (449).
* Added ability to set exact box positions in the interactive maps (433).

Bug fixes

* Circumvent "numpy.float is not defined" error (442)
* Fix parsing of annotation values which are Python list strings (436)
* Fix error message when multiple empty annotations are created (440)

Installation Options

There are three ways to install CNApy:

1. As the easiest way only under Windows, you can use the .exe installer attached to the assets at the bottom of [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).
2. Under any operating system, you can 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).
3. If you want to clone and/or develop CNApy, follow the instruction 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 432 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/433
* set Qt version to 5.15 (LTS) by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/431
* parse lists of annotation values as lists by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/436
* Copy reaction table to UI clipboard by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/438
* Scenario constraints by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/445
* Visual OptMDFpathway by Paulocracy in https://github.com/cnapy-org/CNApy/pull/441
* Fix 439 (error with multiple empty annotations) by Paulocracy in https://github.com/cnapy-org/CNApy/pull/440
* Add automatic blank background with reaction addition by Paulocracy in https://github.com/cnapy-org/CNApy/pull/447
* Add free linear constraints to OptMDFpathway and thermodynamic bottleneck analysis by Paulocracy in https://github.com/cnapy-org/CNApy/pull/446
* Scenario tab updates by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/448
* Add menu entry for storing reaction list content by Paulocracy in https://github.com/cnapy-org/CNApy/pull/449
* Move website data to master branch by sthiele in https://github.com/cnapy-org/CNApy/pull/444
* In out fluxes additions by Paulocracy in https://github.com/cnapy-org/CNApy/pull/451
* Flux feasibility with biomass modification by axelvonkamp in https://github.com/cnapy-org/CNApy/pull/450
* Bump to 1.1.5 by Paulocracy in https://github.com/cnapy-org/CNApy/pull/452


**Full Changelog**: https://github.com/cnapy-org/CNApy/compare/v1.1.4...v1.1.5

***CNApy has got a [Gitter chat room](https://gitter.im/cnapy-org/community) where you can talk to CNApy's developers and stay informed about new releases***

This is primarily a maintenance release with some new small features and many bug fixes.

New features

* Annotation values can now be searched in the search bar if selected (412).
* Annotations can now be deleted using a "-" button and can be directly opened in the web browser by using identifiers.org (412)
* Gene annotations are now shown and can be edited (412)

Bug fixes

* Fix model saving problem (427).
* Fix error when editing scenario using backspace (424).
* Various error messages when opening files and performing calculations are now catched (413, 414)

Further changes

* Reactions selected in the reaction list are now automatically highlighted in the map (418).
* The most recent opened .cna files are now shown as a File menu entry (415, 419).

Installation Options

There are three ways to install CNApy:

1. As the easiest installation way which only works under Windows, you can use the .exe installer attached to the assets at the bottom of [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).
2. Under any operating system, you can 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).
3. If you want to develop CNApy, follow the instruction for the successful cloning of CNApy in section [Setup the CNApy development environment](https://github.com/cnapy-org/CNApy#setup-the-cnapy-development-environment).