Cnapy

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

Major new feature

* CNApy can now use **interactive Escher maps**, including the ability to load, save and edit them thanks to axelvonkamp's integration of the Escher in CNApy. From now on, Escher maps are the 2nd type of possible interactive metabolic model maps in CNApy, together with the "traditional" CNApy maps (401). If you encounter any problems with Escher maps in CNApy, please let us know through [our GitHub issues](https://github.com/cnapy-org/CNApy/issues).

Bug fixes

* Editing a GPR rule does not create many new orphaned genes anymore (329)
* CNApy now always downloads the latest CNApy projects version (398)
* Scenario objectives are not deleted when using flux history values (404)
* [StrainDesign](https://github.com/klamt-lab/straindesign) now comes in version 1.9, fixing some crashes with GLPK.
* Escher also works within cobra packages and the .exe installer version (406)

Further changes

* Again, some vertical space is saved by rearranging the reaction view's content, making it more readable with smaller screens (402)
* Various optimizing refactorings (396, 400)

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).

*Beta release*

*Important note if you're using the cnapy-dev Anaconda environment: Since the 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.*

New features

* Scenarios can now get an optional objective and description (388)
* Separate objective tab added (388)
* Scenario-bound reactions can now be pinned in the reaction list (388)
* The flux feasibility routine now shows all made changes for feasibility in the iPython console (385)
* New first start-up routine specifically asking for the download of CNApy's example projects (388)

Bug fixes

* Resolve CNApy installer issue, which led to no CNApy start-up, by using sthiele's JVM-searching routine (386)
* Resolve CNApy installer issue in common folders (386)
* Resolve update_item() error when changing reaction elements (390)
* Resolve error with in/out metabolite fluxes on some devices (389)

Further changes

* Reordered Scenario menu tab for more consistency (388)
* Some vertical space is saved by rearranging the reaction view's content (388), making it more readable with smaller screens
* VonAlphaBisZulu's StrainDesign package was updated to its latest version 1.6

Install

There are two ways to install CNApy:

1. Under any operating system, by installing CNApy as a conda package (see [https://github.com/cnapy-org/CNApy#install-cnapy-with-conda](https://github.com/cnapy-org/CNApy#install-cnapy-with-conda))
2. As an alternative installation way under Windows, by using the .exe installer attached to [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).

*Beta release*

*Important note if you're using the cnapy-dev Anaconda environment: Since the 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 update which contains many significant changes and additional features:

New features

* **VonAlphaBisZulu's [StrainDesign ](https://github.com/klamt-lab/straindesign) package is now integrated within CNApy**. You can access it under CNApy's GUI under the "Analysis" menu entry. By using StrainDesign's GUI and functions, one can easily create powerful combinations of several strain design methods such as OptKnock, RobustKnock and generalized Minimal Cut Sets (MCS). StrainDesign makes use of state-of-the-art model compression algorithms in order to minimize the computational complexity of all calculations as much as currently possible, thus making calculations faster and less memory-intensive. Further major features are: One can also define knock-ins instead of knock-outs; Aside of reaction-based knock-outs, one can also define gene-based knock-outs.
* Right now only for the StrainDesign features, the open-source solver **[SCIP](https://scipopt.org/) is now usable with CNApy**. You still have to install and configure SCIP by yourself. In the future, this will be facilitated and SCIP will be usable with all CNApy functions.
* Since almost all legacy functions are now programmed in Python, **all *CellNetAnalyzer* legacy bindings are now removed**, so that no MATLAB or Octave is needed for them anymore.
* The **community versions of IBM CPLEX and Gurobi** are now installed by default. These community versions are restricted to models up to 1000 variables. In order to facilitate the integration of both solver's full versions (usable for big versions), wizards were added to CNApy which you may find under the "Config" menu entry.
* The **standard [CNApy projects](https://github.com/cnapy-org/CNApy-projects) can now be downloaded** under the respective field in the "Projects" menu entry even after the first start.

Bug fixes

* GLPK is now the standard solver in order to prevent typical IBM CPLEX or Gurobi errors (376)
* Numerous potential IBM CPLEX and Gurobi errors are now catched (368, 373)
* WIth the newest [CNApy projects](https://github.com/cnapy-org/CNApy-projects) release, a map resolution error under Linux affecting the map's text was resolved (#377)
* An error while using the Escher SVG integration was resolved (355)
* Maps are now automatically zoomed in the start-up such that no scroll bars have to appear (354)

Install

There are two ways to install CNApy:

1. Under any operating system, by installing CNApy as a conda package (see [https://github.com/cnapy-org/CNApy#install-cnapy-with-conda](https://github.com/cnapy-org/CNApy#install-cnapy-with-conda))
2. As an alternative installation way under Windows, by using the .exe installer attached to [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).

*Beta release*