*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