CNApy 1.1.6

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 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.
2. Under any operating system, you can install CNApy as a conda package as described in section 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.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

• Fix #432 by @Paulocracy in #433
• set Qt version to 5.15 (LTS) by @axelvonkamp in #431
• parse lists of annotation values as lists by @axelvonkamp in #436
• Copy reaction table to UI clipboard by @axelvonkamp in #438
• Scenario constraints by @axelvonkamp in #445
• Visual OptMDFpathway by @Paulocracy in #441
• Fix #439 (error with multiple empty annotations) by @Paulocracy in #440
• Add automatic blank background with reaction addition by @Paulocracy in #447
• Add free linear constraints to OptMDFpathway and thermodynamic bottleneck analysis by @Paulocracy in #446
• Scenario tab updates by @axelvonkamp in #448
• Add menu entry for storing reaction list content by @Paulocracy in #449
• Move website data to master branch by @sthiele in #444
• In out fluxes additions by @Paulocracy in #451
• Flux feasibility with biomass modification by @axelvonkamp in #450
• Bump to 1.1.5 by @Paulocracy in #452
• Fix concentration setting by @Paulocracy in #453

Full Changelog: v1.1.4...v1.1.5
and
Full Changelog: v1.1.5...v1.1.6