Releases: cnapy-org/CNApy
v1.1.9
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:
- If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
- 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.
- 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.
- 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.
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
- Unify scenario_file_name label and load scenario_button by @sthiele in #476
- Schedule old MapViews for deletion by @sthiele in #477
- Escher profile by @axelvonkamp in #479
- if a loaded scenario is modified mark the displayed filename as changed by @axelvonkamp in #482
- Apply button by @axelvonkamp in #483
- Misc by @axelvonkamp in #485
- Small fixes by @Paulocracy in #484
- Bump to version 1.1.9 by @Paulocracy in #486
Full Changelog: v1.1.8...v1.1.9
Contributors
Assets 4
CNApy 1.1.8
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:
- If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
- 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.
- 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.
- 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.
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 #434 and other minor enhancements by @axelvonkamp in #458
- Fix small bugs and expanded search features by @Paulocracy in #457
- Enhanced readme by @Paulocracy in #459
- some bug fixes by @axelvonkamp in #460
- Add default concentration ranges in thermodynamic dialog by @Paulocracy in #461
- popup list with recently viewed model items, various small GUI improvemets by @axelvonkamp in #464
- Add new installation instructions by @Paulocracy in #465
- Misc updates by @axelvonkamp in #469
- replace deprecated add_reaction with add_reactions by @axelvonkamp in #474
- Bump to 1.1.8 by @Paulocracy in #475
Full Changelogs:
- v1.1.6...v1.1.7 (version 1.1.7 is skipped due to blocking errors fixed in 1.1.8)
- v1.1.7...v1.1.8
Contributors
Assets 4
CNApy 1.1.7
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.
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:
- If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
- 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.
- 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.
- 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.
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 #434 and other minor enhancements by @axelvonkamp in #458
- Fix small bugs and expanded search features by @Paulocracy in #457
- Enhanced readme by @Paulocracy in #459
- some bug fixes by @axelvonkamp in #460
- Add default concentration ranges in thermodynamic dialog by @Paulocracy in #461
- popup list with recently viewed model items, various small GUI improvemets by @axelvonkamp in #464
- Add new installation instructions by @Paulocracy in #465
- Misc updates by @axelvonkamp in #469
- Version 1.1.7 by @Paulocracy in #471
Full Changelog: v1.1.6...v1.1.7
Contributors
Assets 2
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:
- 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.
- Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
- 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
Contributors
Assets 6
CNApy 1.1.5
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:
- 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.
- Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
- 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
Full Changelog: v1.1.4...v1.1.5
Contributors
Assets 3
CNApy 1.1.4
CNApy has got a Gitter chat room 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:
- 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.
- Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
- If you want to develop CNApy, follow the instruction for the successful cloning of CNApy in section Setup the CNApy development environment.
CNApy 1.1.3
CNApy has got a new Gitter chat room 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.
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 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:
- 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.
- Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
- If you want to develop CNApy, follow the instruction for the successful cloning of CNApy in section Setup the CNApy development environment.
Contributors
Assets 3
CNApy 1.1.2
Beta release
CNApy 1.1.1
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:
- Under any operating system, by installing CNApy as a conda package (see https://github.com/cnapy-org/CNApy#install-cnapy-with-conda)
- As an alternative installation way under Windows, by using the .exe installer attached to CNApy's latest release.
Contributors
Assets 3
CNApy 1.1.0
Beta release