CNApy 1.2.4

This is (another) hotfix for CNApy, this time for a jpype problem that caused a Java Virtual Machine (JVM) error after installation.

Installation Options

There are 4 alternative ways to install CNApy:

1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see Using CNApy installer for more.
2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through pip install cnapy in your console. Afterwards, you can start CNApy's GUI by running either cnapy or, if this doesn't work, python -m cnapy where "python" must call your Python 3.10 installation.
3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named cnapy-1.2.2 as follows: 1) Run conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge, 2) run conda activate cnapy-1.2.2, 3) run pip install cnapy. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either cnapy or, if this doesn't work, python -m cnapy. Note that the cnapy conda package is currently not being updated due to licensing uncertainties.
4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section Setup the CNApy development environment.

What's Changed

• Correct license in toml by @Paulocracy in #530
• Version 124 by @Paulocracy in #531

Full Changelog: v1.2.3...v1.2.4

CNApy 1.2.3

This is a hotfix regarding issue #528 and, if you use the installer, an occassional "numpy.bool" error".
While this hotfix mitigates the Gurobi error in the former, the newest Gurobi version (starting from version 12) are currently unsupported until this issue in CNApy's dependency is fixed.

Installation Options

There are 4 alternative ways to install CNApy:

1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see Using CNApy installer for more.
2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through pip install cnapy in your console. Afterwards, you can start CNApy's GUI by running either cnapy or, if this doesn't work, python -m cnapy where "python" must call your Python 3.10 installation.
3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named cnapy-1.2.2 as follows: 1) Run conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge, 2) run conda activate cnapy-1.2.2, 3) run pip install cnapy. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either cnapy or, if this doesn't work, python -m cnapy. Note that the cnapy conda package is currently not being updated due to licensing uncertainties.
4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section Setup the CNApy development environment.

What's Changed

• Gurobi hotfix by @Paulocracy in #529

Full Changelog: v1.2.2...v1.2.3

v1.2.2

This release contains two major changes for CNApy:

1. The much-improved installation process is introduced, now with an automatic installer for Windows, Linux and MacOS. For more details, see the 1st point in the "Installation Options" below.
2. Due to licensing issues, we suspend providing new conda packages for CNAPy. Instead, CNApy can now be installed using pip as it is now available as a PyPI package, see the 2nd point in the "Installation Options" below. For instructions on still using CNApy in a conda/mamba environment, see the 3rd point in the "Installation Options" below.

Installation Options

There are 4 alternative ways to install CNApy:

1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see Using CNApy installer for more.
2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through pip install cnapy in your console. Afterwards, you can start CNApy's GUI by running either cnapy or, if this doesn't work, python -m cnapy where "python" must call your Python 3.10 installation.
3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named cnapy-1.2.2 as follows: 1) Run conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge, 2) run conda activate cnapy-1.2.2, 3) run pip install cnapy. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either cnapy or, if this doesn't work, python -m cnapy. Note that the cnapy conda package is currently not being updated due to licensing uncertainties.
4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section Setup the CNApy development environment.

What's Changed

• Pypi by @axelvonkamp in #525
• Version 122 by @Paulocracy in #526

Full Changelog: v1.2.1...v1.2.2

1.2.1

Important note for those who are 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.

Major changes

This release bumps CNApy's Python requirement from Python 3.8 to Python 3.10. While this makes CNApy a bit more performant and easier to delevop, this also means that external solver versions that do not support Python 3.10 will not work with CNApy anymore.
Furthermore, this release includes a multitude of important bug fixes (see below) as well as a much better Escher map integration and small quality-of-life enhancements.

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.
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.
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.
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.

Changes in this release

What's Changed

• File management by @axelvonkamp in #510
• Fix annoying OptMDFpathway bugs by @Paulocracy in #511
• Scenario in clipboard by @Paulocracy in #512
• Push to Python 3.10 by @Paulocracy in #514
• fix #515 and ensure that a changed objective is always set by @axelvonkamp in #518
• improved Escher integration by @axelvonkamp in #513
• Per default use system font size by @sthiele in #517
• Store EFMs as JSON by @Paulocracy in #522
• possible fix for #520 by @axelvonkamp in #521
• unified strain design by @axelvonkamp in #519
• Bump to 1.2.1 by @Paulocracy in #523

Full Changelog: v1.1.11...v1.2.1

CNApy 1.1.11

Main changes

This update provides a multitude of bug fixes, including the solution for a crash during plotting when it was installed using the Windows installer. Furthermore, one can now easily take a map screenshot under the respective options in the "Map" menu, EFMs can now be easily normalized and scenario-dependent annotations were added (e.g., for scenario-dependent variances or thermodynamic parameter values).

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.
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.
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.
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.

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 SDS loading by @Paulocracy in #500
• Addressing #489 by @Paulocracy in #502
• Add screenshot capability for CNApy maps by @Paulocracy in #501
• Add EFM normalization button (#503) by @Paulocracy in #504
• Add Scenario annotations by @Paulocracy in #506
• explicitaly show unchanged IDs as such by @axelvonkamp in #507
• Improved installation guide by @Paulocracy in #508

Full Changelog: v1.1.10...v1.1.11

v1.1.10

Important note for those who are 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 update provides a multitude of bug fixes and several small enhancements such as an improved Compute MCS dialog with a reaction auto-completion and the ability to use the "-" sign.

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.
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.
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.
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.

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 several bugs by @Paulocracy in #492
• small improvements by @axelvonkamp in #493
• sequential editing of scenario values using up/down arrow keys in sce… by @axelvonkamp in #497
• Multiple MCS dialog improvements by @Paulocracy in #496
• Version 1.1.10 by @Paulocracy in #494

Full Changelog: v1.1.9...v1.1.10

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:

1. If you use Windows, the easiest way is to use our Windows installer, see section 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.
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.
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.

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

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:

1. If you use Windows, the easiest way is to use our Windows installer, see section 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.
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.
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.

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

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:

1. If you use Windows, the easiest way is to use our Windows installer, see section 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.
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.
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.

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

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