CNApy v1.2.7

This is (another) hotfix release to resolve the gurobipy version conflict-related install error #551

What's Changed

• explicitly create empty default map when loading SBML file by @axelvonkamp in #550
• Bump to 1.2.7 by @Paulocracy in #552

Full Changelog: v1.2.6...v1.2.7

CNApy 1.2.6

This is a hotfix release which should solve a major installer bug, as well as some small bug, and now also offers compatibility with the very latest CPLEX version.

What's Changed

• Hotfixes; V 1.2.6 by @Paulocracy in #549

Full Changelog: v1.2.5...v1.2.6

CNApy 1.2.5

This release contains a multitude of important bug fixes as well as the following new features:

• A new dark mode option that you an acivate in CNApy's config dialog
• If you have performance problems with StrainDesign, you can now try to use the "Big M" option for an alternative formulation without indicator constraints, which may be significantly faster in some cases
• If started from the console, you can now specify a model and model that is automatically loaded during start-up by using the model path as first command argument, and (optionally) the path to the scenario as second argument
• More robust thermodynamic calculations based upon the COBRA-k package

What's Changed

• cnapy.spec for use with pyinstaller by @axelvonkamp in #532
• Change cplex package to ARM-MacOS-compatible version by @Paulocracy in #533
• Small setuptools dependency fix by @Paulocracy in #534
• Update python-publish.yml by @Paulocracy in #539
• Add ability to load project and scenario as command-line arguments by @Paulocracy in #540
• Fix #535 by @Paulocracy in #541
• Add first stage of COBRA-k integration by @Paulocracy in #542
• simplify Escher initialization by @axelvonkamp in #543
• Bug fixes/improvements by @axelvonkamp in #544
• Add BigM option by @Paulocracy in #546
• Fix dark mode by @Paulocracy in #547
• Bump to 1.2.5 by @Paulocracy in #548

Full Changelog: v1.2.4...v1.2.5

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