PSAMM 0.28

• The YAML model format now allows users to specify compartment information and compartment boundaries in the model.yaml file. See the file format documentation for more information.
• The media key in the model.yaml has changed name to exchange to reflect the fact that not only uptake exchange must be defined here. The media key is still supported but has been deprecated.
• The gap-filling command gapfill and fastgapfill now use the compartment information to determine which artificial transport and exchange reactions to add. This means that a model must specify compartments and compartment boundaries when using gap-filling commands.
• The gapcheck command now has two new methods for detecting blocked compounds. The new prodcheck is a more robust version of the GapFind check which was previously used. The new sinkcheck method will find compounds that cannot be produced in excess. This can find some additional blocked compounds that were not detected by the other methods.
• The gapcheck command now reports blocked compounds in the extracellular space. Previously, these compounds were excluded. An option is available to switch back the old behavior of excluding these from the final output.
• The gapcheck command now has an option to run the check with unrestricted exchange reactions.
• The gapfill command can now be run without implicit sinks. This makes it possible to use this command to solve additional model gaps. It is still recommended to first solve gaps using implicit sinks, then later disable implicit sinks when all other gaps have been closed.
• The gapfill command now has an option to enable the bounds expansion proposals (e.g. making irreversible reactions reversible). By default this option is now off.
• The fastgapfill has improved output that contains less superfluous information. The output format is now identical to the gapfill command. The fastgapfill also no longer runs an FBA on the induced model since this caused some confusion.
• Added new command checkduplicates which detects whether the model has multiple reactions with the same (or similar) reaction equation.
• The sbmlexport command now allows the user to specify a file path. The command can also optionally output the SBML file in a more readable format with an option.
• Fixed support for the latest CPLEX release 12.7. A change in their API made PSAMM incompatible with the 12.7 release. This is now fixed.
• We now officially support Python 3.5 and Python 3.6.