PSAMM 1.2.1

• fix bug in generate-database
• revise formatting of doc

PSAMM 1.2

• Adds the new psamm-generate-model command with the options of
  generate-database, generate-transporters, and generate-biomass,
  which construct metabolic models in the KEGG namespace
• Adds the new option translated-reactions to the tableexport command
• Added translated reactions to excelexport
• Fixed compatibility in documentation for Gurobi for python versions 3.7
• Adds support for Python 3.8 and 3.9

PSAMM 1.1.2

• Drops support for Python 2.7 (deprecated Jan. 01, 2020), 3.3, and 3.4
• Adds the --phin and --phout options to the tmfa command
• Adds descriptive counts of the number of reactions and compounds
  curated in the manual curation option of modelmapping

PSAMM 1.1.1

• Fix bug where the psamm modelmapping translate_id command requires
  the undefined parameter --dest-model

PSAMM 1.1

• Adds the new vis command for visualizing metabolic pathways and
  networks
• Adds the new tmfa command to implement the approach as described
  in Henry et al., 2007 (PMID: 17172310) and Hamilton et al., 2013
  (PMID: 23870272).
• Performance updates to the model-mapping command
• Updates to export full models from gimme and psammotate
• Added the --fva option to the robustness command

PSAMM 1.0

• Adds the new modelmapping command for mapping reactions and
  compounds ids between different GEMs.
• Adds the new psammotate command for generating draft GEMs
  using a template model and a mapping of orthologous genes to
  another organism.
• Adds the new gimme command which implements the GIMME algorithm
  as described in Becker and Palsson, 2008 (PMID: 18483554).
• Updates the search command to allow for searching of strings
  within any reaction or compound property.
• Updates to the tableexport and excelexport commands to allow
  for the export of additional gene and reaction information.
• Adds new section to the tutorial to detail how to use the
  findprimarypairs commands.
• Renamed duplicatescheck command to dupcheck.

PSAMM 0.31

• The psamm-import tool has been moved from the psamm-import package to
  the main PSAMM package. This means that to import SBML files the
  psamm-import package is no longer needed. To use the model-specific Excel
  importers, the psamm-import package is still needed. With this release
  of PSAMM, the psamm-import package should be updated to at least 0.16.
• The tutorial was updated with additional sections on using gap-filling
  procedures on models.

PSAMM 0.30

• Adds the new command primarypairs for predicting reactant/product element transfers using the new FindPrimaryPairs method as well as the MapMaker method.
• A new option has been added to the genedelete command which allows use of minimization of metabolic adjustments to simulate biomass production for gene knockouts.
• Fixes a bug where the epsilon parameter was accidentally ignored by fastgapfill.
• Fixes a bug where the psamm-sbml-model command did not ignore boundary species. With this change, the boundary species are also ignored by default when using the API to read SBML models.
• Fixes a performance issues with gap-filling that made the gapfill and fastgapfill commands take much longer time to run on large models than necessary.

PSAMM 0.29

• The tutorial in the PSAMM documentation has been updated and expanded to include additional information on using PSAMM for model curation and constraint-based analyses.
• The experimental command psamm-sbml-model was added which makes it possible to run any command from psamm-model (e.g. fba, robustness, etc.) directly on an SBML file. For now this only supports SBML level 3 files with FBC. This provides a quick way of running basic analyses on SBML files. We still recommend importing the SBML file to YAML format with psamm-import for anyone wishing to make changes to a model.
• Fixes access to charge parameter parsed from SBML files. The charge is now correctly imported with psamm-import.
• Fixes import of compartments from SBML files. The empty boundary compartments are now no longer included in the import.
• Fixes bug in writing the reaction flux limits sheet of the excelexport command.
• The console command was changed to only provide the model variable since the metabolic model can easily be created.

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.