v2.10.0

• fix:
  • importModel only removes identifier prefixes (like R_ for reactions) when present in all entries of a certain type; gives a warning that this happened; and has a removePrefix flag that can be set to false if desired
  • exportModel only adds identifier prefixes (like R_ for reactions) when one or more entries of a certain type are not compatible with SBML (i.e. do not start with a letter or _); gives a warning that this happened; and has a neverPrefix flag that can be set to true if desired. Previously, prefixes were always added
  • importModel allows for empty parameters when not specified
  • constructS gives correct error message when a metabolite is missing
  • importExcelModel can ignore faulty MIRIAM entries (note: import of Excel models is strongly discouraged!)
  • checkModelStruct to determine if reaction is reversible, consider all combinations of LB and UB, not just whether LB < 0 or not
  • checkModelStruct checks that all genes in grRules field are also in genes field (solves #556)
• feature:
  • checkModelStruct queries if the model has any identifiers that are not SBML compatible (i.e. do not start with a letter or _)
  • new removeIdentifierPrefix function can remove identifier prefixes like R_ for reactions if desired
  • new addIdentifierPrefix function can add identifier prefixes like R_ for reactions if required
  • support for model.proteins as field, which matches model.genes and is also supported by SBML and YAML
  • getExchangeRxns has more options to select reactions based on their reaction bounds, whether they represent uptake, excretion etc. (solves #555)
• docs:
  • getKEGGModelForOrganism explicitly refers to the correct dataDir options (i.e. prok90_kegg105 or euk90_kegg105 at this time)