Psamm

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- Fixed an error parsing decimal values in reactions which resulted in a
failure to run FBA and other analyses on certain models.
- The `fastgapfill` command no longer tries to unblock exchange reactions by
default. Only internal reactions will be unblocked by default.
- The `fastgapfill` command has a new `--subset` option to explicitly specify
set of reactions to unblock. This means that the command can now be used to
unblock a specific reaction.
- The weight options on `fastgapfill` have changed name to `--db-penalty`,
`--tp-penalty` and `--ex-penalty` for consistency with the existing
`--penalty` option.
- Fixed an error in `gapfill` that in some cases would result in a compound
incorrectly marked as non-blocked.
- The `sbmlexport` command now follows the FBCv2 specification for writing
flux bounds, biomass reaction, gene products and various other properties to
SBML files.
- The `sbmlexport` command now uses the same ID for compartment IDs as used
in the YAML files.
- The order of compounds in the output from commands now reflects the order
of compounds in the reactions as specified in the model files.
- Experimental support for solving MILP problems with GLPK has been activated.

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- When specifying flux bounds in media and limits, the `fixed` key can now be
used when lower and upper limits are the same.
- New column in output of `excelexport` and `tableexport` commands to
indicate if reactions and compounds are in the model.
- Zero mass compounds are now omitted from the output of the `massconsistency`
command.
- When exporting SBML file using the `sbmlexport` command, the exported
compounds and reactions now have IDs that are based on the YAML model IDs.
Characters that are not allowed in SBML IDs are transformed in a way that is
compatible with COBRA.

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- Fix a bug where no output of the `randomsparse` command was produced.
- Make Cplex interface in PSAMM compatible with earlier versions
(12.6 and 12.6.1) again.

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- Better unicode handling in commands.
- When running the `gapfill` command the epsilon parameter can now be
specified on the command line.
- When parsing reaction and compound entities from the YAML files, produce
better error messages when IDs are invalid.
- Work around a bug in Cplex that in rare causes a segmentation fault when a
linear programming problem is solved repeatedly.
- API: Add `fastgapfill` module which allows access to run the fastGapFill
algorithm.
- API: Add `randomsparse` module which allows access to generate a random
minimal model which satisfies the flux threshold of the objective reaction.

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- Add `genedelete` command to allow users to delete one or more genes and
perform a viability check on the model after all related reactions are
deleted.
- Add `balancecheck` module which allows API access to charge balance and
formula balance checks.
- When a compound in the extracellular space doesn't have an exchange reaction,
a warning would be provided so that the user may add the compound to the
medium.
- If a compartment is not given for a medium, it will now be assumed to have
the extracellular compartment.
- When using Gurobi and Cplex, the default optimality tolerance and feasibility
tolerance has been decreased to 1e-9.
- Fixed a bug where the reaction IDs are not printed properly in the result of
`chargecheck` command.

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- Added experimental support for GLPK solver. MILP problems are not yet
supported with this solver. GLPK also appears to have some issues with
`fastgapfill`.
- The `gapfill` command can now take a list of compounds on the command line
that it will try to unblock. If a list of compounds is given, the command
will not run GapFind but instead only use those compounds.
- Remove the assumption that the extracellular compartment is always called
`e`. The user can now specify the name of the extracellular compartment with
the option `extracellular` in `model.yaml`.
- In a previous release, the code interfacing with Cplex was updated and is now
using an interface in Cplex that was introduced in version 12.6.2. The
documentation now makes it clear that at least version 12.6.2 is required.
- Update YAML format documentation on the model definition table format.
- Work around issue with `pkg_resources` that resulted in import errors when
running from IPython.