Psamm

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- This software is now GPLv3 licensed. A copy of the license is included in
[LICENSE](LICENSE).
- Allow setting the default flux limit in `model.yaml`. Previously a limit
of 1000 units was used, and this value is still used if not specified.
- Allow setting the reaction name of the implicit exchange reactions
specified in the medium definition.
- sbml: Change the SBML writer to avoid negative values for reaction
stoichiometry. Some software packages do not handle negative values
correctly when loading SBML files.
- command: Add a new option to `fluxcheck` where the restrictions imposed on
the exchange reactions are removed before the consistency check.
- cplex: Use numerical emphasis mode by default.

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- Add methods the internal metabolic model representation to provide the
compartments. This is used by commands instead of hardcoding specific
model compartments when running `gapfill` or `fastgapfill`.
- docs: Update documentation on `psamm-model` commands.
- docs: Update information on installing the linear programming solvers.

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- The name of the project (in `setup.py`) changed name to `psamm`.
- The name of the main package changed from `metnet` to `psamm`.
- Remove unused scripts related to obsolete GAMS modeling.
- Assume TSV format for `.tsv` compound files. This removes the need for
explicitly specifying `format: tsv` in the include.
- By default FVA and the flux consistency check will apply thermodynamic
constraints. A command line option was added to go back to the previous
behavior.
- Properly report compound names when multiple files are included.
- Add possibility of supplying additional solver parameters through the command
line. Currently, the Cplex solver supports the parameters `threads` (the max
number of threads allowed globally) and `feasibility_tolerance` (how much the
basic variables of a model are allowed to violate their bounds).
- command: The command `randomsparse` now defaults to normal FBA without
thermodynamic constraints. This is much faster and the additional constraints
are guaranteed to not change the result in this case.
- docs: Enabled napoleon Sphinx extension for Google-style docstring support.
This makes docstrings more readable while at the same time improving the
generated docs. The `fluxanalysis` module was updated with additional
documentation in this format.
- fluxanalysis: Change the API so that the `tfba` parameter can be given to
functions that support thermodynamic constraints to select this mode. The
support for thermodynamic constraints was extended to the flux consistency
check and FVA.
- fluxanalysis: Slightly improve FVA by avoiding copying the model.
- sbml: Provide access to species charge.
- qsoptex: Fix error when calling the `status()` method of a result.
- command: Add option to see current version.

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- Change name of `model` script to `psamm-model`.
- native: Add YAML format for flux limits. The documentation has been updated
to include more information on this format. This changes the `limits` key in
`model.yaml` to a list of dicts.
- Add `--exchange` option to the `randomsparse` command to find random
minimal sets of exchange reactions.
- Change name of `fluxconsistency` command to `fluxcheck`.
- Allow compounds to be marked as zero-mass (e.g. photons) by setting
`zeromass: yes`. These compounds will be exempt from the mass requirements
in the `masscheck` command.
- sbml: Provide access to model ID and name.
- sbml: Add option to skip boundary condition species when parsing.
- massconsistency: Fix bugs occurring when zero-mass compounds are specified.
- command: Log number of consistent reactions in `masscheck`.
- sbml: Fix a number of minor bugs.
- command: Fix search command when no alternative compound names are present

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- sbml: Fix bug where boundary conditions were parsed incorrectly.

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- Apply changes to the SBML parser in order for it to interoperate with
`model-import`. This makes it easier to implement the SBML importer in
`model-import`.
- Add non-strict mode to the SBML parser. This makes it possible to load
almost-compliant SBML documents that are accepted by COBRA.
- `masscheck` command: Allow reactions to be marked as checked.
- cplex: Consider status `optimal_tolerance` to be successful.
- docs: Expand documentation on the `masscheck` command.
- docs: Change order of API documentation to `bysource`.