Psamm

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- Add `sbmlexport` command to export current model as an SBML file.
- Add a generic interface to the linear programming solvers that delegates to
an actual solver that is installed and has the required features. This adds
a `--solver` option to a number of command which can be used to influence
which solver is selected.
- Add `--epsilon` option to a number of commands that previously had the
epsilon value hardcoded.
- Refactor functions in `fastcore` for easier use.
- docs: Extend docstring documentation of various modules.
- docs: Add DOI links for references.

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- Add documentation generated by Sphinx. The main contents of the
[README](README.md) file has been moved to the new documentation.
- Generate the entry-point script using `setup.py`. This ensures that the
package is correctly installed before the main script can be called. This
also changes the name of the entry-point from `model.py` to `model`.
- Refactor functions in `massconsistency` for easier use.
- Add `__version__` attribute to main module.
- docs: Move references to separate section.
- docs: Fix file format documentation for medium file.
- Unit tests: Skip tests requiring a linear programming solver if Cplex is
present.

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- Require reaction files to be explicitly listed in `model.yaml`.
- Add support for TSV reaction file format.
- Change format of YAML reactions (see [README](README.md) for details).
- Add tables of recognized compounds and reaction properties to
[README](README.md).
- `masscheck` command: Automatically exclude biomass reaction from check.

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- Allow compounds to be specified using YAML, TSV or ModelSEED format. This
changes the format of the `compounds` key in `model.yaml` (see
[README](README.md) for more information).
- Allow specifying biomass reaction in `model.yaml` using the `biomass` key.
The biomass reaction will be used by default for FBA, FVA, etc.
- Allow explicit definition of media. This can be defined using a table format
or YAML format. See [README](README.md) for more information.
- `chargecheck`/`formulacheck` commands: Only check reactions where all
compounds have charge/formula specified. The number of skipped reactions is
reported separately.
- `chargecheck` command: Use charge information from model definition instead
of requiring a separate charge table file.

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- Initial release.