Psamm

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- Change parsing of medium definitions to combine all parts of the medium into
one final medium used for simulations. Previously, the entries in the
`media` key would be considered as separate media and only the first entry
would be used.
- Fix parsing of limits table format to make it consistent with the medium
table format.
- Change the name of option `--reaction` to `--objective` for commands that
take an optional reaction flux to maximize.
- Change the default of commands that use thermodynamic constraints on FBA
problems to _not_ apply the additional constraints by default. The commands
have an option to enable thermodynamic constraints.
- Change the `--no-tfba` option of the commands `fba` to `robustness` to
`--loop-removal`. The loop removal option allows the L1 minimization method
to be selected as a loop removal method in addition to the thermodynamic
constraints.
- Add option to `robustness` command to print all fluxes. By default only the
objective is shown.
- In `robustness`, obtain the lower and upper bounds of the varying reaction
by minimizing and maximizing the reaction flux. This avoids trying to solve
many LP problems that are infeasible and instead provides more samples from
the flux range that is known to be feasible.
- Fix a bug in `robustness` that caused thermodynamic constraints to never be
enabled properly.
- Fix bug where parsing medium from table would fail.
- Produce a warning when a compound is referenced from a reaction but not
defined in the list of compounds.
- During SBML import produce a warning when `_b`-suffix compounds are
converted to boundary compounds in non-strict mode.
- Improve the efficiency of creating long linear expressions for the LP
solver interface. This should speed up certain procedures that use long
expression as objectives or constraints.
- Improve the efficiency of resolving variable names in Cplex LP problems by
using column indices directly. This significantly speeds up procedures using
many variables when using Cplex as the solver.

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- Fix tiny bug in setup.py resulting in failure to upload the 0.12 package to
PyPI.

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- Add support for the Gurobi LP solver (Python 2.7 only).
- Fix a bug in the `fastgapfill` command that caused the biomass reaction to
never be found in the model.
- Add command line tool `psamm-list-lpsolvers` which will list the available
solvers, and report their attributes and whether they can be successfully
loaded.
- Change the way the threshold parameter on the `randomsparse` command is
parsed. A threshold relative to the maximum flux is now given using
percentage notation (e.g. `95%`) while an absolute flux threshold is given as
a number (e.g `1.34`).
- Log the model name at the beginning of every command. If the model exists in
a Git repository, the current Git commit ID is also reported.
- Produce warnings when encountering invalid SBML constructs using non-strict
parsing. Previously, some of these could only be noticed when using the
strict mode.
- Improve error reports from commands. This means that usage information is now
printed when a command fails to parse an argument.
- Improve the API in the `fluxanalysis` module to allow commands to more
easily reuse LP problems. This improves the speed of robustness analysis in
particular.
- Improve and expand the install instructions in the documentation.
- Reorganize implementations of commands into the `psamm.commands` package. The
commands are now discovered through the entry point mechanism from
`setuptools` allowing any package to install additional commands into the
PSAMM user interface.
- Use a simpler output format for log messages unless the environment variable
`PSAMM_DEBUG` is set. If set, this variable determines the logging level
(e.g. `PSAMM_DEBUG=debug` enables more messages).
- Include Python 3.3 in the tox test suite.

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- Add new flux coupling analysis command and API module.
- Add parser for KEGG reaction files.
- Export COBRA-compatible flux constraints when exporting to SBML.
- Improve the command descriptions in the command line interface.
- Extend the search command to report information on which file the
compound/reaction was parsed from.
- Add support for Python 3.4.
- Fix Fastcore unit tests that failed using an exact solver.
- Change unit tests to allow covering solvers other than Cplex.
- Optionally use tox for unit test management. This allows independently
testing with multiple versions of Python and with different solvers.
- Adapt code to conform to PEP-8.

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- Various minor documentation and packaging updates. PSAMM is now available
through [PyPI](https://pypi.python.org/pypi/psamm) and the documentation has
been updated to reflect this. The documentation is available through
[Read the Docs](https://psamm.readthedocs.org/). Lastly, the test suite is
automatically run by [Travis CI](https://travis-ci.org/zhanglab/psamm).

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- Update README with new repository names and improved install instructions.
- docs: Add improved install instructions based on README.