Psamm

------------------

- The `psamm-import` tool has been moved from the `psamm-import` package to
the main PSAMM package. This means that to import SBML files the
`psamm-import` package is no longer needed. To use the model-specific Excel
importers, the `psamm-import` package is still needed. With this release
of PSAMM, the `psamm-import` package should be updated to at least 0.16.
- The tutorial was updated with additional sections on using gap-filling
procedures on models.

------------------

- Adds the new command `primarypairs` for predicting reactant/product element
transfers using the new FindPrimaryPairs method as well as the MapMaker
method.
- A new option has been added to the `genedelete` command which allows use of
_minimization of metabolic adjustments_ to simulate biomass production for
gene knockouts.
- Fixes a bug where the epsilon parameter was accidentally ignored by
`fastgapfill`.
- Fixes a bug where the `psamm-sbml-model` command did not ignore boundary
species. With this change, the boundary species are also ignored by default
when using the API to read SBML models.
- Fixes a performance issues with gap-filling that made the `gapfill` and
`fastgapfill` commands take much longer time to run on large models than
necessary.

------------------

- [The tutorial](https://psamm.readthedocs.io/en/stable/tutorial.html) in the
PSAMM documentation has been updated and expanded to include additional
information on using PSAMM for model curation and constraint-based analyses.
- The experimental command `psamm-sbml-model` was added which makes it possible
to run any command from `psamm-model` (e.g. `fba`, `robustness`, etc.)
directly on an SBML file. For now this only supports SBML level 3 files with
FBC. This provides a quick way of running basic analyses on SBML files. We
still recommend importing the SBML file to YAML format with `psamm-import`
for anyone wishing to make changes to a model.
- Fixes access to charge parameter parsed from SBML files. The charge is now
correctly imported with `psamm-import`.
- Fixes import of compartments from SBML files. The empty boundary compartments
are now no longer included in the import.
- Fixes bug in writing the reaction flux limits sheet of the `excelexport`
command.
- The `console` command was changed to only provide the `model` variable since
the metabolic model can easily be created.

------------------

- The YAML model format now allows users to specify compartment information and
compartment boundaries in the `model.yaml` file. See the file format
documentation for more information.
- The `media` key in the `model.yaml` has changed name to `exchange` to
reflect the fact that not only uptake exchange must be defined here. The
`media` key is still supported but has been deprecated.
- The gap-filling command `gapfill` and `fastgapfill` now use the compartment
information to determine which artificial transport and exchange reactions
to add. This means that a model *must* specify compartments and compartment
boundaries when using gap-filling commands.
- The `gapcheck` command now has two new methods for detecting blocked
compounds. The new `prodcheck` is a more robust version of the GapFind check
which was previously used. The new `sinkcheck` method will find compounds
that cannot be produced in excess. This can find some additional blocked
compounds that were not detected by the other methods.
- The `gapcheck` command now reports blocked compounds in the extracellular
space. Previously, these compounds were excluded. An option is available to
switch back the old behavior of excluding these from the final output.
- The `gapcheck` command now has an option to run the check with unrestricted
exchange reactions.
- The `gapfill` command can now be run without implicit sinks. This makes it
possible to use this command to solve additional model gaps. It is still
recommended to first solve gaps using implicit sinks, then later disable
implicit sinks when all other gaps have been closed.
- The `gapfill` command now has an option to enable the bounds expansion
proposals (e.g. making irreversible reactions reversible). By default this
option is now off.
- The `fastgapfill` has improved output that contains less superfluous
information. The output format is now identical to the `gapfill` command.
The `fastgapfill` also no longer runs an FBA on the induced model since this
caused some confusion.
- Added new command `checkduplicates` which detects whether the model has
multiple reactions with the same (or similar) reaction equation.
- The `sbmlexport` command now allows the user to specify a file path. The
command can also optionally output the SBML file in a more readable format
with an option.
- Fixed support for the latest CPLEX release 12.7. A change in their API made
PSAMM incompatible with the 12.7 release. This is now fixed.
- We now officially support Python 3.5 and Python 3.6.

------------------

- When exporting a model with `excelexport`, `sbmlexport` or `tableexport`, the
current Git commit ID of the model is now part of the export.
- The `gapfill` command has been split into two separate commands. The new
command `gapcheck` only reports which compounds are blocked without
trying to fill gaps. The `gapfill` command now only reports the suggested
reactions for gap-filling.
- The `tableexport` command has been made more robust when the model properties
contain special characters or structured data. Strings containing tabs or
newline characters are now quoted in the output.
- Improved error messages for multiple commands when reactions with forced
flux (e.g. ATP maintenance reactions) impose impossible constraints.

------------------

- All commands that perform loop removal now use the option `--loop-removal` to
set the type of loop removal. The `--tfba` option is no longer available for
the `fva`, `fluxcheck` and `randomsparse` commands, instead
`--loop-removal=tfba` should be used.
- All simulation commands that perform a maximization of an objective now take
an `--objective` option that can be used to override the `biomass` reaction
set in the model. The commands `fba` and `fva` no longer allow positional
arguments to set the objective, instead the `--objective` option should be
used.
- All user data in the model is now exported with the `sbmlexport` command.
User data that cannot be translated into a standard machine-readable SBML
form will instead be stored in the SBML notes section.
- The output from the `gapfill` command now shows the complete induced model
(like `fastgapfill`) and also lists the compound IDs of the blocked
compounds.
- The `gapfill` command will now propose the removal of flux bounds if such a
modification can unblock the model.
- The `gapfill` command now excludes the biomass reaction from being modified
in the induced model. Previously the biomass reaction was sometimes reversed
in the induced model but this is usually not a desired solution.
- The `gapfill` command now allows the user to specify penalties on added or
modified reactions (like `fastgapfill`).
- The `gapfill` command was changed so the `--epsilon` option now
specifies the threshold for non-zero reaction fluxes (like the `--epsilon`
in other PSAMM commands).
- The `gapfill` command was changed to be more robust when handling small
epsilon values. It will now lower the solver thresholds if necessary and will
generate a warning when epsilon is too low. This fixes an issue where
`gapfill` would previously fail or generate incorrect results with some
models.
- Fixed: The `--exclude` option in the `formulacheck` command did not work
correctly.