Psamm

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- fix bug in `generate-database`
- revise formatting of doc

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- Adds the new `psamm-generate-model command` with the options of
`generate-database`, `generate-transporters`, and `generate-biomass`,
which construct metabolic models in the KEGG namespace
- Adds the new option _translated-reactions_ to the `tableexport` command
- Added translated reactions to `excelexport`
- Fixed compatibility in documentation for Gurobi for python versions 3.7
- Adds support for Python 3.8 and 3.9

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- Drops support for Python 2.7 (deprecated Jan. 01, 2020), 3.3, and 3.4
- Adds the --phin and --phout options to the `tmfa` command
- Adds descriptive counts of the number of reactions and compounds
curated in the _manual curation_ option of `modelmapping`

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- Fix bug where the `psamm modelmapping translate_id` command requires
the undefined parameter `--dest-model`

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- Adds the new `vis` command for visualizing metabolic pathways and
networks
- Adds the new `tmfa` command to implement the approach as described
in Henry et al., 2007 (PMID: 17172310) and Hamilton et al., 2013
(PMID: 23870272).
- Performance updates to the `model-mapping` command
- Updates to export full models from `gimme` and `psammotate`
- Added the --fva option to the `robustness` command

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- Adds the new `modelmapping` command for mapping reactions and
compounds ids between different GEMs.
- Adds the new `psammotate` command for generating draft GEMs
using a template model and a mapping of orthologous genes to
another organism.
- Adds the new `gimme` command which implements the GIMME algorithm
as described in Becker and Palsson, 2008 (PMID: 18483554).
- Updates the `search` command to allow for searching of strings
within any reaction or compound property.
- Updates to the `tableexport` and `excelexport` commands to allow
for the export of additional gene and reaction information.
- Adds new section to the tutorial to detail how to use the
`findprimarypairs` commands.
- Renamed `duplicatescheck` command to `dupcheck`.