- Filter the presence of seeds in the scope by removing seeds absent from the network (issue #15)
- Modify if statement that will be deprecated in the future
- Replace use of pkg_resources that will become deprecated
- Move from
setup.py/setup.cfgtopyproject.toml - Update license year
Mene scope_incidentifies the number of steps needed either to produce targets or all producible compounds (computed with menescope) starting from nutrients- tests and doc for
Mene scope_inc - CHANGELOG.md file
- Remove uneeded imports
- Update license year
- Latest clyngor versions led to errors that can be preventing by not using the clingo module when calling solver #12
- Tests are no longer done for Python 3.6 but for versions 3.7, 3.8, 3.9
- A small typo is fixed
.gitignorehas been updated
Mene seedidentifies compounds that would be considered as seeds in network expansion because they are produced by exchange reactions
- Update with Meneseed
- New tests for Meneseed
- The MeneTools project is now mirrored on Gitlab Inria via GH CI.
MeneTools is now under the LGPL licence.
Update documentation with the latest citation for MeneTools.
mene scopenow returns (in the json output and API call) a dictionnary with 2 keys:- the usual list of compounds in the scope
- the list of seeds that are also predicted to be produced by the organism
- new tests for the latest version of
mene scope
- Menedead: to identify deadends in metabolic network.
- Windows and MacOS tests in GitHub Actions.
- Windows compatibility.
- Error message if SBML files have no reactions.
- Merge all commands into one command with subcommands: e.g.
menescopebecomesmene scope - Version can now be retrieved with
mene --version
- Typos
- Meneacti to retrieve activable reactions from nutrients
- Documentation for Meneacti
- typos
- output format of Menecheck in console
- Use of Clyngor for ASP computations
- Improved documentation
- Calls directly from python scripts are possible
- Use of loggers
- Beta developments of Menepath and Menecof