MeneTools v3.4.0

Modify

• 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.cfg to pyproject.toml
• Update license year

MeneTools v3.3.0

Add

• Mene scope_inc identifies 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

Modify

• Remove uneeded imports
• Update license year

MeneTools v3.2.1

Fix

• Latest clyngor versions led to errors that can be preventing by not using the clingo module when calling solver #12

Test

• Tests are no longer done for Python 3.6 but for versions 3.7, 3.8, 3.9

Doc

• A small typo is fixed

Others

• .gitignore has been updated

MeneTools v3.2.0

Add

• Mene seed identifies compounds that would be considered as seeds in network expansion because they are produced by exchange reactions

Doc

• Update with Meneseed

Tests

• New tests for Meneseed

Others

• The MeneTools project is now mirrored on Gitlab Inria via GH CI.

MeneTools v3.1.1

Licence

MeneTools is now under the LGPL licence.

Doc

Update documentation with the latest citation for MeneTools.

MeneTools v3.1.0

Add

• mene scope now 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

Tests

• new tests for the latest version of mene scope

MeneTools v3.0.2

Add

• Menedead: to identify deadends in metabolic network.
• Windows and MacOS tests in GitHub Actions.
• Windows compatibility.

MeneTools v3.0.1

Add

• Error message if SBML files have no reactions.

MeneTools v3.0.0

Add

• Merge all commands into one command with subcommands: e.g. menescope becomes mene scope
• Version can now be retrieved with mene --version

Fix

• Typos

MeneTools v2.1.0

Add

• Meneacti to retrieve activable reactions from nutrients
• Documentation for Meneacti

Fix

• typos
• output format of Menecheck in console