miscoto - MiSCoTo v3.2.0

New

• CHANGLEOG.md showing the different versions and the associated changes.

Modify

• Miscoto focus can be run from a LP instance (issue #17).
• Copy but do not modify given instance in miscoto scopes and mincom (issue #8).
• Replace use of pkg_resources that will become deprecated.
• Update license year.
• Modify if statement that will be deprecated in the future.
• Move from setup.py/setup.cfg to pyproject.toml.

- Python
Published by ArnaudBelcour almost 2 years ago

miscoto - MiSCoTo v3.1.2

New

• miscoto focus can now be run systematically for all species with the --all option

Fix

• Latest clyngor versions led to errors that can be preventing by not using the clingo module when calling solver #14

Test

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

Doc

• Update miscoto focus section

CI

• Mirror to Inria Gitlab

- Python
Published by cfrioux almost 4 years ago

miscoto - MiSCoTo v3.1.1

New

miscoto focus calculates the producible metabolites for one metabolic network of interest in two conditions. First when considered alone in the given nutritional conditions. Secondly, among its community, in the same nutritional conditions but those are necesarily altered by what other species are likely to produce.

Doc

• usage of miscoto focus
• fix docstringd

Tests

• test miscoto focus

Licence

MiSCoTo is now under the LGPL licence

- Python
Published by cfrioux about 5 years ago

miscoto - MiSCoTo v3.1.0

Fix

• consider reversible reactions to characterise targetproducercoop_initcom
• remove adding a host fact in miscoto instancewhen no host argument was provided

Test

• test the second fix

- Python
Published by cfrioux about 5 years ago

miscoto - MiSCoTo v3.0.3

Add

• test for key species in mincom.

Replace

• "keystone species" by "key species".

- Python
Published by ArnaudBelcour about 5 years ago

miscoto - MiSCoTo v3.0.2

Add

• Windows and MacOS tests in GitHub Actions.
• Windows compatibility.

- Python
Published by ArnaudBelcour over 5 years ago

miscoto - MiSCoTo v3.0.1

Add

• Error message if SBML files have no reactions.

- Python
Published by ArnaudBelcour over 5 years ago

miscoto - MiSCoTo v3.0.0

Add

• Merge all commands into one command with subcommands: e.g. miscoto_scopes becomes miscoto scopes
• Version can now be retrieved with miscoto --version
• Output messages are clearer than before

Update

• Documentation
• Help of subcommands

Fix

• Typos

- Python
Published by cfrioux over 5 years ago

miscoto - MiSCoTo v2.1.2

New Features

• In mincom -o soup return in the json output a new predicate that contains all producible targets in a minimal community. This new predicate is stored as "producible" in the json output. This featyre is useful in 2 cases:
  • In case there are compounds in targets that are also nutrients (seeds): they would not have appeared in newly_producible
  • In case a host is provided: the target compounds that the host can produce by itself would not have been stored in the json

Fix

• Issue with the display of target producers in selected communities

CI & Tests

• Add a new test and its associated target file in toy related to returning all producible targets

- Python
Published by cfrioux over 5 years ago

miscoto - Miscoto v2.1.1

Add

• final producers for the targets. Miscoto will search for the organisms able to activate the reaction producing each of the targets. This is computed in the full community with miscoto_scopes and in the selected minimal communities with miscoto_mincom. The information is stored in the targets_producers key in the json output.

CI

• test for the new final producer feature.

- Python
Published by ArnaudBelcour over 5 years ago

miscoto - Miscoto v2.1.0

Modify mincom json ouput

• rename optimum_inter into score_optimum_inter

• rename optimum_union into score_optimum_union

• add result of --optsol in json with the one_model key.

• add keystone_species, essential_symbionts and alternative_symbionts in json if --union and --intersection are used together.

- Python
Published by ArnaudBelcour over 5 years ago

miscoto - Miscoto v2.0.8

Fix

• minexch behaviour (missing solution) when running without host

CI

• add new tests for the above cases

- Python
Published by cfrioux over 5 years ago

miscoto - Miscoto v2.0.7

Improvement of tests, better documentation, Github actions

- Python
Published by cfrioux almost 6 years ago

miscoto - Miscoto v2.0.2 (clyngor)

First release that uses Clyngor rather than Pyasp for ASP support.

- Python
Published by cfrioux over 6 years ago

miscoto - Miscoto v1.2.0

This is the last release of Miscoto using Pyasp as a support for ASP computing. This version and the ones before are not compatible with metage2metabo

- Python
Published by cfrioux over 6 years ago