Releases: cfrioux/miscoto
Releases · cfrioux/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
topyproject.toml
.
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
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
MiSCoTo v3.1.0
Fix
- consider reversible reactions to characterise target_producer_coop_initcom
- remove adding a host fact in
miscoto instance
when no host argument was provided
Test
- test the second fix
MiSCoTo v3.0.3
Add
- test for key species in mincom.
Replace
- "keystone species" by "key species".
MiSCoTo v3.0.2
Add
- Windows and MacOS tests in GitHub Actions.
- Windows compatibility.
MiSCoTo v3.0.1
Add
- Error message if SBML files have no reactions.
MiSCoTo v3.0.0
Add
- Merge all commands into one command with subcommands: e.g.
miscoto_scopes
becomesmiscoto scopes
- Version can now be retrieved with
miscoto --version
- Output messages are clearer than before
Update
- Documentation
- Help of subcommands
Fix
- Typos
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
- In case there are compounds in targets that are also nutrients (seeds): they would not have appeared in
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
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 withmiscoto_mincom
. The information is stored in thetargets_producers
key in the json output.
CI
- test for the new final producer feature.