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Metage2Metabo v1.6.0
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@ArnaudBelcour ArnaudBelcour released this 01 Mar 12:49
1.6.0
b61c001

WARNING: change for individual and community scopes:

  • for individual scope: only seeds that are producible, ie associated with activated reactions are now shown in the results. Additional information on producible, non-producible and absent seeds are available in the json output. This requires MeneTools version >= 3.4.0.
  • for community scope: use of miscoto focus for computation in order to retrieve the metabolite producers in community. This requires MiSCoTo version >= 3.2.0.

Add

  • Test in m2m_analysis to check if combination of powergraph predicted by bubbletools is the same as the ones found in minimal communities.
  • Creation of boolean equation summarizing the powergraph if it is simple enough.
  • New option --target-com-scope to use all the community scope as targets for minimal community prediction (issue #21).
  • Add a function to modify xml created by Pathway Tools (issue #60).
  • Troubleshooting page in readthedocs (issue #24 and #25).
  • Metadata json file created when using command line (both for m2m and m2m_analysis).
  • Essential and alternative symbiont in producibility_targets.json (issue #19).
  • Test for host for m2m metacom.

Fix

  • Fix potential error when reading taxon_id file (issue #22).
  • Fix issue with etree in reconstruction.
  • Issues with readthedocs.
  • GitHub Actions not working.

Modify

  • Better deal with seeds that are absent from networks or not produced in iscope and also the seeds that are produced through interactions in cscope (issue #53).
  • Exit m2m_analysis when there are unproducible targets (issue #23).
  • Check forbidden characters during targets file creation.
  • Do not allow abbreviation in command arguments by argparse (issue #54).
  • Sanitize use of tarfile extractall (issue #55).
  • Remove unused dependency.
  • First step in replacing pkg_resources (which will become deprecated in the future) with importlib.metadata or import of __version__.
  • Move from setup.py/setup.cfg to pyproject.toml.
  • Update tutorial.
  • Update docs and readme.
  • Update license year and affiliation.
  • Move support for CI to Python 3.8 and 3.9.
  • Remove import in __init__.py to avoid loading m2m_analysis dependencies when using only m2m.
  • Avoid using os.unlink() function on Windows as it can lead to Permission Error.
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