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Padmet 5.0.2
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@ArnaudBelcour ArnaudBelcour released this 30 Oct 16:05
· 2 commits to master since this release
5.0.2
21af2e1
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Learn about vigilant mode.

Add

  • Add getter for pathway with reactions.
  • Add metexploreviz_export script.
  • Add script to create input for GNN from padmet or sbml.
  • Add pathway_production in padmet exploration.
  • Implement adding uniprot ids refs from protein-seq-ids-reduced-70.dat file in pgdb_to_padmet.

Fix

  • Bug in --enhance functionality from pgdb_to_padmet, reaction IDs were put in dicOfNode instead of reactant IDs (issue #12). Add a test to check this.
  • Check if output file is writable for sbmlGenerator.
  • Fix issue with pvclust dendrogram using old reactions.tsv.
  • Fix an issue with multiprocessing in prot2genomes.
  • Fix numerous issues in visualisation scripts.
  • Fix doc building.

Modification

  • Replace setup.py and setup.cfg by pyproject.toml.
  • Extract inchi from PGDB.
  • Update enhanced_meneco_output.py: add json + reactions options argument to consider json meneco output format and be able to extract other set of reactions than union (intersection, minimal, essential).
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