Integrate refinegems

[cb-Hades]

The idea is to export the utility functions of SPECIMEN to refinegems and have SPECIMEN load refinegems to use those. In other words, SPECIMEN will focus on the pipeline for building the strain-specific model automatically, while refinegems is the toolbox containing the functionalities applicable to more than just SPECIMEN.

Overview:

• 🔴 Integrations of functions into refingems (see issue there)
• [x] changing / deleting functions in SPECIMEN to use refinegems
• [x] check and fix links between modules
• [x] test
• [x] change docs
  • [x] 🟦 IDEA: change type of documentation to the one used in refinegems to have the same standard for easier development and maintenance

Updated Modules:

• [x] classes
  • [x] reports
  • [x] medium 🟥 deleted, after complete integration
• [x] core
  • [x] bidirectional_blast 🟪 no function for handling models, not integration necessary
  • [x] generate_draft_model 🟧 keep everything, maybe change remote - see notebook in refinegems
  • 🔴 refinement -> needs further extension, see other
    • 🔴 extension
    • 🔴 clean_up
    • [x] annotation
    • 🔴 smoothing
  • [x] validation 🟪 not necessary, no complex functions, skipped
  • [x] analysis
• [x] util
  • [x] cobra_models 🟥 deleted, after adding everything to rg HOWEVER connections not fully checked
  • [x] io 🟥 deleted, after adding everything to refinegems
  • [x] set_up
  • [x] util 🟧 check connections in SPECIMEN
  • [x] cmd_access
  • [x] workflow

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🔴 WARNING 🔴 Due to restructuring of refinegems, recheck all import and connection to ensure it still works properly.

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[cb-Hades]

Regarding analysis.py module: all parts have been added to refinegems save for the statistical report.

The statistical report in its current form is quite rigidly bound to SPECIMEN, however one idea 🟦 might be to create a super class in refinegems that can be extended in SPECIMEN.

Overall, reports were reduced to statistical only, rest as added successfully to refinegems.

[cb-Hades]

Functionalities of util.io were added to the io submodule of refinegems in their entirety.,

[cb-Hades]

The medium submodule was complete transferred to refinegems and connected to the newly established media database of refinegems.

[cb-Hades]

util.util - functions about DIAMOND and NCBI mapping are kept in SPECIMEN (too specific), function for BiGG namespace have been transferred to refine gems and merged with the existing database that contains the BiGG names and mapping.

same goes for set_up.py - testing still required after deleting all BiGG

[cb-Hades]

🟥 Warning 🟥 started further adjustment to the new changes in refinegems - including the media_config, biomass_presence, namespace option and more.
▶ this means that the programs - all the run functions - will no longer work as expected
🟧 extensive TESTING - and probably bug-fixing - required

[cb-Hades]

SPECIMEN = Workflows; refineGEMs = Toolbox

successful separation