Issues

• refactor: Improve type adnotations quality

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#34 · Filter by author Fasamik39 opened on Oct 15, 2026 · Stage1

• [EPIC] Repository organization

  epic
  Tomasz-Lab/microbiomeGPT-benchmarks#29 · Filter by author purbancz opened on Oct 13, 2026

• Test NMF via pytest

  CI/CDtests
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#28 · Filter by author Fasamik39 opened on Oct 13, 2026 · Stage1
  

• Consider different way of picking up the best nmf fit

  help wantedquestion
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#26 · Filter by author Fasamik39 opened on Oct 12, 2026 · Stage1
  

• Automate Changelog Generation via CI/CD Bot

  choreCI/CDdocumentation
  Tomasz-Lab/microbiomeGPT-benchmarks#25 · Filter by author Fasamik39 opened on Oct 12, 2026 · Stage1

• NMF module refactor

  epic
  Tomasz-Lab/microbiomeGPT-benchmarks#23 · Filter by author Fasamik39 opened on Oct 12, 2026
  

• Decouple Execution Logic into a Lightweight Runner/Engine

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#19 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Modularize BacteriaModel into Composable Components

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#18 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Extract Unified Data Pipeline (BacteriaDataModule)

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#17 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Refactor hardcoded logic and file conventions into config-driven architecture

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#16 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Refactor Bi-Cross-Validation (BiCV) NMF script

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#15 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Redundant subfolder creation in find_output_path usage

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#14 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Enhance logging configuration with module, level, and timestamp details

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#13 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Introduce MLflow

  featurerefactor
  Feature

  Tomasz-Lab/microbiomeGPT-benchmarks#12 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Separate bicrossvalidation and nmf into distinct modules

  refactor
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#11 · Filter by author Fasamik39 opened on Oct 10, 2026 · Stage1
  

• Set up standardized GitHub Issue templates

  chore
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#7 · Filter by author Fasamik39 opened on Oct 9, 2026 · Stage1
  

• Create a standardized Pull Request template

  chore
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#6 · Filter by author Fasamik39 opened on Oct 9, 2026 · Stage1
  

• Introduce tool for metadata profiling

  feature
  Task

  Tomasz-Lab/microbiomeGPT-benchmarks#3 · Filter by author Fasamik39 opened on Oct 8, 2026 · Stage1