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CHANGELOG.md

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Changelog

2.3.1 --- Minority Complex (WIP)

  • Restructure example description and organization
  • Add auxotroph example
  • Fix issue with output in same directory

2.3.0 --- Multiplexing Catharsis (Feb 07, 2024)

  • Fix selected community not being reported
  • REVERT: check_feasibility is no longer used to assess feasibility
  • REVERT: Execution and reporting of multiple optimization targets
  • Only one optimization target will be assessed and reported
  • Upgrade reframed

2.2.0 --- Consistency Crisis (Feb 21, 2023)

  • Use a separate environment for the MILP and the LPs
  • Fix incorrect addition of knowledge constraints when optimizations fail

2.1.3 --- Reporting Madness (Feb 3, 2023)

  • Log community members when community solution is stored
  • Missing reaction warnings will be sorted
  • Setup custom environment for solver

2.1.0 --- Transparency Dilemma (Sep 6, 2022)

  • Report feasible communities if optimization fails
  • Report which optimizations succeeded
  • Report if parsimony variables are set
  • Fix missing check_feasibility method.

2.0.0 --- Numerical Exercise (Sep 2, 2022)

  • Build new community models candidate solutions for verification

1.3.1 --- Speedup Inclination (Sep 1, 2022)

  • Use yaml C loader and dumper

1.3.0 --- Linearization Effort (Aug 18, 2022)

  • Linear parsimony optimization

1.2.1 --- Reporting Bias (NONE)

  • Report feasible communities, even if optimization fails
  • Add function to get supplier and community frozensets.
  • Update crossfeed to report as frozensets.
  • Add functions to gather statistics.

1.2.0 --- Caching Interference (Mar 1, 2022)

  • Add argument --media-select to choose subset of media
  • Add argument --cache-file to cache intermediate constraints
  • Add module misosoup.library.minimizer.
  • Changed minimization to use state-aware minimizer class
  • Removed module misosoup.library.solve
  • Removed module misosoup.library.load

1.1.0 --- Optimization Indifference (Feb 3, 2022)

  • Enable gurobi logging to file
  • Community feasibility test without optimization

1.0.0 --- Standalone Practice (Dec 23, 2021)

  • Create LayeredCommunity subclass for reframed.Community
  • Create GurobiEnvSolver subclass of reframed.solvers.GurobiSolver
  • Remove loading bars
  • Remove tqdm dependency
  • Provide package on pypi

0.6.0 --- Interface Recalibration (Dec 20, 2021)

  • Pass media as dictionaries
  • Rework how we screen multiple carbon sources
  • Command line argument --media added
  • Command line argument --carbon-sources removed
  • Command line argument --base-medium removed
  • Maintenance requirements in the model are now supported

0.5.0 --- Operating Generalization (Dec 9, 2021)

  • RESTRUCTURED PROJECT to support Windows
  • Added argument to adjust objective
  • Focal strain is now constraint by its binary variable

0.4.0 --- Documentation Expansion (May 11, 2021)

  • Reaction Ids in medium need to exactly match the Ids in the models now
  • Add warning if reactions Ids are not contained in the model
  • Support expansion in code for large input expansion
  • Minimal growth CLI argument now controls any minimal growth setting
  • Always choose dual simplex method
  • Add a brief description of the content of output to the argparse description.

0.3.0 --- Gut Conformity (April 29, 2021)

  • Add support for biomass exchange reactions
  • Add script that selects strains and populates the current directory with symbolic links
  • Change the naming convention for species specific exchange reactions to _i
  • Fix issue where target could not be an arbitrary relative path
  • Fix issue with internal metabolites not being separated in some cases

0.2.0 --- Selective Procedures (April 19, 2021)

  • Add simple solution validation taste_soup
  • Add simple solution filter filter_soup
  • Add unit and integration tests for new scripts.

0.1.0 --- Community Emergence (April 17, 2021)

  • Initial version of MiSoS(oup)