diff --git a/NEWS.md b/NEWS.md index a11bb107..67144969 100755 --- a/NEWS.md +++ b/NEWS.md @@ -5,6 +5,24 @@ This includes a list of major changes for each minor version starting from 0.19. For information on how to use `micom` please refer to [the documentation](https://micom-dev.github.io/micom). +### 0.35.0 + +`plot_fit` got renamed to `plot_association` and will not use LASSO coefficients anymore +as a proxy for univariate associations. Instead univariate non-parametric tests are +run for each metabolite. This should be more stable and avoid issues with low reproducibility +of coefficients. LASSO model performance is still reported as a global measure +of association. In case you need access to the previous `plot_fit` function you can simply +install a prior version of micom in a python or conda environment. + +Visualizations are updates requiring less dependencies now and using a current version +of vega-lite. + +The transition to the hybrid solver is now completed and the installation does not require +manual steps anymore. + +Lowered the iteration limit for the OSQP step in the hybrid solver as more iterations +did usually not lead to an improvement or convergence. + ### 0.34.1 Fix a typo in the hybrid settings. diff --git a/micom/util.py b/micom/util.py index 698a408c..ce2a4733 100755 --- a/micom/util.py +++ b/micom/util.py @@ -322,7 +322,7 @@ def adjust_solver_config(solver): solver.problem.Params.Threads = 1 solver.problem.Params.LogToConsole = 0 if interface == "hybrid": - solver.problem.settings["optimality_tolerance"] = 1e-5 + solver.problem.settings["optimality_tolerance"] = 1e-6 solver.problem.settings["lp_method"] = "interior point" solver.problem.settings["iteration_limit"] = 20000 solver.problem.settings["presolve"] = "auto"