Issues

• Cycle closure dataframe hangs on large networks

  OpenFreeEnergy/cinnabar#238 · Filter by author jthorton opened on Sep 8, 2026
  

• CLD Labels change depending on the sources provided

  OpenFreeEnergy/cinnabar#237 · Filter by author jaclark5 opened on Sep 4, 2026
  

• Make all plotting functions return subplots

  OpenFreeEnergy/cinnabar#235 · Filter by author jthorton opened on Aug 21, 2026

• Support multiple sources on plots?

  OpenFreeEnergy/cinnabar#226 · Filter by author jthorton opened on Jun 17, 2026

• get_cycle_closure_dataframe does not consider self loop edges

  OpenFreeEnergy/cinnabar#219 · Filter by author hannahbaumann opened on Jun 3, 2026

• Cycle enumeration strategy in get_cycle_closure_dataframe

  OpenFreeEnergy/cinnabar#218 · Filter by author hannahbaumann opened on Jun 3, 2026

• Rework bootstrap_statistic to align with metric functions

  OpenFreeEnergy/cinnabar#217 · Filter by author jthorton opened on Jun 3, 2026

• Rework pair_plot mega function

  OpenFreeEnergy/cinnabar#214 · Filter by author jthorton opened on Jun 1, 2026

• Support multiple experimental measures

  OpenFreeEnergy/cinnabar#196 · Filter by author jthorton opened on Mar 26, 2026

• Adding documentation on how to go from openfe gather results to cinnabar

  OpenFreeEnergy/cinnabar#195 · Filter by author IAlibay opened on Mar 12, 2026

• Update defaults on everything

  OpenFreeEnergy/cinnabar#179 · Filter by author jthorton opened on Jan 26, 2026
  1

  

• Add function to draw network with calculated values

  OpenFreeEnergy/cinnabar#176 · Filter by author jthorton opened on Jan 19, 2026
  

• Old readme file

  OpenFreeEnergy/cinnabar#165 · Filter by author jthorton opened on Oct 21, 2025
  

• Documentation: CLI examples

  documentationusability
  Task

  OpenFreeEnergy/cinnabar#142 · Filter by author jthorton opened on Aug 26, 2025
  1

  

• Linear regression (R2) fails when boostrapping on very few data points

  OpenFreeEnergy/cinnabar#124 · Filter by author IAlibay opened on Aug 22, 2024
  3

• wrong estimates with FEMap with single experimental value

  OpenFreeEnergy/cinnabar#123 · Filter by author ijpulidos opened on Jul 10, 2024
  6

  

• add option for get_absolute_dataframe to shift values

  OpenFreeEnergy/cinnabar#111 · Filter by author richardjgowers opened on Nov 15, 2023
  2

• make FEMap a gufe tokenizable

  OpenFreeEnergy/cinnabar#108 · Filter by author richardjgowers opened on Nov 6, 2023
  4

  

• Seaborn calls in WhyNotToUseR2ForDDG notebook fail

  OpenFreeEnergy/cinnabar#104 · Filter by author richardjgowers opened on Oct 23, 2023

• Add plot_bar to plotly example notebook

  OpenFreeEnergy/cinnabar#103 · Filter by author richardjgowers opened on Oct 23, 2023
  

• not catching node name mismatch

  enhancement
  OpenFreeEnergy/cinnabar#101 · Filter by author JenkeScheen opened on Oct 18, 2023
  3

• the value of the x/y axis from plot_DGs function does not reflect the true DGs

  OpenFreeEnergy/cinnabar#93 · Filter by author wenchangzhou-qtx opened on Jul 18, 2023
  6

• Refactor stats into base and derived class so we can drop in different MLE solvers?

  OpenFreeEnergy/cinnabar#89 · Filter by author jchodera opened on Jun 29, 2023
  1

  

• [Question] Allow arbitrary xy tick frequency when plotting

  OpenFreeEnergy/cinnabar#88 · Filter by author kntkb opened on Jun 6, 2023

• Compare different systems/targets in a single plot

  enhancement
  OpenFreeEnergy/cinnabar#87 · Filter by author ijpulidos opened on Jun 5, 2023