OpenFreeEnergy/cinnabar

Issues

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

  #124 opened 4 months ago by IAlibay
  0

• wrong estimates with FEMap with single experimental value

  #123 opened 6 months ago by ijpulidos
  2

• MLE ddG errors != calculated ddG errors for open cycle

  #120 opened 8 months ago by jeremyaq
  0

• Update API docs

  #116 opened a year ago by IAlibay
  0

• Update changelog docs

  #118 opened a year ago by IAlibay
  0

• Add userguide docs

  #117 opened a year ago by IAlibay
  0

• Rework FEMap API

  #55 opened 3 years ago by IAlibay
  14

• add option for get_absolute_dataframe to shift values

  #111 opened a year ago by richardjgowers
  1

• FEMap add to/from networkx method

  #110 opened a year ago by richardjgowers
  0

• make FEMap a gufe tokenizable

  #108 opened a year ago by richardjgowers
  4

• Versioneer causing failures on conda-forge builds

  #105 opened a year ago by richardjgowers
  1

• base class for MLE estimation-like methods

  #109 opened a year ago by richardjgowers
  0

• add controllable guidelines on plots

  #106 opened a year ago by richardjgowers
  0

• Seaborn calls in WhyNotToUseR2ForDDG notebook fail

  #104 opened a year ago by richardjgowers
  0

• Add plot_bar to plotly example notebook

  #103 opened a year ago by richardjgowers
  0

• not catching node name mismatch

  #101 opened a year ago by JenkeScheen
  3

• Update readme and examples

  #102 opened a year ago by IAlibay
  0

• refactoring bootstrap stats

  #99 opened a year ago by RiesBen
  2

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

  #93 opened a year ago by wenchangzhou-qtx
  6

• Error of exactly zero will trigger SVD failure when generating absolute values

  #97 opened a year ago by IAlibay
  0

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

  #89 opened 2 years ago by jchodera
  1

• readthedocs is deeply unhappy

  #94 opened a year ago by richardjgowers
  0

• [Question] Allow arbitrary xy tick frequency when plotting

  #88 opened 2 years ago by kntkb
  0

• Compare different systems/targets in a single plot

  #87 opened 2 years ago by ijpulidos
  0

• feature: error per cycle graph

  #86 opened 2 years ago by richardjgowers
  0

• Warn if node is overwritten

  #65 opened 2 years ago by mikemhenry
  1

• Extend to support the case where multiple edges span two nodes

  #44 opened 2 years ago by jchodera
  1

• Make sure we annotate the units for experimental error

  #66 opened 2 years ago by mikemhenry
  2

• When some of the expriments data is missing?

  #67 opened 2 years ago by kexul
  3

• Easier exposure for calculations where there isn't experimental data to compare against

  #82 opened 2 years ago by hannahbruce
  2

• Add tests for plotting functions

  #77 opened 2 years ago by zhang-ivy
  1

• 95% CI sometimes doesn't contain the RMSE or MUE

  #73 opened 2 years ago by zhang-ivy
  9

• Effect of centralizing

  #75 opened 2 years ago by djhuggins
  0

• basic cli usage broken

  #70 opened 2 years ago by richardjgowers
  1

• Catch the exception for the R2 computation

  #62 opened 2 years ago by xiki-tempula
  2

• Separate out stats calls from plotting

  #48 opened 3 years ago by richardjgowers
  1

• [proposal] Clear up Python support - NEP29?

  #57 opened 3 years ago by IAlibay
  2

• Update conda-forge package

  #61 opened 3 years ago by mikemhenry
  0

• Clean up the CI yaml files

  #59 opened 3 years ago by IAlibay
  0

• Fix badges

  #54 opened 3 years ago by IAlibay
  0

• Test notebooks

  #51 opened 3 years ago by IAlibay
  1

• Clean up readme for data folder

  #53 opened 3 years ago by IAlibay
  1

• Cleanup setup.py / setup.cfg, add pyproject.toml

  #56 opened 3 years ago by IAlibay
  0

• Add module level docstring or general info about what each module does

  #52 opened 3 years ago by IAlibay
  0

• Expand example notebooks & add static versions to docs page

  #50 opened 3 years ago by IAlibay
  0

• Expand getting started docs

  #49 opened 3 years ago by IAlibay
  0

• Add zenodo badge and/or CITATION.cff to make this repo citable

  #43 opened 3 years ago by jchodera
  0

• Fix uncertainty factor naming in stats.mle

  #45 opened 3 years ago by jchodera
  0

• Standardize plotly and matplotlib plotting interfaces

  #46 opened 3 years ago by jchodera
  1

• [proposal] Rename to arsenic?

  #47 opened 3 years ago by IAlibay
  1