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_example_plot_rbfe.py incompatible with cinnabar #151
Description
Describe the bug
When running with new cinnabar there is an error.
To Reproduce
Install env with software versions defined below and run _example_plot_rbfe.py
Software versions
- Which operating system and version did you use? MacOS 15.1
- Which method did you use to install this package? Micromamba
- Copy/paste the output of
conda list(or the equivalent for your package manager): - Before: openfe=1.8.1; cinnabar=0.5.0
- After: openfe=1.12; cinnabar=0.6.1
Output
/Users/jenniferclark/bin/openfe-benchmarks/openfe_benchmarks/scripts/_example_plot_rbfe.py:53: DeprecationWarning: to_legacy_graph() is deprecated and will be removed in a future release. Use get_relative_dataframe() and get_absolute_dataframe() to access the underlying data, or generate_absolute_values() to run MLE explicitly. The plot functions plot_DDGs, plot_DGs, and plot_all_DDGs now accept a FEMap directly.
legacy_graph = femap.to_legacy_graph()
Traceback (most recent call last):
File "/Users/jenniferclark/bin/openfe-benchmarks/openfe_benchmarks/scripts/_example_plot_rbfe.py", line 67, in <module>
main()
File "/Users/jenniferclark/bin/openfe-benchmarks/openfe_benchmarks/scripts/_example_plot_rbfe.py", line 54, in main
plotting.plot_DDGs(
TypeError: plot_DDGs() missing 2 required positional arguments: 'femap' and 'source'
Expected behavior
No error
AI disclosure
None
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[-]_example_plot_rbfe.py incompatible with cinnebar[/-][+]_example_plot_rbfe.py incompatible with cinnabar[/+]jthorton commentedon Oct 7, 2026
Ah good catch the API changed in the 0.6 update do we want to support both versions or just move to the new API? I can open a PR for either option.
jaclark5 commentedon Oct 7, 2026
@jthorton I think we can just move to the most recent version, BUT right now the tests are being run in an env compatible with the old alchemiscale stack (i.e., openfe=1.8.0) which the new version of cinnabar is not compatible with. The tests also pass with openfe=1.12 so we can update the pin to there.
BUT will you need an env to pull any more data from alchemiscale? (I've pulled all the data I need). If so, the current env file is convenient for that.
If the answer is no, then I think we can:
jaclark5 commentedon Oct 7, 2026
Note: I needed to test this on the branch #150 to run since pontibus is not compatible with OpenFE >1.12