conda-forge / yank-feedstock Goto Github PK
View Code? Open in Web Editor NEWA conda-smithy repository for yank.
License: BSD 3-Clause "New" or "Revised" License
A conda-smithy repository for yank.
License: BSD 3-Clause "New" or "Revised" License
@ijpulidos and @mikemhenry: We could really use your help as maintainers of the YANK feedstock (our absolute free energy tool which uses openmmtools). Would that be OK?
With pyyaml 6.0, yank analyze fails:
(openmm) mjw@ubu:~/workspace/yank-examples/examples/hydration/phenol/explicit_1$ yank analyze --store=experiments
Traceback (most recent call last):
File "/home/mjw/miniconda3/envs/openmm/bin/yank", line 10, in <module>
sys.exit(main())
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/commands/analyze.py", line 148, in dispatch
single_run()
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper
return run_single_node(rank, task, *args, **kwargs)
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node
result = task(*args, **kwargs)
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/commands/analyze.py", line 143, in single_run
output = analyze.analyze_directory(args['--store'], **analyzer_kwargs)
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/analyze.py", line 782, in analyze_directory
auto_experiment_analyzer = ExperimentAnalyzer(source_directory, **analyzer_kwargs)
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/analyze.py", line 299, in __init__
analysis = yaml.load(f)
TypeError: load() missing 1 required positional argument: 'Loader'
Exception ignored in: <function ExperimentAnalyzer.__del__ at 0x7f8bdf6b5d30>
Traceback (most recent call last):
File "/home/mjw/miniconda3/envs/openmm/lib/python3.9/site-packages/yank/analyze.py", line 336, in __del__
for phase, analyzer in self.analyzers.items():
AttributeError: 'ExperimentAnalyzer' object has no attribute 'analyzers'
See also:
yaml/pyyaml#576
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