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getting the following error when running yank analyze report --store=experiments --output=yank_output.ipynb --format ipynb:
yank analyze report --store=experiments --output=yank_output.ipynb --format ipynb
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Rendering notebook as a .ipynb file... Processing notebook now, this may take a while... Traceback (most recent call last): File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/bin/yank", line 10, in <module> sys.exit(main()) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 123, in dispatch return dispatch_report(args) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 322, in dispatch_report run_notebook(store, output, notebook_serial_file, **analyzer_kwargs) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 281, in run_notebook processed_notebook, resources = ep.preprocess(loaded_notebook, resource_data) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 91, in preprocess self.preprocess_cell(cell, resources, index) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 85, in wrapped return just_run(coro(*args, **kwargs)) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 60, in just_run return loop.run_until_complete(coro) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nest_asyncio.py", line 90, in run_until_complete return f.result() File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/futures.py", line 201, in result raise self._exception.with_traceback(self._exception_tb) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/tasks.py", line 232, in __step result = coro.send(None) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 1019, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 913, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ from matplotlib import pyplot as plt from yank.reports import notebook %matplotlib inline report = notebook.HealthReportData(store_directory, **analyzer_kwargs) report.report_version() ------------------ --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In [2], line 4 2 from yank.reports import notebook 3 get_ipython().run_line_magic('matplotlib', 'inline') ----> 4 report = notebook.HealthReportData(store_directory, **analyzer_kwargs) 5 report.report_version() File ~/.conda/envs/myenv/lib/python3.10/site-packages/yank/analyze.py:299, in ExperimentAnalyzer.__init__(self, store_directory, **analyzer_kwargs) 297 raise RuntimeError(err_msg) 298 with open(analysis_script_path, 'r') as f: --> 299 analysis = yaml.load(f) 300 phases_names = [] 301 signs = {} TypeError: load() missing 1 required positional argument: 'Loader' TypeError: load() missing 1 required positional argument: 'Loader' 2022-11-03 15:14:21,028: CRITICAL - mpiplus.mpiplus - MPI node 1/1 raised an exception and called Abort()! The exception traceback follows Traceback (most recent call last): File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/bin/yank", line 10, in <module> sys.exit(main()) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 123, in dispatch return dispatch_report(args) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 322, in dispatch_report run_notebook(store, output, notebook_serial_file, **analyzer_kwargs) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/yank/commands/analyze.py", line 281, in run_notebook processed_notebook, resources = ep.preprocess(loaded_notebook, resource_data) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 91, in preprocess self.preprocess_cell(cell, resources, index) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 85, in wrapped return just_run(coro(*args, **kwargs)) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/util.py", line 60, in just_run return loop.run_until_complete(coro) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nest_asyncio.py", line 90, in run_until_complete return f.result() File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/futures.py", line 201, in result raise self._exception.with_traceback(self._exception_tb) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/asyncio/tasks.py", line 232, in __step result = coro.send(None) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 1019, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/net/pulsar/home/koes/rishal/.conda/envs/myenv/lib/python3.10/site-packages/nbclient/client.py", line 913, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ from matplotlib import pyplot as plt from yank.reports import notebook %matplotlib inline report = notebook.HealthReportData(store_directory, **analyzer_kwargs) report.report_version() ------------------ --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In [2], line 4 2 from yank.reports import notebook 3 get_ipython().run_line_magic('matplotlib', 'inline') ----> 4 report = notebook.HealthReportData(store_directory, **analyzer_kwargs) 5 report.report_version() File ~/.conda/envs/myenv/lib/python3.10/site-packages/yank/analyze.py:299, in ExperimentAnalyzer.__init__(self, store_directory, **analyzer_kwargs) 297 raise RuntimeError(err_msg) 298 with open(analysis_script_path, 'r') as f: --> 299 analysis = yaml.load(f) 300 phases_names = [] 301 signs = {} TypeError: load() missing 1 required positional argument: 'Loader' TypeError: load() missing 1 required positional argument: 'Loader'
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getting the following error when running
yank analyze report --store=experiments --output=yank_output.ipynb --format ipynb:The text was updated successfully, but these errors were encountered: