Analysis errors on SymmetricalLogScale #30
Description
I am trying to use goeffel-analysis for the first time to plot cpu percentage but it is erroring out regardless of the metric I use.
The capture command/output looks ok:
[foxx@foxx-arch crowdsecBench]$ sudo goeffel --pid 2711735
250922-11:17:26.728 INFO: Collect time series for the following metrics:
unixtime
isotime_local
monotime
proc_pid
proc_cpu_util_percent_total
proc_cpu_util_percent_user
proc_cpu_util_percent_system
proc_cpu_id
proc_ctx_switch_rate_hz
proc_disk_read_throughput_mibps
proc_disk_write_throughput_mibps
proc_disk_read_rate_hz
proc_disk_write_rate_hz
proc_num_ip_sockets_open
proc_num_threads
proc_num_fds
proc_mem_rss_percent
proc_mem_rss
proc_mem_vms
proc_mem_dirty
system_loadavg1
system_loadavg5
system_loadavg15
system_mem_available
system_mem_total
system_mem_used
system_mem_free
system_mem_shared
system_mem_buffers
system_mem_cached
system_mem_active
system_mem_inactive
250922-11:17:27.244 INFO: Create HDF5 file: ./goeffel-timeseries__20250922-111726.hdf5
250922-11:17:27.258 INFO: Updated HDF5 file: wrote 1 sample(s) in 0.01365 s
250922-11:17:37.253 INFO: Updated HDF5 file: wrote 20 sample(s) in 0.00634 s
250922-11:17:47.256 INFO: Updated HDF5 file: wrote 20 sample(s) in 0.00651 s
250922-11:17:57.259 INFO: Updated HDF5 file: wrote 20 sample(s) in 0.00697 s
250922-11:18:07.261 INFO: Updated HDF5 file: wrote 20 sample(s) in 0.00684 s
250922-11:18:11.249 INFO: Process went away. Exit, indicate success
250922-11:18:11.249 INFO: Wait for producer buffer to become empty
250922-11:18:11.249 INFO: Wait for consumer process to terminate
250922-11:18:11.256 INFO: Updated HDF5 file: wrote 7 sample(s) in 0.00671 s
250922-11:18:11.258 INFO: Consumer process terminated
The error I get when running analysis:
[foxx@foxx-arch crowdsecBench]$ goeffel-analysis plot goeffel-timeseries__20250922-11172
6.hdf5 --metric proc_cpu_util_percent_system
250922-11:18:50.000 INFO: Read data from HDF5 file: goeffel-timeseries__20250922-111726.hdf5
250922-11:18:50.042 INFO: Convert `unixtime` column to pandas' timestamps
250922-11:18:50.043 INFO: Number of samples (rows): 88
250922-11:18:50.043 INFO: Check monotonicity of time index
250922-11:18:50.043 INFO: Time series start time (UTC): 2025-09-22 15:17:27.238580942
250922-11:18:50.043 INFO: Time series time span: '43s'
250922-11:18:50.123 INFO: Plot column {'y_label': 'Proc CPU util (total) [%]', 'rolling_wdw_width_seconds': 10} from proc_cpu_util_percent_total
250922-11:18:50.189 INFO: Perform rolling window analysis
250922-11:18:50.213 INFO: Plot column {'y_label': 'Proc RSS mem [%]', 'rolling_wdw_width_seconds': 10} from proc_mem_rss_percent
250922-11:18:50.237 INFO: Perform rolling window analysis
250922-11:18:50.262 INFO: Plot column {'y_label': 'Proc read() rate [Hz]', 'rolling_wdw_width_seconds': 10, 'yscale': 'symlog'} from proc_disk_read_rate_hz
250922-11:18:50.287 INFO: Perform rolling window analysis
250922-11:18:50.314 INFO: symlog: set lower ylim to 0
Traceback (most recent call last):
File "/home/foxx/.local/bin/goeffel-analysis", line 7, in <module>
sys.exit(main())
~~~~^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/goeffel/analysis.py", line 106, in main
cmd_simpleplot()
~~~~~~~~~~~~~~^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/goeffel/analysis.py", line 380, in cmd_simpleplot
fig, custom_tight_layout_func = plot_simple_magic(dataframe, metadata)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/goeffel/analysis.py", line 565, in plot_simple_magic
plot_subplot(axs[idx-1], column_plot_config, series, subplotsettings)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/goeffel/analysis.py", line 788, in plot_subplot
ax.set_yscale(
~~~~~~~~~~~~~^
'symlog',
^^^^^^^^^
...<2 lines>...
subsy=[2, 3, 4, 5, 6, 7, 8, 9]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/matplotlib/axes/_base.py", line 74, in wrapper
return get_method(self)(*args, **kwargs)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/matplotlib/axis.py", line 794, in _set_axes_scale
ax._axis_map[name]._set_scale(value, **kwargs)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/matplotlib/axis.py", line 763, in _set_scale
self._scale = mscale.scale_factory(value, self, **kwargs)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
File "/home/foxx/.local/pipx/venvs/goeffel/lib/python3.13/site-packages/matplotlib/scale.py", line 728, in scale_factory
return scale_cls(axis, **kwargs)
TypeError: SymmetricalLogScale.__init__() got an unexpected keyword argument 'linthreshy'. Did you mean 'linthresh'?
The same error occurs for all metrics I've tried to plot. I tried with two different capture files, both produce the same error. I can't attach the files but I have them to here to download, if you'd like:
https://i.foxxmd.dev/K95zrEYg42An.hdf5
https://i.foxxmd.dev/EEQxP03F3jMq.hdf5
I am running goeffel version 0.3.0 installed using pipx.
Can you please help me figure out what is going wrong here? Thanks