Matplotlib error is_decade

[MHunt-tools]

Flowcal plot functions are not working for clean install of FlowCal. Seems like matplotlib has deprecated the is_decade function for ticker. Full traceback is as follows:

FlowCal.plot.hist1d(s, channel='FL1-H')
Traceback (most recent call last):
File "", line 1, in
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/FlowCal/plot.py", line 1285, in hist1d
plt.xlim((edges[0], edges[-1]))
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/pyplot.py", line 1961, in xlim
ret = ax.set_xlim(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axes/_base.py", line 3664, in set_xlim
return self.xaxis._set_lim(left, right, emit=emit, auto=auto)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axis.py", line 1243, in _set_lim
self.set_view_interval(v0, v1, ignore=True)
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axis.py", line 2272, in setter
setattr(getattr(self.axes, lim_name), attr_name, (vmin, vmax))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axes/_base.py", line 849, in viewLim
self._unstale_viewLim()
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axes/_base.py", line 844, in _unstale_viewLim
self.autoscale_view({f"scale{name}": scale
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axes/_base.py", line 2936, in autoscale_view
handle_single_axis(
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/matplotlib/axes/_base.py", line 2932, in handle_single_axis
x0, x1 = locator.view_limits(x0, x1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/MaxwellHunt/opt/anaconda3/envs/flowc/lib/python3.12/site-packages/FlowCal/plot.py", line 648, in view_limits
if not matplotlib.ticker.is_decade(abs(vmin), b):
^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'matplotlib.ticker' has no attribute 'is_decade'. Did you mean: '_is_decade'?

Suggested update to is_decade following https://matplotlib.org/stable/api/prev_api_changes/api_changes_3.8.0.html:
instead of ticker.is_decade; use y = numpy.log(x)/numpy.log(base); numpy.isclose(y, numpy.round(y))

[castillohair]

@MHunt-tools thanks for submitting this. If you want, you could make a branch starting from develop with your proposed solution and, after testing it, submit a pull request. This website explains the workflow we have used to work with FlowCal.

@JS3xton what would be the process to approve a bug/deprecation fix these days? I would think that just making sure the plots are generated as before would suffice for this particular case, but it's been a while since I've worked with FlowCal's code.

Thanks.

[JS3xton]

Thanks for pointing this out, Max.

The last release process was very tedious--I'd like to automate some of the testing if possible, e.g., with GitHub Actions. There are also several other outstanding deprecation issues that should probably be resolved--and it's probably time to officially drop support for Python 2. I don't expect any of this to happen quickly, though, so yeah, Max I'd rely on your own fork in the short term.

[MHunt-tools]

Hey all, thanks for looking into this! I updated the plot script and tested with the example data (minor updates in those processing scripts as well). Pull request has been submitted!