'LipdSeries' attribute error in TimeEmbeddedSeries function

[frozenarchives]

Current version of Ammonyte (after installing from the instructions in the readme file) installs the latest version of Pyleoclim (1.2.1), which throws the following error for TimeEmbeddedSeries function.

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[7], line 1
----> 1 air_td = amt.TimeEmbeddedSeries(air_series,air_m,air_tau)

File [/opt/homebrew/anaconda3/envs/pyleo/lib/python3.11/site-packages/ammonyte/core/time_embedded_series.py:77](http://localhost:8892/opt/homebrew/anaconda3/envs/pyleo/lib/python3.11/site-packages/ammonyte/core/time_embedded_series.py#line=76), in TimeEmbeddedSeries.__init__(self, series, m, tau, embedded_data, embedded_time, value_name, value_unit, time_name, time_unit, label)
     73     self.tau = tau_search(self.series)
     75 if self.embedded_data is None:
---> 77     if isinstance(self.series, (pyleo.core.Series, pyleo.core.LipdSeries)):
     78         values = self.series.value
     79         time_axis = self.series.time[:(-self.m*self.tau)]

AttributeError: module 'pyleoclim.core' has no attribute 'LipdSeries'

This appears to be an issue caused by mismatched versions of the Pyleoclim package and its dependencies. The Pyleoclim version must be between less than 0.14 and greater than 0.7.0.

The temporary workaround for this problem is to force the installation of Python 3.11, Pyleoclim 0.14, and pandas 2.3.2 (pandas 2.3.2 to eliminate the ''values fall before the last bin during resampling '' error.)

Looking forward to the next stable version of Ammonyte. Thanks!

[CommonClimate]

Thanks for uncovering this error @frozenarchives ! It seems to me that the issue is with the fact that LipdSeries is no longer a class in Pyleoclim. @alexkjames how essential is it to the package? Can we use GeoSeries instead?

[alexkjames]

There is no reason to have that LipdSeries isinstance check there anymore, it should be changed to GeoSeries.

[CommonClimate]

That's what I thought. @niatimary would you be able to make the required change, testing it, and making a pull request for me to review? We might need to ask Claude to write unit tests for Ammonyte. Now that we have our first official user outside of USC, it's becoming important!

[CommonClimate]

@frozenarchives I am not sure how this happened as I don't see any commit implementing this change, but the code no longer references LipdSeries, so the bug should be gone. Can you please:

• uninstall the version of Ammonyte you currently have
• reinstall using the latest code (which has not been released yet): pip install git+https://github.com/LinkedEarth/Ammonyte.git
• try your test again
  ?