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lbl-anp / becquerel

Becquerel is a Python package for analyzing nuclear spectroscopic measurements.
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Isotopes notebook has errors #325

Closed jaromrax closed 2 years ago

jaromrax commented 2 years ago

Comment 1

activated_qty = IsotopeQuantity(iso2, date='2017-05-01', bq=103.2)
na23_qty = ni.activate(barns, initial=iso, activated=activated_qty)

gives nan g

Comment 2

/home/ojr/.local/lib/python3.8/site-packages/becquerel/tools/isotope_qty.py:351: DeprecationWarning: bq_now() is deprecated and will be removed in a future release. Use bq_at(date=None) instead.

is shown many times....

Comment 3

/usr/local/lib/python3.8/dist-packages/ipykernel/ipkernel.py:283: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.

appears also sometimes in different notebooks.

Comment 4

Also JSON from compendium may not be loaded with all materials...

jccurtis commented 2 years ago

Hi @jaromrax, thanks for the notes! I've added some sections to your description to improve our ability to address each one.

  1. Can you expand this to a MWE, i.e. what are the iso2, barns, iso and activated_qty vars?
  2. See #326, this will go in soon. Thanks for the head's up!
  3. I cannot find this text in any of our notebooks. I believe this was fixed here: https://github.com/ipython/ipykernel/pull/617. If you don't want to update ipykernel you can downgrade ipython to 7.10 as mentioned here: https://github.com/ipython/ipykernel/issues/540#issuecomment-699566981. FYI if you are using a conda env (highly recommended) you can update this with conda update ipykernel jupyter.
  4. @markbandstra is this related to #324?
markbandstra commented 2 years ago

Yes, I'm guessing comment 4 pertains to #324, and I hope to get in a fix soon.

jccurtis commented 2 years ago

Excellent, thanks @markbandstra!

jvavrek commented 2 years ago

Comment 1

activated_qty = IsotopeQuantity(iso2, date='2017-05-01', bq=103.2)
na23_qty = ni.activate(barns, initial=iso, activated=activated_qty)

gives nan g

Here iso and iso2 are Na-23 and Na-24, respectively. Na-23 is stable, so the division by self.decay_const (which is 0) produces the nan. @jccurtis @markbandstra I think there's a physics error in the example, not in the IsotopeQuantity code.

jccurtis commented 2 years ago

@jvavrek thanks for the context. Totally makes sense. I think the comments have all been addressed.

@jaromrax let us know if these comments address the issues you have encountered. Thanks!

jvavrek commented 2 years ago

Closed by #339 #333 #326. @jaromrax please let us know if any problems persist by opening a new issue.