Replacing PyNE with radioactivedecay for radionuclide decay calculations #1813

lemointm · 2021-10-15T22:17:41Z

This PR is designed to replace the functionality of PyNE in TARDIS with the python package radioactivedecay.

Description

TARDIS uses PyNE to perform decay caluclations, and to handle nuclide name parsing. The main change will be with handling nuclide decays in tardis/io/decay.py with radioactivedecay, and to replace the usage of PyNE's nucname function with the radioactivedecay.Nuclide class' name parsing functionality throughout TARDIS. Nuclide decays will now use the radioactivedecay.Inventory objects and the decay() method.

Motivation and context

This PR is meant to solve problems outlined in issue #1654.

How has this been tested?

Testing pipeline.
Other.

Examples

Type of change

Bug fix.
New feature.
Breaking change.
None of the above.

Checklist

My change requires a change to the documentation.
- I have updated the documentation accordingly.
- (optional) I have built the documentation on my fork following the instructions.
I have assigned and requested two reviewers for this pull request.

tardis-bot · 2021-10-18T15:58:59Z

Before a pull request is accepted, it must meet the following criteria:

Is the necessary information provided?
Is this a duplicate PR?
- If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
- If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
Does it pass existing tests and are new tests provided if required?
- The test coverage should not decrease, and for new features should be close to 100%.
Is the code tidy?
- No unnecessary print lines or code comments.

tardis-bot · 2021-10-18T15:58:59Z

Before a pull request is accepted, it must meet the following criteria:

Is the necessary information provided?
Is this a duplicate PR?
- If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
- If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
Does it pass existing tests and are new tests provided if required?
- The test coverage should not decrease, and for new features should be close to 100%.
Is the code tidy?
- No unnecessary print lines or code comments.

tardis_env3.yml

tardis/io/decay.py

andrewfullard · 2022-02-17T23:14:14Z

Need to format to black standards

wkerzendorf · 2022-02-23T16:14:35Z

@lemointm the tests are failing - can you make sure it reruns.

lemointm · 2022-02-23T19:49:08Z

Just pushed a commit for formatting, I will check the other tests next

afloers · 2022-02-28T15:02:24Z

pyne also needs to be replaced in the tests

ImportError while loading conftest '/home/vsts/work/1/s/tardis/tardis/conftest.py'.
tardis/init.py:15: in
import pyne.data
E ModuleNotFoundError: No module named 'pyne'

epassaro · 2022-02-28T22:24:36Z

There are several references to pyne in the tardis package, use Ctrl+Shift+F on VSCode to find them.

tardis/util/base.py

lemointm · 2022-03-02T23:51:09Z

There's an ongoing test failure where radioactivedecay says Ni-58 doesn't exist, this is a small issue with the package due to Ni-58 not being a progeny of any of the nuclides in the dataset (since it's produced by spontaneous fission only). I will try to get this fixed in radioactivedecay asap.

tardis/io/decay.py

tardis/model/base.py

tardis/visualization/widgets/custom_abundance.py

lemointm · 2022-03-23T22:54:46Z

@andrewfullard I added a util to tardis to perform those checks that I had rewritten in a few different places. The code should be a little cleaner now.

lemointm · 2022-03-23T23:58:48Z

@andrewfullard I added a util to tardis to perform those checks that I had rewritten in a few different places. The code should be a little cleaner now.

I spoke too soon, I just discovered that radioactivedecay can input grams, commit coming shortly!

lemointm · 2022-03-24T00:04:52Z

There also was an error where Inventory.mass_fractions() wasn't working properly since each nuclide is stored in a different Inventory. This was fixed by switching to Inventory.masses('g') instead, with an update to having inventories stored in grams.

lemointm · 2022-03-24T01:09:56Z

Now there should be only the Ni-58 test error (for now). I will give an update once the fixes are made to radioactivedecay.

lemointm · 2022-03-25T21:55:53Z

After the newest release (0.4.12) to radioactivedecay, all tests pass. I marked the code for review, please let me know if there are any other changes anyone would like to see.

codecov · 2022-03-28T14:54:25Z

Codecov Report

Merging #1813 (c99a4a0) into master (f541e73) will increase coverage by 0.05%.
The diff coverage is n/a.

❗ Current head c99a4a0 differs from pull request most recent head 5ee7ca1. Consider uploading reports for the commit 5ee7ca1 to get more accurate results

@@            Coverage Diff             @@
##           master    #1813      +/-   ##
==========================================
+ Coverage   58.74%   58.80%   +0.05%     
==========================================
  Files          70       70              
  Lines        7847     7853       +6     
==========================================
+ Hits         4610     4618       +8     
+ Misses       3237     3235       -2

Impacted Files	Coverage Δ
tardis/tardis/io/logger/logger.py	`70.68% <0.00%> (-1.45%)`	⬇️
tardis/tardis/io/atom_data/base.py	`89.71% <0.00%> (-0.06%)`	⬇️
tardis/tardis/model/base.py	`88.92% <0.00%> (-0.04%)`	⬇️
tardis/tardis/io/decay.py	`89.65% <0.00%> (ø)`
tardis/tardis/plasma/properties/atomic.py	`53.12% <0.00%> (ø)`
...rdis/plasma/properties/transition_probabilities.py	`24.03% <0.00%> (ø)`
tardis/tardis/io/model_reader.py	`97.77% <0.00%> (+0.06%)`	⬆️
...s/tardis/visualization/widgets/custom_abundance.py	`14.14% <0.00%> (+0.11%)`	⬆️
...s/tardis/montecarlo/montecarlo_numba/estimators.py	`34.61% <0.00%> (+0.13%)`	⬆️
...dis/montecarlo/montecarlo_numba/formal_integral.py	`51.36% <0.00%> (+0.16%)`	⬆️
... and 2 more

📣 Codecov can now indicate which changes are the most critical in Pull Requests. Learn more

Rodot- · 2022-03-28T15:06:58Z

Can you update the astropy version to >=4.1 to remove the distutils warnings?

lemointm · 2022-03-29T07:05:16Z

Can you update the astropy version to >=4.1 to remove the distutils warnings?

I also added radioactivedecay>=0.4.12 to ensure that the latest version with Ni-58 is installed.

lemointm · 2022-03-29T07:20:47Z

There still seems to be an issue with astroPy, now with importing astropy.modeling.blackbody. The documentation mentions that the module are deprecated as of version 4.0.

andrewfullard · 2022-04-04T14:05:36Z

Reminder to revert the astropy version change in this PR so we can merge it

epassaro · 2022-04-04T19:32:32Z

Also, please try to build the documentation before merging!

epassaro · 2022-04-04T19:33:03Z

Black check is failing.

andrewfullard · 2022-04-06T20:39:31Z

Black check is failing.

#1940 is the reason

epassaro · 2022-04-06T20:42:47Z

Black check is failing.

#1940 is the reason

Thanks, I think we should update black in https://github.com/tardis-sn/tardis/blob/master/.github/workflows/black-check.yml instead of doing in the env file.

lemointm · 2022-04-06T21:21:38Z

I just reverted the astropy version, and ran the docs on my machine - everything looks good!

epassaro · 2022-04-11T14:17:53Z

tardis_env3.yml

@@ -14,7 +14,7 @@ dependencies:
  - astropy=3
  - numba=0.53
  - numexpr
-  - pyne=0.7=nomoab_openmc*  # Issue #1537
+  - radioactivedecay>=0.4.12


Is a good idea to pin the bugfix number? Maybe just minor version it's ok, what do you think @lemointm ?

I talked to Alex about this, we think that in the future the functionality TARDIS needs won't get deprecated

but that shouldn't affect the bugfix number, right?

I see what you're saying, sorry I misunderstood. The "bugfix" added some functionality, so it needs to be pinned... which is not the standard but that's how it ended up I suppose

Added rd decay calculations to decay.py

c0eddab

andrewfullard requested review from afloers, wkerzendorf and andrewfullard October 18, 2021 15:58

andrewfullard added atomic priority - high 🔥 restructure labels Oct 18, 2021

epassaro reviewed Oct 19, 2021

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epassaro reviewed Oct 19, 2021

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andrewfullard requested changes Dec 2, 2021

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minor tweaks after review

5f078e7

andrewfullard marked this pull request as ready for review February 17, 2022 22:57

andrewfullard approved these changes Feb 17, 2022

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Ran black formatter

351f01a

andrewfullard self-requested a review February 28, 2022 16:29

removed pyne references from tardis files

a1aa4f9

andrewfullard reviewed Mar 2, 2022

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revert tqdm changes to util base file

7028908

andrewfullard requested changes Mar 9, 2022

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lemointm and others added 2 commits March 9, 2022 15:32

Merge branch 'master' into decayedits

07c475d

Add util to check if str is valid elem or nuclide

66228ac

fixed how inventories are updated, units to grams

3bc5d72

lemointm added 2 commits March 23, 2022 17:24

Updated decay test with more accurate decay data

c273076

Fixed convert_abundances_format util test error

b9355c6

lemointm requested review from andrewfullard and epassaro March 25, 2022 21:51

Updated astropy, set radioactivedecay version

95a32f1

lemointm mentioned this pull request Mar 30, 2022

Set astroPy version #1939

Closed

10 tasks

revert astropy fixed version

5ee7ca1

andrewfullard approved these changes Apr 11, 2022

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epassaro approved these changes Apr 11, 2022

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andrewfullard merged commit 929b0ec into tardis-sn:master Apr 11, 2022

This was referenced Apr 12, 2022

Update TARDIS environment after replacing PyNE #1948

Merged

Add pyne installation issue to TARDIS installation troubles #1860

Closed

pyne holding back newer python releases #1537

Closed

Add pyne installation instructions to documentation #1256

Closed

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Replacing PyNE with radioactivedecay for radionuclide decay calculations #1813

Replacing PyNE with radioactivedecay for radionuclide decay calculations #1813

lemointm commented Oct 15, 2021

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Replacing PyNE with radioactivedecay for radionuclide decay calculations #1813

Replacing PyNE with radioactivedecay for radionuclide decay calculations #1813

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