Update IPython notebooks #1735
Update IPython notebooks #1735
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mliu49
added
the
Status: Ready for Review
Codecov Report
@@ Coverage Diff @@
## master #1735 +/- ##
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+ Coverage 32.6% 32.61% +<.01%
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Files 87 87
Lines 26116 26124 +8
Branches 6875 6878 +3
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+ Hits 8516 8521 +5
+ Misses 16642 16633 -9
- Partials 958 970 +12
Continue to review full report at Codecov.
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@mjohnson541 and @alongd, it would be really nice to get this in before the IPython session on Wednesday. Do you have time to look at it or should I request other reviewers? |
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I'm sorry, I won't have time for a decent review by Wednesday. |
| " },\n", | ||
| " terminationTime=('''+str(sim_time/1000.0)+''','s'),\n", | ||
| " }},\n", | ||
| " terminationTime=({sim_time/1000.0!s},'s'),\n", |
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The !s formatting might not be necessary
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For this specific one or in general?
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I think in general for the cases I saw in this file
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Quick comment on running the IPython notebooks: uncommenting the line |
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I think this PR is good to go. Rebase to update this and I'll merge it in |
It was leading to circular imports, and was only used for an isinstance check, which was refactored
Main motivation is that None can no longer be compared to ints in Python 3 This changes how the sorting process is implemented but maintains the same behavior as before
In cases where there may have been a line break in the middle of the reaction template, which is very likely with automatically generated families.
Was accidentally renamed
The R_Recombination family was changed for auto tree generation There is only a single template now, and duplicate * labels This copies template handling from __generate_reactions A unit test is also added
Motivation or Problem
This PR updates the notebooks located in
RMG-Py/ipythonto work with Python 3 and RMG API changes.The only exception is
globalUncertainty.ipynb, which will be updated along with the MUQ changes in a separate PR.Description of Changes
In the process of updating the notebooks, a few bugs were also discovered and fixed.
The parse_source example model also had to be updated to reflect RMG-database changes (in particular, the replacement of the R_Recombination tree with auto-generated groups).
Testing
I have run all of the notebooks locally. To confirm, the reviewer can do the same. All of the notebooks can be executed in their entirety without changing any user inputs, and should run without any errors.