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[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (juliaup and pythoncall), Add Tests for Arkane Network Algorithms #2687

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Commits on Jun 28, 2024

  1. switch to branch

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  2. Use pyjuliacall instead of pyjulia

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  3. No need to install julia from conda

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  4. update

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  5. update

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  6. Swap the order

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  7. update

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  8. doc

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  9. Use the preexisting mamba

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  11. Add channels

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  12. skip make for now for debugging

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  13. Trying to use juliaup

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  14. Don't need to install diffeqpy

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  15. Uncomment make step

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  16. Don't need julia plug in

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  17. Use mamba

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  18. No need to add channels

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  19. import juliacall

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  20. Don't track coverage

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  21. debug

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  22. debug

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  23. convert empty list

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  24. Add additional test file for sls

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  25. Should be seval

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  26. debug

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  27. update doc

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  28. Add tests

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  29. Don't track plots

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  30. don't track yaml files

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  31. update name

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  32. track yaml files

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  33. See where we get julia from

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  34. Add Pkg.

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  35. debug

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  36. update

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  37. debug

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  40. Convert to julia object

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  41. Remove duplicate test

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  42. Add comments and juliaup status

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  44. Don't change release note

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  45. Add docstring

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  46. Update rmgpy/rmg/reactors.py

    Co-authored-by: Jackson Burns <[email protected]>
    hwpang and JacksonBurns committed Jun 28, 2024
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  47. Fix

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  48. Avoid duplicating

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  49. Avoid casting to list

    hwpang authored and JacksonBurns committed Jun 28, 2024
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  51. Add changelog

    hwpang authored and JacksonBurns committed Jun 28, 2024
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Commits on Jul 1, 2024

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  3. fix cython compilation errors (0.23 -> 3.n), SEE EXTENDED!!

    here are all the solutions that were implemented:
     - in a couple places we were implicitly casting a double to a numpy float, now need to explicitly grad the _real_ part of the double
     - Cython does not allow nested function declaration inside cpdef functions, move all of these outside of their parent functions or redefine them to be purely functional where practical
     - similar to the above, lambda function are no longer allowed - get the same treatment. what's different here is that usually we are using lambda in sorting calls, so we can replace these with operator.itemgetter or attrgetter, where relevant. this also involves re-writing a couple reduce calls, which also used lambda
     - modern cython does not allow re-declaring existing Cython variables (in previous versions this was a warning I think), so I just remove these where needed. (btw Cython is super cool, actually points out both of the declaration so that you can delete one)
    
    i made these fixes while listening to The Metal by Tenacious D, Talk Too Much by Renee Rapp, BEST INTEREST by Tyler, The Creator (love the bass line), mos thoser by food house, and Doritos & Fritos by 100 Gecs
    JacksonBurns committed Jul 1, 2024
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  4. add newly defined functions to pxd files

    as requested in: #2687 (comment)
    JacksonBurns committed Jul 1, 2024
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Commits on Jul 2, 2024

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  3. Use Sundials from RMS

    hwpang committed Jul 2, 2024
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  5. DROP ME comment out failing lpsolve test for now

    want to see if the problem comes up again elsewhere
    JacksonBurns committed Jul 2, 2024
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Commits on Jul 3, 2024

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Commits on Jul 8, 2024

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  2. passthrough args to same_object

    for some reason `functools.partial` is allowed, but not `lambda`
    JacksonBurns committed Jul 8, 2024
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