WIP - Rebasing Python 3.9 Update #2741
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These squashed commits contain all of the initial efforts by HWP to switch from pythoncall to JuliaCall
These were the first commits to change to Python 3.9, and they do not work on their own but instead open the door to finding issues to make the rest of the changes
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
as requested in: #2687 (comment)
These commits are the second (and final) round of attempting JuliaCall debugging by HWP
These commits reflect the initial effort by XD to re-implement the MILP for Clar optimization in SciPy. They were unsuccessful because at the time RMG could not actually run a required version of Python to install SciPy with MILP.
These commits rescued some abandoned work from another branch
This is a collection of largely unordered commits which implement all of the changes discussed in the commit name
…lopment, gone on main
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@jonwzheng @donerancl the current unit test failure seems to indicate that benzene is not being perceived as aromatic, preventing it from being matched in the tree (maybe?) |
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Need to check (1) if resonance structure generation happens during the failing test and (2) does the new implementation work on benzene, with and without the bonds already being of order 1.5 (aromatic)? |
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WIP