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duartegroup / autodE

automated reaction profile generation
https://duartegroup.github.io/autodE/
MIT License
171 stars 52 forks source link

Add combination of bonds primitive and trust radius optimiser #345

Closed shoubhikraj closed 3 months ago

shoubhikraj commented 3 months ago

(1) Adds a linear combination of bonds as a primitive (2) Trust radius quasi-Newton optimiser

Checklist

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 98.45758% with 6 lines in your changes missing coverage. Please review.

Project coverage is 97.43%. Comparing base (76398fc) to head (fb4328b).

Files Patch % Lines
autode/opt/optimisers/qa.py 92.53% 5 Missing :warning:
autode/opt/optimisers/crfo.py 98.91% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## v1.4.4 #345 +/- ## ========================================== + Coverage 97.39% 97.43% +0.04% ========================================== Files 202 204 +2 Lines 23278 23626 +348 ========================================== + Hits 22672 23021 +349 + Misses 606 605 -1 ``` | [Flag](https://app.codecov.io/gh/duartegroup/autodE/pull/345/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=duartegroup) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/duartegroup/autodE/pull/345/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=duartegroup) | `97.43% <98.45%> (+0.04%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=duartegroup#carryforward-flags-in-the-pull-request-comment) to find out more.

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shoubhikraj commented 3 months ago

@t-young31 Hi, do you know why the tests are failing with a RecursionError on a numpy allclose call? I have no idea how this error is happening.

t-young31 commented 3 months ago

looks like a major numpy update (https://github.com/duartegroup/autodE/actions/runs/9922667636/job/27421474592?pr=345#step:5:148) – will have a look for a solution.

edit: Looks like we're hitting:

https://github.com/numpy/numpy/blob/7bff2754f64cb855c39b59cf6d0b7bc51fe49a61/numpy/_core/numeric.py#L2419 https://github.com/duartegroup/autodE/blob/2f3af32fc7806b7175133220506f0eb54c66ab13/autode/values.py#L622 ♻️

shoubhikraj commented 3 months ago

@t-young31 Could you have one last check before merge please?