Add egfr_extended codegen and simulation to benchmarks #527
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jmuhlich
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Sorry, I just realized the egfr_extended codegen and simulation benchmarks that this PR introduces are completely new. I created this branch by cherry-picking some commits from another branch where I'd introduced a combined egfr_extended simulator benchmark, and it was so long ago that I forgot that benchmark was only on that branch! |
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I edited the PR title to make more sense in light of this revelation. |
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Also remove Earm10 test with empty cython_directives since it's broken after a previous refactoring and is about to be obviated by an upcoming improvement in ScipyOdeSimulator.
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* Move python version window up to only currently-supported versions. * Specify extra dependencies in matrix req rather than a conda env. * Add OMP_NUM_THREADS=1 to the env to avoid useless BLAS threading.
| // "six": ["", null], // test with and without six installed | ||
| // "pip+emcee": [""], // emcee is only available for install with pip. | ||
| // }, | ||
| "matrix": { |
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I can't find this format for matrix documented anywhere, and asv run gives me the error TypeError: sequence item 1: expected str instance, dict found. The required format seems to match what's commented out above. Am I missing something?
| "python-dateutil": "2.8.1", | ||
| "cython": "0.29.21", | ||
| "alubbock::bionetgen": "2.5.1", | ||
| "alubbock::cupsoda": "v1.1_986c895" |
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CupSODA is not available as an Anaconda package for Mac (Macs haven't had NVIDIA GPUs for a while now, and although an eGPU might work, I haven't had access to one to try it). There doesn't seem to be a way to specify a package for specific platforms either, unfortunately. Maybe we should just leave a comment for Mac users to comment this line out, unless there's a better solution?
Codecov Report
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## master #527 +/- ##
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Coverage 80.16% 80.16%
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Files 100 100
Lines 10650 10650
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Hits 8538 8538
Misses 2112 2112 📣 Codecov can now indicate which changes are the most critical in Pull Requests. Learn more |
This lets us track codegen and simulation performance separately. Also:
after a previous refactoring and is about to be obviated by an upcoming
improvement in ScipyOdeSimulator.