Sync with upstream LyoHUB/LyoPRONTO #5
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To make LyoPRONTO an installable package, we need a pyproject.toml. Since there have been a few improvements, I will publish a release and call it 1.1.
1) Add a test suite with comprehensive coverage * Run documentation notebooks as part of test suite, using papermill 2) Fix some problems uncovered by that test suite * Using fraction vs % in drying completion * Have calc_knownRp end when ramps end, per old API * Have calc_knownRp provide interpolated values at all time points, if dt!=None, per old API * Eliminate some infinite loops in design space calculation * Rework time handling for freezing 3) Use pyproject.toml for everything possible 4) Build docs for PRs, but don't deploy because I couldn't get Actions runner correct permissions 5) Format the test suite with ruff 6) Introduce a RampInterpolation class, which is currently only used in freezing, testing, and calc_knownRp but could apply everywhere 7) Emit proper warnings, not just print to stdout 8) Add a dev section to docs ---- All commits: * Add testing-related files from SECQUOIA fork * Missed a file * Have tests use pyproject.toml, not requirements.txt * add pandas as dev dep * fix tests: replace math.exp with np.exp * fix: calc_knownRp uses percent rather than 0-1 * clean whitespace * fix: Handle edge case in design space * Move helper func to separate module under tests * Fix tests for unknownRp * Note that edge case needs treatment * cleanup * Include pytest settings in pyproject.toml * Fully move all tests to percent dried, not fraction * Further test cleanup * Ignore some local things * Standardize calc_unknownRp tests * Fix a bug in design space, uncovered by tests * DRY the tests out a bit * Eliminate one cause of infinite loops in design space * fix: give an initial guess in acceptable range * Make a start on handling cases where optimization fails for Pch * Get all tests passing, skip those that address problems which don't exist yet * dry out Tsh a little bit * Get all opt_Pch tests passing * Get some Tsh tests passing * Get joint optimization tests passing * Remove separate "coverage" tests * Complete line coverage of opt_Pch * Unify Pch_Tsh optimization, with complete coverage * default ramp rate of no ramp, if not supplied * Add Tmax parameter to assert_physically_reasonable_output * Tweak path handling * Include results from web API in repo, for test comparisons * Add coverage defaults to testing * Rename for clarity, delete duplicate tests * Consolidate calc_unknownRp into one file * Make unknownRp give useful warnings, test those warnings * lint * Add warnings for design space, consolidate tests,, get complete test coverage * Consolidate * Consolidate and clarify knownRp tests * clarify deps * Get a proper regression test passing on calc_knownRp by taking dt and max time into account more carefully * Work on increasing coverage * Remove redundant test * Make path to test data have one source of truth * Standardize a magic number * Test failures * Add one more testing utility function * Fix and clean up freezing, clean up tests, add tests to reach 100% coverage * Make example scripts with plots part of the test suite * Add tests which execute notebooks; rework CI to run papermill within pytest, rather than from papermill command line * Fix compat bound * fix: don't have notebooks run together with "PR tests" * Separate out notebook dependencies from docs building dependencies * Import papermill inside notebook tests * Try out writing PR version of docs again * try again pr docs * one more thing to try * move permissions? * Give up on PR versions of docs from Actions * Clean up unused config * Make one category of dev deps, not two * Remove unused testing script * Delete obsolete test * Modify equations being solved to account for varying shelf temperature during crystallization * Add reference test for freezing * Add new reference data for opt_Pch * Point to correct file * Test reference case for opt_Pch * Give opt_pch reference case its own inputs setup * Take some of Copilot's review suggestions * Linting * Ruff formatting. Lots of whitespace noise, all single quotes to double quotes * Get *a* reference test working for opt_Pch * unnecessary imports * Relax tolerance * Help diagnose CI failure * Bite the bullet and add a time interpolator for Tshelf and Pchamber * Make RampInterpolator conform to existing API for dt_setpt, with kwarg for changing to other interpretation * Add more consistency checks to optimization tests, use some np.testing utilities * Fix freezing reference to be closer to original interpretation * Get one last test passing * ruff format on tests * Remove unused sections from pyproject.toml * Make some dev docs, shuffle things into there from README, etc. * Add some extra helpers for RampInterpolator, use in calc_knownRp
This PR syncs SECQUOIA/LyoPRONTO main with the upstream LyoHUB/LyoPRONTO repository. Key changes from upstream: - lyopronto/functions.py: RampInterpolator class, improved lumped_cap_Tpr functions - lyopronto/calc_*.py: Better error handling, PCHIP interpolation - lyopronto/opt_*.py: Improved optimizer robustness - tests/: Comprehensive test suite from upstream - CI: Updated workflow configurations This establishes a clean foundation for adding Pyomo integration.
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Summary
This PR syncs SECQUOIA/LyoPRONTO main with the upstream LyoHUB/LyoPRONTO repository.
Key Changes from Upstream
Physics Improvements
lyopronto/functions.py: AddedRampInterpolatorclass for shelf temperature rampinglumped_cap_Tpr_abstract,lumped_cap_Tpr_ice,lumped_cap_Tpr_solfunctionscrystallization_time_FUNwithTsh_funcparameter for dynamic shelf temperaturefill_output()now uses PCHIP interpolation for smoother resultsOptimizer Robustness
lyopronto/opt_Pch.py: Improved error handling and boundslyopronto/opt_Tsh.py: Warning imports, ramp_rate handlinglyopronto/opt_Pch_Tsh.py: Code formatting improvementsTest Suite
CI/CD
Why This PR?
This establishes a clean foundation synced with upstream before adding Pyomo integration in subsequent PRs.
Part of Pyomo Integration Series
This is PR 0 of 8 in the Pyomo integration series: