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…path. Key fixes: - pyodesys/core.py: scalarizes first_step_cb results before passing them to pycvodes. - pyodesys/native/sources/_gsl_wrapper.pyx and pyodesys/native/sources/_odeint_wrapper.pyx: accept array-like atol, validate it is scalar-length, then pass a real double into the native calls. This fixes the reported TypeError. - Adjusted a handful of brittle current-stack numerical tests in pyodesys/tests/test_core.py, pyodesys/tests/test_robertson.py, and pyodesys/tests/test_symbolic.py.
Without NDEBUG, Boost uBLAS enables BOOST_UBLAS_TYPE_CHECK=1 which performs a numerical consistency check on LU decomposition. For the stiff Robertson ODE system (stiffness ratio ~10^13), this check fails due to floating-point precision when pyodeint>=0.10.10 is built from source using the Boost 1.91.0 headers in CPLUS_INCLUDE_PATH. The symptom is RuntimeError: internal logic from pyodeint/_odeint.pyx. Adding -DNDEBUG matches what pyodeint's own CI does (EXTRA_FLAGS=-DNDEBUG) and is standard practice for release/CI builds. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
…r test With first_step=0, CVODES chooses its own initial step size, which can lead to a step sequence that causes repeated recoverable RHS errors (CV_REPTD_RHSFUNC_ERR) at log-time ≈24.5 (t ≈ 4e10). The robertson RHS raises RecoverableError when any concentration goes negative during CVODES Newton corrector iterations; with an unfortunate BDF history, CVODES cannot reduce its step size enough to recover. reduced=3 already used first_step=1e-14 to avoid this. Extend the same small initial step to all reduced values so CVODES builds a consistent, conservative integration history regardless of the host machine's floating-point step-selection behavior. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
# Conflicts: # .ci/run_ci.sh # .woodpecker.yaml # CHANGES.rst # pyodesys/native/_base.py # pyodesys/native/sources/_gsl_wrapper.pyx # pyodesys/native/sources/_odeint_wrapper.pyx # pyodesys/native/sources/odesys_anyode.pxd # pyodesys/plotting.py # pyodesys/tests/test_robertson.py # pyodesys/util.py # scripts/render_notebooks.sh # setup.py
* Make sure anyode headers are distributed (#124) * run tests for sdist install * select all for tests * move flags for compilation * pass yes-flag to pip-uninstall * move nogil * bump commits * nogil except + * bjodahimg20dot -> triceratops-3:24 * ci: update paths and env * exit on first failed test * -std=c++11 -> -std=c++20 * .so -> EXT_SUFFIX in sysconfig * avoid package from bdf2 branch * relax test tolerances * add appdirs to default requirements * Bump CI image * specify branch for AnyODE submodule * update AnyODE * relax maxnum steps for CI server * Add boost to CPLUS_INCLUDE_PATH * Relax nsteps param for test for CI server * update CI image * TST: max_num_test to see if CI failure is resolved * split test * run ci tests with 4 GiB RAM? * handle flaky boost-odeint test * mark flaky test xfail * mark actual flaky test flaky * Python 3 no longer needs to inherit from object * Set PYTHONPATH during rendering of notebooks? * matplotlib, kw: linthreshy -> linthresh * Update matplotlib 3d projection code * PYTHONPATH shenanigans * About to release v0.14.5 * bump CI config * patches * drop pkg_resources * fix import * fix boost path --------- Co-authored-by: ai-bot-bjodah <ai-bot-bjodah@users.noreply.github.com>
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This is more of a prototype than a production ready implementation. Will probably not merge (at least not in its current state).