MesoHOPS 1.7.0#5
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Imported from MesoscienceLab/pyhops master at commit 10beb3f4 via the
release_to_mesohops.py tool. Identifier renames (pyhops -> mesohops) and
display-string renames (PyHOPS -> MesoHOPS) applied during import; private
files (README.md, LICENSE, .gitignore) preserved from mesohops master.
Highlights of v1.7.0 (vs. mesohops 1.6.0):
Build stability:
- pyproject.toml: pin all dependency ranges. numba and numpy pinned tight
(numba >=0.63,<0.64; numpy >=2.3,<2.4) to guard against a history of
stochastic test failures and memory issues that tracked numba minor bumps;
numba binds against a specific numpy ABI per release. Other deps loose-
pinned at the major.
- pyproject.toml: tighten requires-python to >=3.12,<3.14 (matches what CI
validates and what the numba pin allows).
- pyproject.toml: replace malformed "Development Status :: full release
1.6.0" classifier with the standard trove classifier.
- .github/workflows/coverage.yml: matrix CI on Python 3.12 + 3.13 and add
a gating clean-install smoke job that runs `pip install .` (non-editable)
+ level-1 tests; catches packaging bugs the editable-install coverage
job hides.
Cleanup:
- src/mesohops/noise/hops_noise.py: fix __title__ casing typo.
- tests/test_git_utils.py: skip test_get_git_commit_hash_success when the
installed package is not inside a git working tree (the function returns
the git error message string in that case, by design).
- Remove two orphan test fixtures (pyhops_testing_noise{,_v0}.npy) that
were never referenced by any test.
Test results on the imported snapshot: level-2 suite passes 319/319 in a
fresh venv with the pinned dep ranges resolving cleanly.
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MesoHOPS 1.7.0
This commit upgrades MesoHOPS to support million-state-class adaptive simulations, expands nonlinear spectroscopy to full third-order rephasing/non-rephasing pathways, and includes stability and quality improvements across checkpointing, storage, and core numerical routines.
Key improvements and features:
Million-state-class scalability: Adaptive-basis construction, operator-assembly, and noise-memory bookkeeping were redesigned to remain size-invariant on million-state-class systems. The new
HopsNoiseMemoryclass manages z-memory indexing with O(1) updates as the adaptive basis grows; modes that have left the basis but not yet decayed below precision persist inz_memuntil they do, with separate index lists tracking the full set vs. the active subset. Reduced/masked sparse paths were strengthened to avoid full-system constructions in critical routines.HOPS Nonlinear Spectroscopy (NLS):
DyadicSpectranow supports full third-order rephasing and non-rephasing pathways (GSB / SE / ESA) in a unified workflow.Dyadic checkpoint robustness: Strengthened save/load validation and restore behavior for
DyadicTrajectorycheckpoints. Selective permanent-state / adaptive interactions added and validated for stable spectroscopy-focused adaptive runs.Checkpoint storage-time fix:
HopsStorage.storage_timeis now correctly reloaded from checkpoint data; previously it reset on restore.Storage default refinement:
list_aux_normis no longer saved by default inHopsStorage; users who depend on it must opt in viastorage_dic={'list_aux_norm': True}. Reduces default RAM cost. Whenz_memis saved (adaptive checkpoints),list_zmemmodeidx_absis now auto-enabled so the mode-index mapping survives checkpoint round-trips.General Brownian-oscillator BCF:
bcf_convert_dl_ud_to_expis removed. Usebcf_convert_bo_to_exp(lambda_bo, gamma_bo, omega_bo, temp, k_matsubara=0)instead. The new function uses an exact contour integration over the upper half-plane and handles both underdamped (γ < Ω) and overdamped (γ > Ω) regimes in one workflow, with optional Matsubara corrections. Critical damping (γ = Ω) raisesValueError; near-critical damping warns. Numerical results for simulations that previously usedbcf_convert_dl_ud_to_expwill differ from 1.6.x; re-run convergence checks against the new implementation.Numerical robustness guards: Divide-by-zero protection added to system and hierarchy timescale calculations.
Vestigial code removal: The unused
NoiseTrajectoryclass was removed.These enhancements collectively improve the scalability, spectroscopic capability, and numerical robustness of MesoHOPS for current and future applications.