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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update particle weight normalization to global convention (breaking change for old databases) and fix minor bugs. * migration for old databases
arrjon
marked this pull request as ready for review
July 30, 2026 14:19
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I bumped the version to 0.13.0, as we have breaking changes in the database. Ready for the new release now. |
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Pull request overview
Copilot reviewed 78 out of 79 changed files in this pull request and generated no new comments.
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pyabc/storage/history.py:350
get_distributionnormalizes weights viaw_arr / w_arr.sum()without guarding against a zero sum. If a model has only zero-weight particles stored (possible when a model is effectively dead but still present), this will divide by zero and return NaNs / raise warnings. Consider keeping the new within-model renormalization, but fail fast on a zero sum with a clear error message.
pyabc/visualization/walltime.py:50_prepare_plot_total_walltimefalls back to(abc.end_time - abc.start_time)when per-generationwall_timeis missing. For unfinished runs (end_time is None), this will raiseTypeError. Consider handlingend_time=Noneexplicitly (e.g., usedatetime.datetime.now()or another reasonable fallback) so plotting doesn’t crash on in-progress histories.
pyabc/storage/migrate.py:106- On unsupported database identifiers,
migrate()prints an error andreturns, which causes the CLI to exit with status 0. This makes it hard to detect migration failures in scripts/CI. Consider exiting with a non-zero status after printing the error.
* FIX broken docstring * CHG: Update PETab intersphinx inventory location * Update external deendencies information
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kilianvolmer
requested changes
Jul 31, 2026
kilianvolmer
approved these changes
Jul 31, 2026
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General:
time, and within it the population size calculation and distance function ´
adaptation. The timings are also returned by
run_generation. Resolves Profiling #325.Visualization:
plot_walltimeandplot_total_walltimenow report the actualper-generation walltimes and no longer include the idle time that passed
between a stored analysis and a later resumed run. Resolves Walltime plots do not show actual walltime if stored abc runs are resumed #667.
Storage:
wall_timecolumn,database version 2). Databases created with older pyABC versions must be
migrated via
abc-migratebefore they can be resumed; for such databasesthe walltime plots fall back to the previous, end-time-based behavior.
to 1 across all particles of all models, matching the in-memory
Populationrepresentation). This is bundled into database version 2 andhandled by
abc-migratefor existing databases. Resolves Normalization of weights #47.