Prepare Release 0.12.19

[arrjon]

General:

• Add support of python3.14
• Add execution time profiling to the ABC-SMC run, reporting pure simulation time, parallel-pipeline setup, in-between-iterations
  time, and within it the population size calculation and distance function ´
  adaptation. The timings are also returned by run_generation. Resolves Profiling #325.
• Minor bug fixes and improved type setting.

Visualization:

• plot_walltime and plot_total_walltime now report the actual
  per-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:

• Store the per-generation walltime in the database (new wall_time column,
  database version 2). Databases created with older pyABC versions must be
  migrated via abc-migrate before they can be resumed; for such databases
  the walltime plots fall back to the previous, end-time-based behavior.
• Particle weights are now stored using the global normalization (weights sum
  to 1 across all particles of all models, matching the in-memory
  Population representation). This is bundled into database version 2 and
  handled by abc-migrate for existing databases. Resolves Normalization of weights #47.

[codecov-commenter]

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Codecov Report

❌ Patch coverage is 90.00000% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.21%. Comparing base (3cbd1ce) to head (3340ca9).

Files with missing lines	Patch %	Lines
pyabc/inference_util/inference_util.py	94.11%	1 Missing and 1 partial ⚠️
pyabc/sampler/util.py	60.00%	1 Missing and 1 partial ⚠️
pyabc/sampler/redis_eps/cli.py	50.00%	1 Missing ⚠️
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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #671      +/-   ##
==========================================
- Coverage   79.23%   79.21%   -0.03%     
==========================================
  Files         141      141              
  Lines        8327     8337      +10     
  Branches     1110     1111       +1     
==========================================
+ Hits         6598     6604       +6     
- Misses       1359     1362       +3     
- Partials      370      371       +1     

Flag	Coverage Δ
base	59.35% <90.00%> (+<0.01%)	⬆️
external-R	36.82% <82.00%> (+<0.01%)	⬆️
external-other-simulators	31.46% <42.00%> (+0.01%)	⬆️
migrate	25.44% <28.00%> (+0.08%)	⬆️
petab	35.51% <56.00%> (+0.01%)	⬆️
visualization	52.81% <44.00%> (+0.03%)	⬆️

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[Copilot]

Pull request overview

Prepares the next pyABC release by updating supported Python/dependency versions, refreshing CI/tox and external-simulator test coverage, and adapting AMICI/PEtab integration to newer upstream APIs.

Changes:

• Update packaging/CI/tooling for newer Python (incl. 3.14) and dependency versions, and reorganize tox environments.
• Adapt AMICI/PEtab imports and solver API usage to AMICI ≥ 1.0.0 across library code, tests, and docs.
• Refactor parts of multiprocessing-based samplers and add new external R/rpy2 storage tests; various doc/example cleanups.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tox.ini	Adjust tox env extras/commands; add PEtab git deps; expand external-R tests; update quality tooling version.
test/petab/test_petab.py	Update AMICI PEtab importer calls to new API (import_petab_problem, create_solver, renamed kwargs).
test/petab/test_petab_suite.py	Update AMICI imports/API usage and simulation dataframe conversion function path.
test/external/test_rpy2_storage.py	Add rpy2-backed History storage roundtrip tests for R objects in sumstats.
test/external/test_rpy2_bytesstorage.py	Add rpy2-backed bytes storage roundtrip tests for R dataframes.
test/base/test_storage.py	Remove rpy2-based sumstat storage checks from base test suite.
test/base/test_integrated_model.py	Fix typo in comment.
test/base/test_bytesstorage.py	Remove rpy2-based bytes-storage cases from base tests.
pyproject.toml	Update Python requirement and bump multiple dependency minimum versions; adjust ruff target version.
pyabc/version.py	Bump library version constant.
pyabc/sampler/util.py	Add helper to select multiprocessing Process constructor (preferring fork).
pyabc/sampler/redis_eps/server_starter.py	Switch worker process creation to use new multiprocessing helper.
pyabc/sampler/redis_eps/cli.py	Switch worker process creation to use new multiprocessing helper.
pyabc/sampler/multicore.py	Switch process creation to use new multiprocessing helper.
pyabc/sampler/multicore_evaluation_parallel.py	Switch process creation to use new multiprocessing helper.
pyabc/petab/amici.py	Update AMICI/PEtab integration code to AMICI ≥ 1.0.0 API; adjust solver settings I/O.
pyabc/inference_util/inference_util.py	Refactor nested closures into top-level helpers and use functools.partial.
pyabc/epsilon/temperature.py	Minor docstring formatting cleanup.
doc/sampler.rst	Whitespace cleanup in docs.
doc/examples/wasserstein.ipynb	Normalize quoting style and small string literal updates.
doc/examples/using_R.ipynb	Normalize quoting style and small string literal updates.
doc/examples/sde_ion_channels.ipynb	Normalize quoting style and small string literal updates.
doc/examples/resuming.ipynb	Normalize quoting style and adjust a couple of cells to print instead of bare expressions.
doc/examples/petab_yaml2sbml.ipynb	Update AMICI API usage (import_petab_problem, create_solver, simulate, etc.).
doc/examples/petab_application.ipynb	Update AMICI API usage (import_petab_problem, create_solver) and minor formatting.
doc/examples/parameter_inference.ipynb	Normalize quoting style and minor string literal updates.
doc/examples/multiscale_agent_based.ipynb	Normalize quoting style and minor string literal updates.
doc/examples/model_selection.ipynb	Normalize quoting style and change a couple of cells from expression display to print/assert.
CHANGELOG.rst	Add new release-note section.
.pre-commit-config.yaml	Update default pre-commit Python version.
.github/workflows/install_deps.sh	Remove R install helper; trim AMICI apt deps.
.github/workflows/deploy.yml	Bump GitHub Actions versions used in deploy workflow.
.github/workflows/ci.yml	Update Python matrix (incl. 3.14), action versions, Julia setup, add setup-r, tweak dependency install logic, and make codecov upload non-blocking.

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

pyabc/sampler/util.py:21

• get_mp_process() can return a Process class from a different multiprocessing context (fork) than the one used to create Queue/Value objects elsewhere (which use the default context). Mixing contexts is known to raise runtime errors (e.g. SemLock/context mismatch) on platforms where the default start method is spawn (macOS) or when users set a non-fork start method.

To avoid cross-context issues, return the Process class from the current/default context (or alternatively expose a get_mp_context() helper and create Queue/Value from that same context).

def get_mp_process():
    """Get a multiprocessing Process constructor.

    On POSIX, prefer ``fork`` when available to support non-picklable
    callables (e.g. local functions in tests) in nested worker setups.
    """
    if 'fork' in mp.get_all_start_methods():
        return mp.get_context('fork').Process
    return mp.Process

[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

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