Add better time tracking

[arrjon]

This pull request adds detailed execution time profiling to the ABC-SMC run, including both wall-clock and fine-grained sub-step timings. Additionally, per-generation walltimes are now stored in the database, and visualizations have been updated to reflect these more accurate timings.

I also cleaned up some minor code.

Resolves #325 and #667

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Codecov Report

❌ Patch coverage is 94.44444% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.28%. Comparing base (1749237) to head (2ec22d1).

Files with missing lines	Patch %	Lines
pyabc/visualization/walltime.py	86.36%	2 Missing and 1 partial ⚠️
...s/versions/2_20260724_add_populations_wall_time.py	90.00%	1 Missing ⚠️
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Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #668      +/-   ##
===========================================
+ Coverage    79.21%   79.28%   +0.07%     
===========================================
  Files          141      142       +1     
  Lines         8337     8386      +49     
  Branches      1111     1116       +5     
===========================================
+ Hits          6604     6649      +45     
- Misses        1362     1365       +3     
- Partials       371      372       +1     

Flag	Coverage Δ
base	59.39% <64.51%> (+0.03%)	⬆️
external-R	36.98% <61.29%> (+0.13%)	⬆️
external-other-simulators	31.61% <61.29%> (+0.16%)	⬆️
migrate	25.44% <25.00%> (+0.01%)	⬆️
petab	35.64% <61.29%> (+0.14%)	⬆️
visualization	52.98% <93.54%> (+0.18%)	⬆️

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[Copilot]

Pull request overview

This PR improves time tracking in pyABC by (1) persisting per-generation walltime in the database to make walltime visualizations accurate across resumed runs, and (2) adding fine-grained per-generation execution-time profiling inside the ABC-SMC loop.

Changes:

• Store per-population walltime (Population.wall_time) in the DB and use it in plot_walltime / plot_total_walltime to avoid counting idle resume gaps.
• Add per-generation execution-time profiling in ABCSMC.run_generation (pipeline setup, simulation, in-between steps) and return these timings to callers.
• Add a regression test for “resume gap” walltime plotting; bump package + DB versions and document in the changelog.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/visualization/test_base_viz.py	Adds a regression test ensuring resume gaps don’t inflate plotted walltime when per-generation walltimes exist.
pyabc/visualization/walltime.py	Uses per-generation wall_time when available for walltime plots; adds low-level support for passing walltimes.
pyabc/version.py	Bumps package version to 0.12.19.
pyabc/storage/version.py	Bumps DB version to 2.
pyabc/storage/history.py	Extends population queries and storage updates to include wall_time; threads walltime through calibration/population storage.
pyabc/storage/db_model.py	Adds wall_time column to the populations table model.
pyabc/inference/smc.py	Adds _Timer and per-generation profiling; stores per-generation walltime in the DB; returns timing data from run_generation.
pyabc/distance/pnorm.py	Type-hint refinements (Optional/None unions).
pyabc/distance/base.py	Type-hint refinements; tightens FunctionDistance typing and allows None in to_distance input typing.
CHANGELOG.rst	Documents new profiling, walltime plotting behavior, and DB format change for 0.12.19.

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[kilianvolmer]

Thank you for implementing all those changes so fast! I left a few minor comments here and there, nothing severe.

[arrjon]

Ready to merge now