Maintenance/checkpointing

[otaub]

Description

This PR replaces the pickle based checkpointing with HDF5.
Main changes:

• candidates will be written to checkpoint on sampling/breeding, so individuals whose evaluation has started are not lost when the run is interrupted.
• pollination now only has one individual per island
• population is now a dict

Minor changes

• fixed some signs in the static surrogate mechanism, closes Check surrogate merge works as intended #157

Fixes # (issue)

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

[github-actions]

Name	Stmts	Miss	Cover	Missing
propulate/__init__.py	15	2	87%	6-7
propulate/_globals.py	5	0	100%
propulate/islands.py	85	5	94%	134, 171, 179, 212, 218
propulate/migrator.py	174	12	93%	220, 275-296
propulate/pollinator.py	153	1	99%	186
propulate/population.py	123	22	82%	56, 73, 101-102, 119, 128, 142, 147, 164, 172, 176, 186, 223, 265-275
propulate/propagators/__init__.py	6	0	100%
propulate/propagators/base.py	103	16	84%	68, 98, 150, 262, 267-272, 343, 397, 450, 524, 527-530
propulate/propagators/cmaes.py	189	22	88%	229-237, 244-246, 262-269, 336, 370, 395, 762, 808-809
propulate/propagators/ga.py	117	52	56%	61, 88-92, 96-98, 159-171, 187-207, 267, 347, 405, 421-427, 469-470, 486-500
propulate/propagators/nm.py	80	0	100%
propulate/propagators/pso.py	120	30	75%	145, 152-154, 341, 524, 554, 560-561, 617-622, 643-674
propulate/propulator.py	296	34	89%	146-148, 151, 206, 246, 417-418, 522, 534, 593-604, 620-627, 648, 651-657
propulate/surrogate.py	138	26	81%	42, 62, 80, 104, 124, 142, 290-292, 462, 466, 477-489, 551, 554, 558, 562, 568, 585
propulate/utils/__init__.py	38	9	76%	79, 140-141, 146-151
propulate/utils/benchmark_functions.py	137	31	77%	586, 609-683
propulate/utils/consistency_checks.py	68	11	84%	58-59, 110-111, 133-136, 147-149
TOTAL	1847	273	85%

[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.81443% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.43%. Comparing base (3d64147) to head (e5dd521).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
propulate/utils/consistency_checks.py	75.92%	13 Missing ⚠️
propulate/propulator.py	95.20%	8 Missing ⚠️
propulate/propagators/pso.py	77.77%	2 Missing ⚠️
propulate/population.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #182      +/-   ##
==========================================
- Coverage   85.88%   85.43%   -0.46%     
==========================================
  Files          16       17       +1     
  Lines        1792     1819      +27     
==========================================
+ Hits         1539     1554      +15     
- Misses        253      265      +12     

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