Update CI configuration and dependencies

[arrjon]

This pull request modernizes and streamlines the project's packaging and CI infrastructure. The most significant changes include migrating all packaging metadata from setup.cfg to pyproject.toml, updating the CI workflows for improved reliability and future compatibility, and enhancing the installation scripts for robustness and cross-platform support.

[codecov-commenter]

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Codecov Report

❌ Patch coverage is 82.73616% with 159 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.93%. Comparing base (00b1c7b) to head (21aed8c).

Files with missing lines	Patch %	Lines
pyabc/visserver/server_dash.py	0.00%	37 Missing ⚠️
pyabc/sampler/redis_eps/cli.py	43.47%	11 Missing and 2 partials ⚠️
pyabc/sge/job_info_redis.py	0.00%	12 Missing ⚠️
pyabc/sge/db.py	25.00%	9 Missing ⚠️
pyabc/sge/sge.py	41.66%	6 Missing and 1 partial ⚠️
pyabc/petab/base.py	60.00%	4 Missing and 2 partials ⚠️
pyabc/visualization/data.py	57.14%	6 Missing ⚠️
pyabc/distance/pnorm.py	81.81%	4 Missing ⚠️
pyabc/storage/history.py	91.30%	2 Missing and 2 partials ⚠️
pyabc/visserver/server_flask.py	84.61%	4 Missing ⚠️
... and 37 more
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Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #656      +/-   ##
===========================================
- Coverage    80.62%   79.93%   -0.69%     
===========================================
  Files          141      141              
  Lines         8533     8325     -208     
  Branches         0     1110    +1110     
===========================================
- Hits          6880     6655     -225     
+ Misses        1653     1298     -355     
- Partials         0      372     +372     

Flag	Coverage Δ
base	59.42% <66.73%> (?)
external-R	36.66% <52.50%> (?)
external-other-simulators	35.44% <50.97%> (?)
migrate	25.35% <44.84%> (?)
petab	35.44% <51.30%> (?)
visualization	52.77% <65.32%> (?)

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[arrjon]

also provides a fix for #655

[arrjon]

Tests now include most notebooks, only the dependency onpetabtests is currently removed, as the installation fails (due to conflicts with pysb and amici dependencies.

[stephanmg]

Looks good to me,
thanks for fixing this.

Could you make sure the checks complete succesfully? Then merge it.

[arrjon]

The old checks are not triggered here anymore, but the new checks are all good, see: https://github.com/ICB-DCM/pyABC/actions/runs/22139072955

[stephanmg]

The old checks are not triggered here anymore, but the new checks are all good, see: https://github.com/ICB-DCM/pyABC/actions/runs/22139072955

Okay great, then should be able to merge.