Ert

<!-- Release notes generated using configuration in .github/release.yml at version-13.0 -->

What's Changed
Bug Fixes
* Backport proper counting of cpu-seconds for subprocesses by berland in https://github.com/equinor/ert/pull/9955
* Backport join_asof fix by yngve-sk in https://github.com/equinor/ert/pull/9951


**Full Changelog**: https://github.com/equinor/ert/compare/13.0.0...13.0.1

<!-- Release notes generated using configuration in .github/release.yml at version-13.0 -->

What's Changed
User impact 🛠
* Use lalr parser for main ert config by eivindjahren in https://github.com/equinor/ert/pull/9735
Breaking Changes 🛠
* Remove SIMULATION_JOB keyword by DanSava in https://github.com/equinor/ert/pull/9606
* Replace interface towards eclrun and flow using fmstep_config by berland in https://github.com/equinor/ert/pull/9108
* Use ert queue options by oyvindeide in https://github.com/equinor/ert/pull/9486
New Features 🎉
* Add post/pre experiment simulation hooks by yngve-sk in https://github.com/equinor/ert/pull/8993
* Add support for multiple occurrences of design matrix by xjules in https://github.com/equinor/ert/pull/9583
Improvements
* Ignore unimportant ConfigWarnings by frode-aarstad in https://github.com/equinor/ert/pull/9656
* Add nicer error message when init fails by frode-aarstad in https://github.com/equinor/ert/pull/9653
* Warn on full disk by eivindjahren in https://github.com/equinor/ert/pull/9745
* Avoid non-informative ValueError in parameter/response configuration by eivindjahren in https://github.com/equinor/ert/pull/9793
* Pretty print index.json files in storage by oyvindeide in https://github.com/equinor/ert/pull/9792
Bug Fixes
* Workaround Python bug for shutil.copytree() exceptions by berland in https://github.com/equinor/ert/pull/9627
* Fix precision loss issue in calculation of standard deviation. by eivindjahren in https://github.com/equinor/ert/pull/9625
* Fixed plotter remembering correct tab when switching plot types by andreas-el in https://github.com/equinor/ert/pull/9635
* Validate derrf distribution parameters on startup by larsevj in https://github.com/equinor/ert/pull/9599
* Show inversion errors in GUI by eivindjahren in https://github.com/equinor/ert/pull/9678
* Handle unopenable files consistently in config by eivindjahren in https://github.com/equinor/ert/pull/9682
* Only have one visual active button in sidepanel by andreas-el in https://github.com/equinor/ert/pull/9693
* Fix missing comma in SUMMARY_KEYS everest by larsevj in https://github.com/equinor/ert/pull/9717
* Ignore OSErrors on subprocess call of bjobs and bhist by berland in https://github.com/equinor/ert/pull/9696
* Remove asyncio.run_in_executor() calls and make scheduler cancel() async by jonathan-eq in https://github.com/equinor/ert/pull/9664
* Set permissions for transaction files to 0o666 by eivindjahren in https://github.com/equinor/ert/pull/9804
* Backport: Transpose the input to get_nr_primary_components in misfit preprocessor by larsevj in https://github.com/equinor/ert/pull/9939
Maintenance
* Remove unused async_run by oyvindeide in https://github.com/equinor/ert/pull/9609
* Remove function that gave impression everest was logging to azure by oyvindeide in https://github.com/equinor/ert/pull/9558
* Remove deprecated queue options by jonathan-eq in https://github.com/equinor/ert/pull/9501
* Avoid repeated logging for each cluster in misfit analysis by berland in https://github.com/equinor/ert/pull/9626
* Change needed for updated everest-models by frode-aarstad in https://github.com/equinor/ert/pull/9634
* Pin iterative_ensemble_smoother by berland in https://github.com/equinor/ert/pull/9644
* Set up dependabot for github actions by eivindjahren in https://github.com/equinor/ert/pull/9647
* Delete duplicate enum by oyvindeide in https://github.com/equinor/ert/pull/9638
* Avoid UserWarning when vmin==vmax in std_dev plot by berland in https://github.com/equinor/ert/pull/9659
* Add GEN_KW to heat equation and turn localization on by dafeda in https://github.com/equinor/ert/pull/9648
* Use resfo for snake_oil_simulator by eivindjahren in https://github.com/equinor/ert/pull/9667
* Make timestamps in dmesg output human readable by berland in https://github.com/equinor/ert/pull/9685
* Make realization number span attribute by HakonSohoel in https://github.com/equinor/ert/pull/9683
* Include spans for dark storage by HakonSohoel in https://github.com/equinor/ert/pull/9535
* Refactor preferred_num_cpu by frode-aarstad in https://github.com/equinor/ert/pull/9680
* Refactor update workflow signature by frode-aarstad in https://github.com/equinor/ert/pull/9688
* Fix run path tests by eivindjahren in https://github.com/equinor/ert/pull/9711
* Use fetch-depth 1024 instead of 0 by eivindjahren in https://github.com/equinor/ert/pull/9715
* Set span status if realization fails by HakonSohoel in https://github.com/equinor/ert/pull/9692
* Refactor BaseRunModel by frode-aarstad in https://github.com/equinor/ert/pull/9676
* Reduce time in update test by eivindjahren in https://github.com/equinor/ert/pull/9725
* Speed up tests by reusing plugin manager by eivindjahren in https://github.com/equinor/ert/pull/9740
* Change min realizations warning test from cli to unit by eivindjahren in https://github.com/equinor/ert/pull/9747
* Remove redundant tests by eivindjahren in https://github.com/equinor/ert/pull/9753
* Update test_model_factory.py by frode-aarstad in https://github.com/equinor/ert/pull/9764
* Clean up ert config tests by eivindjahren in https://github.com/equinor/ert/pull/9768
* Remove default site config by oyvindeide in https://github.com/equinor/ert/pull/9769
* Convert enum to lower case by oyvindeide in https://github.com/equinor/ert/pull/9776
* Add integration tests for parallel flow simulator by berland in https://github.com/equinor/ert/pull/9779
* Fix fetching with tags by eivindjahren in https://github.com/equinor/ert/pull/9795
* Speed up more tests by eivindjahren in https://github.com/equinor/ert/pull/9803
Build System
* Move egg test from komodo-releases by frode-aarstad in https://github.com/equinor/ert/pull/9801
Dependencies
* Bump astral-sh/setup-uv from 4 to 5 by dependabot in https://github.com/equinor/ert/pull/9651
* Bump pypa/gh-action-pypi-publish from 1.10.1 to 1.12.3 by dependabot in https://github.com/equinor/ert/pull/9652
* Bump codecov/codecov-action from 4 to 5 by dependabot in https://github.com/equinor/ert/pull/9650
* Upgrade pre-commits ruff 0.8.3 -> 0.8.6 by larsevj in https://github.com/equinor/ert/pull/9665
* Bump astral-sh/setup-uv from 4 to 5 by dependabot in https://github.com/equinor/ert/pull/9720
Other Changes
* Refactor the everest run model by verveerpj in https://github.com/equinor/ert/pull/9575
* Replace websockets with zmq by xjules in https://github.com/equinor/ert/pull/9173
* Fix changed functionality after refactoring testing for test_logging_setup and test_https_requests by DanSava in https://github.com/equinor/ert/pull/9622
* Use new version of iterative_ensemble_smoother by dafeda in https://github.com/equinor/ert/pull/9645
* Refactor config docs by oyvindeide in https://github.com/equinor/ert/pull/9610
* Add conda support to activation script by cmrqs in https://github.com/equinor/ert/pull/9436
* Remove job validation from everest config code by verveerpj in https://github.com/equinor/ert/pull/9668
* Non optional everest model and nonzero realizations by StephanDeHoop in https://github.com/equinor/ert/pull/9577
* Explicitly sort dicts in test_api_snapshots by yngve-sk in https://github.com/equinor/ert/pull/9675
* Remove test_run_egg_model by yngve-sk in https://github.com/equinor/ert/pull/9686
* Remove EXEC_ENV by berland in https://github.com/equinor/ert/pull/9690
* Update mac testing workflows by andreas-el in https://github.com/equinor/ert/pull/9716
* Speed up batching of events in evaluator by xjules in https://github.com/equinor/ert/pull/9736
* Increase Event reporter timeout after successful Finish event by xjules in https://github.com/equinor/ert/pull/9733
* Fix bug in docstring of ForwardModelStep by dafeda in https://github.com/equinor/ert/pull/9726
* Update forward model doc for FLOW by berland in https://github.com/equinor/ert/pull/9741
* Store everest results in ERT storage by yngve-sk in https://github.com/equinor/ert/pull/9161
* Revert "Store everest results in ERT storage" by yngve-sk in https://github.com/equinor/ert/pull/9756
* Use codspeed instead of benchmark.yml by eivindjahren in https://github.com/equinor/ert/pull/9759
* Use the configuration file as the everest server job name by verveerpj in https://github.com/equinor/ert/pull/9754
* Speedup everest tests by DanSava in https://github.com/equinor/ert/pull/9746
* Add more snapshots to test_api_summary_snapshot by yngve-sk in https://github.com/equinor/ert/pull/9780
* Fix recommended pytest command by eivindjahren in https://github.com/equinor/ert/pull/9786
* Simplify everest visualisation entry test by DanSava in https://github.com/equinor/ert/pull/9778
* Add optimization algorithms section in the documentation for the theory chapter by roliveira in https://github.com/equinor/ert/pull/9698
* Update outdated documentation mentioning archived EVEREST repository by DanSava in https://github.com/equinor/ert/pull/9802
* V13 backports by xjules in https://github.com/equinor/ert/pull/9862
* zmq: make sure to destroy evaluator context in case zmq fails on startup by xjules in https://github.com/equinor/ert/pull/9905
* Backport: Verify selection when refreshing current selection by andreas-el in https://github.com/equinor/ert/pull/9914

New Contributors
* roliveira made their first contribution in https://github.com/equinor/ert/pull/9698

**Full Changelog**: https://github.com/equinor/ert/compare/12.1.2...13.0.0

<!-- Release notes generated using configuration in .github/release.yml at version-13.0 -->

What's Changed
Bug Fixes
* Transpose the input to get_nr_primary_components in misfit preprocessor by larsevj in https://github.com/equinor/ert/pull/9939
* Verify selection when refreshing current selection by andreas-el in https://github.com/equinor/ert/pull/9914


**Full Changelog**: https://github.com/equinor/ert/compare/13.0.0-rc3...13.0.0-rc4

<!-- Release notes generated using configuration in .github/release.yml at version-13.0 -->

What's Changed
Other Changes
* zmq: make sure to destroy evaluator context in case zmq fails on startup by xjules in https://github.com/equinor/ert/pull/9905


**Full Changelog**: https://github.com/equinor/ert/compare/13.0.0-rc2...13.0.0-rc3

<!-- Release notes generated using configuration in .github/release.yml at version-13.0 -->

What's Changed
Other Changes
* V13 backports by xjules in https://github.com/equinor/ert/pull/9862


**Full Changelog**: https://github.com/equinor/ert/compare/13.0.0-rc1...13.0.0-rc2

<!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed
Bug Fixes
* Set permissions for transaction files to 0o660 by eivindjahren in https://github.com/equinor/ert/pull/9804
Maintenance
* Speed up more tests by eivindjahren in https://github.com/equinor/ert/pull/9803
Build System
* Move egg test from komodo-releases by frode-aarstad in https://github.com/equinor/ert/pull/9801
Other Changes
* Add optimization algorithms section in the documentation for the theory chapter by roliveira in https://github.com/equinor/ert/pull/9698
* Update outdated documentation mentioning archived EVEREST repository by DanSava in https://github.com/equinor/ert/pull/9802

New Contributors
* roliveira made their first contribution in https://github.com/equinor/ert/pull/9698

**Full Changelog**: https://github.com/equinor/ert/compare/13.0.0-rc0...13.0.0-rc1