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Make v24.3 #220

Merged
merged 430 commits into from
Mar 25, 2024
Merged

Make v24.3 #220

merged 430 commits into from
Mar 25, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Feb 8, 2024

  1. style: pre-commit fixes

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  2. Update UKF example plotting

    @NicolaCourtier
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  3. Update simulate

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Commits on Feb 9, 2024

  1. Add BaseModel tests

    @BradyPlanden
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  2. Merge pull request #167 from pybop-team/162-update-design-optimisatio… 

    …n-functionality

Design Optimisation Refactor and Additions
    @BradyPlanden
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  3. Add M1 GitHub runners, Updt. self-hosted

    @BradyPlanden
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  4. Updt changelog

    @BradyPlanden
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  5. Remove M1 tests on unsupported python versions

    @BradyPlanden
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  6. Add VolumetricEnergyDensity example (#191) 

    * Add VolumetricEnergyDensity example

* Update CHANGELOG.md

* Update test_cost.py

* Update example to pass coverage tests

* Split cost classes by type

* Add DesignCost to init

* Update error checking
    @NicolaCourtier
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  7. Revert file names

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  8. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  9. Re-implement change to BaseCost

    @NicolaCourtier
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  10. Separate off plot_parameters

    @NicolaCourtier
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  11. style: pre-commit fixes

    @pre-commit-ci
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  12. Move plot_parameters in init

    @NicolaCourtier
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  13. Update spm_electrode_design.ipynb

    @NicolaCourtier
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  14. Re-implement design changes to quick_plot

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Commits on Feb 11, 2024

  1. #123 rename: release-action to release_action

    @agriyakhetarpal
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  2. #123 add custom script to dynamically generate matrix

    @agriyakhetarpal
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  3. #123 run script, pass generated matrix to next job

    @agriyakhetarpal
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  4. #123 make script executable prior to running it

    @agriyakhetarpal
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  5. #123 don't allow running M-series builds on forks

    @agriyakhetarpal
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  6. #123 don't use git update-index for file permissions

    @agriyakhetarpal
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  7. #123 move script to a dedicated scripts/ci/ folder

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  8. #123 correctly sparse checkout the matrix script

    @agriyakhetarpal
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  9. #123 fix up script to return valid JSON

    @agriyakhetarpal
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  10. #123 simplify GitHub Actions output processing

    @agriyakhetarpal
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  11. #123 convert JSON to string before parsing

    @agriyakhetarpal
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  12. #123 move output before all jobs and test

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  13. #123 don't convert JSON output to raw strings

    @agriyakhetarpal
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  14. #123 matrix script is working now, clean it up

    @agriyakhetarpal
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  15. #123 specify a prettified job name via matrix variables

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Commits on Feb 12, 2024

  1. #123 temporarily fetch last three versions, not four

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  2. #123 add PYBOP_SCHEDULED and PYBAMM_VERSION

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  3. #123 configure PYBAMM_VERSION env var

    @agriyakhetarpal
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  4. chore: update pre-commit hooks 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.2.1](astral-sh/ruff-pre-commit@v0.2.0...v0.2.1)
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Commits on Feb 13, 2024

  1. Merge pull request #194 from pybop-team/pre-commit-ci-update-config 

    chore: update pre-commit hooks
    @BradyPlanden
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  2. Lengthen test data, updat init_soc for test, flip higher cost solutio… 

    …n point
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  3. Merge branch 'develop' into 187-add-m-series-github-runners-to-tests

    @BradyPlanden
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  4. Merge branch '187-add-m-series-github-runners-to-tests' into 196-bug-… 

    …observer-tests-fail-on-m-series-hardware-macos-140
    @BradyPlanden
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  5. Merge pull request #197 from pybop-team/196-bug-observer-tests-fail-o… 

    …n-m-series-hardware-macos-140

Fixes failing observer tests
    @martinjrobins
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  6. Updt. Changelog for #196 addition

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  7. Merge pull request #188 from pybop-team/187-add-m-series-github-runne… 

    …rs-to-tests

Add M1 GitHub runner and update scheduled tests
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  8. #123 merge develop

    @agriyakhetarpal
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  9. #123 add feature note to CHANGELOG

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Commits on Feb 14, 2024

  1. #123 moving forward with PyBaMM parameter set check 

    Coverage is already up for this, this is just for PyBaMM 23.5
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  2. #123 update CHANGELOG under bug fixes

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Commits on Feb 16, 2024

  1. Update subplot widths, test_plotting dataset access, remove square br… 

    …ackets from plots as per SI standard, quick plot for varying length signals, add pybop.is_numeric and restore design cost exception for optimisation
    @BradyPlanden
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  2. Update pybop/plotting/plot_convergence.py 

    Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
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  3. Update pybop/plotting/plot_cost2d.py 

    Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
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  4. Merge pull request #193 from agriyakhetarpal/test-against-pybamm 

    Create dynamic GitHub Actions matrix to test against PyBaMM
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  5. docs: update README.md [skip ci]

    @allcontributors
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  6. docs: update .all-contributorsrc [skip ci]

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  7. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  8. Update plot_cost2d.py

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  9. Update README.md

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  10. Merge pull request #199 from pybop-team/all-contributors/add-agriyakh… 

    …etarpal

docs: add agriyakhetarpal as a contributor for code, and infra
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  11. Make PyBOP version private attr, use importlib.metadata

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  12. Remove distutils & metadata boilerplate, shift to PEP517

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  13. Move pytest, ruff config to pyproject.toml

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  14. Migrate to pyproject.toml (declarative metadata)

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  15. Add CHANGELOG entry for pyproject.toml

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  16. Split integration and unit tests, update pytest --examples, additiona… 

    …l scheduled workflow trigger, add test_parameterisation cost/optimiser test matrix
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  17. Merge branch 'develop' into 139-split-integration-unit-tests

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  18. updt coverage action for style

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Commits on Feb 17, 2024

  1. Add matrix to m-series runner

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  2. Add filtered matrix job, update m-series env

    @BradyPlanden
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  3. Update .github/workflows/scheduled_tests.yaml 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
    @BradyPlanden @agriyakhetarpal
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  4. Restores pyenv environment initialisation

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  5. os bug patch

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  6. revert to single item nox calls

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  7. updt. filtered item name

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  8. Merge develop

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  9. Merge branch 'develop' into 18-how-to-handle-structural-parameters

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  10. revert @staticmethod definition for list_of_examples

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  11. Merge pull request #205 from pybop-team/193-patch-m-series 

    Patch for #193 - Add matrix to M-series runner
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Commits on Feb 19, 2024

  1. Merge pull request #182 from MarkBlyth/develop 

    Allow square-brackets access to dataset objects
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  2. update Python version requirements to remove 3.12 

    Co-Authored-By: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
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  3. Merge branch 'develop' into 139-split-integration-unit-tests

    @BradyPlanden
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  4. Make notes about [dev] and [docs] extras, revise config

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  5. Add the [dev] extras (pytest, nbmake, pre-commit)

    @agriyakhetarpal
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  6. Use [dev] extras for nox session invocations

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  7. Merge branch 'develop' into 177-plotting-capabilities

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  8. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  9. Remove duplicate getitem

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  10. Merge pull request #203 from agriyakhetarpal/add-pep517/518-pyproject 

    Add PEP517/518 `pyproject.toml` support
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  11. Inital benchmarking setup, suite

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  12. Merge branch 'develop' into 179-add-airspeed-velocity-for-automated-b… 

    …enchmarking
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  13. Updt. asv config, changelog, parameterisaton benchmarks

    @BradyPlanden
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  14. chore: update pre-commit hooks 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](astral-sh/ruff-pre-commit@v0.2.1...v0.2.2)
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  15. Merge branch 'develop' into 18-how-to-handle-structural-parameters

    @BradyPlanden
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  16. Change spm_CMAES example to geometric parameters, add true_value to p… 

    …arameter cls, bigfix geometric logic in problem cls
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Commits on Feb 20, 2024

  1. Add tests for pybop parameters

    @BradyPlanden
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  2. Merge pull request #208 from pybop-team/pre-commit-ci-update-config 

    chore: update pre-commit hooks
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  3. bump upper python version

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  4. updt test_on_push workflow for 3.12

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  5. Updts python matrix for scheduled tests

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  6. Updt. matrix generation for incompatible pybamm/python versions

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  7. updt workflow order to ensure self-hosted runner starts in parallel

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  8. Update .github/workflows/scheduled_tests.yaml 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  9. Updt to filter with jq

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Commits on Feb 21, 2024

  1. revert build trigger, requires create_matrix for matrix, filter_matri… 

    …x for timing
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  2. Updt Changelog, rm redundant example

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  3. Add 23.9 / 3.12 to filter

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  4. Add tests for rebuild, and increase pybop.parameter tests

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  5. Updt problem tests, revert model_tests

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  6. remove redundant rebuild condition

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  7. remove missed merge delete

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  8. Merge pull request #169 from pybop-team/18-how-to-handle-structural-p… 

    …arameters

Add fitting functionality for geometric parameters
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  9. Merge pull request #209 from pybop-team/206-support-python-312 

    Add Python 3.12
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  10. Patch: add changelog entry for #206

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  11. Merge branch 'develop' into 179-add-airspeed-velocity-for-automated-b… 

    …enchmarking
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  12. Add peridoci benchmark workflow and nox session

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  13. updt results path for upload

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  14. Merge branch 'develop' into 139-split-integration-unit-tests

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  15. Create --plots pytest marker, add xdist to non-plots nox test session… 

    …s, automate the skip marker procedure
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  16. Merge branch 'develop' into 177-plotting-capabilities

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Commits on Feb 22, 2024

  1. Add plotting support for notebook rendering, adds kaleido as dependancy

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  2. + diffevolution notebook

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  3. Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

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  4. fix missed deletion during merge

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  5. Update test_on_push workflow to add examples and integration, updates… 

    … coverage to use parallel workers where possible
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  6. relax integration asserts

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  7. Split test_on_push jobs, reduce integration and example tests to 3.11

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  8. Add PR template, updt. docs conf.py path definition, add doc tests, a… 

    …dd noxfile sessions
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  9. Merge branch '139-split-integration-unit-tests' into 185-add-pull-req… 

    …uest-template
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  10. Updt. conftest for --docs arg

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Commits on Feb 23, 2024

  1. Update .github/workflows/test_on_push.yaml 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  2. Update noxfile.py 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  3. Update noxfile.py 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  4. style: pre-commit fixes

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  5. convert to session.install()

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  6. updt pytest default opts, test_on_push python vers

    @BradyPlanden
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  7. 139b Add unit tests for plotting and Thevenin model (#212) 

    * Create test_plots.py

* Parametrize test_models

* Add check on n_states

* Add test for json parameter set

* Add test for json export

* Add test for invalid max values

* Add optimisation tests

* Add observer tests

* Add tests on observer evaluate

* Add tests on invalid parameter inputs

* Add invalid sample size tests
    @NicolaCourtier
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  8. Updt. CHANGELOG

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  9. Merge pull request #204 from pybop-team/139-split-integration-unit-tests 

    Splits integration / examples / unit tests
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  10. Merge branch 'develop' into 185-add-pull-request-template

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  11. Updt. Changelog

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  12. Merge branch 'develop' into 177-plotting-capabilities

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  13. Add release_workflow.md, updt. release_action.yaml

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  14. Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

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  15. Update test_plots.py

    @NicolaCourtier
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  16. Update .github/release_workflow.md 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  17. remove API tokens

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  18. Add condition for main repository only on publish

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  19. Updt. Changelog

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  20. markdown format fix

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  21. Merge pull request #215 from pybop-team/157-add-release_workflowmd 

    Update release workflow
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  22. Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

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Commits on Feb 24, 2024

  1. Increment to Python 3.12, fix typos, add push trigger to workflow 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  2. Updt. nox session name

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  3. Updt. nox benchmarks session, tests for CI on benchmark workflow, rem… 

    …ove unused pandas dependancy
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  4. Merge branch 'develop' into 179-add-airspeed-velocity-for-automated-b… 

    …enchmarking
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  5. asv installation, calls

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Commits on Feb 26, 2024

  1. Add gaussian likelihoods, update optimisation cls to for likelihood d… 

    …efinition, add probablilitybased cost function, Add MLE example
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  2. fix mistyped min_iterations

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  3. add property decorator for private n_paramters

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  4. increment versions

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Commits on Feb 28, 2024

  1. updt architecture image, remove stale assets

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Commits on Feb 29, 2024

  1. Merge pull request #221 from pybop-team/update-readme-remove-assets 

    Remove stale assets, update architecture fig
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  2. Update to allow no bounds (#213) 

    * Remove bounds from Adam example

* Add tests with no bounds

* Remove unused bounds from examples

* Update to allow subset of bounds

* Add mean and sigma as properties

* Update CHANGELOG.md

* Improve readability of bounds and sigma logic

Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>

* Fix sigma0 description for SNES
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  3. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  4. Merge branch 'develop' into 177-plotting-capabilities

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Commits on Mar 1, 2024

  1. Revamp model, problem, and cost object from numpy arrays to dictionar… 

    …y. Update tests, add base model classes to init, cleaner multi-signal interaction
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  2. Fix ukf examples, temporarily limits ukf to signal output model

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Commits on Mar 2, 2024

  1. default_variables to additional_variables w/ docstrings, updt. observ… 

    …er tests, dict output observer.evaluate()
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Commits on Mar 4, 2024

  1. Fix integration test logic, add gradient landscape plots, pin pytest … 

    …version due to breaking change in 8.1.0
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  2. Add tests for gradient plots, up coverage

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  3. Set default SciPyMinimize method to Nelder-Mead, clean-up repo

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  4. Merge branch 'develop' / Add unit tests

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Commits on Mar 5, 2024

  1. _sigma -> sigma0, updt tests

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  2. Add ProbabilityBased cost tests, Updt. changelog

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  3. updt cost tests, add set_fail_gradient to RootMeanSquared cost function

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  4. Merge branch 'develop' into 185-add-pull-request-template

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  5. fix nox doctest session, pytest docs update

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  6. add plots session, update nox session installs

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Commits on Mar 6, 2024

  1. update contributing.md

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  2. Merge pull request #214 from pybop-team/185-add-pull-request-template 

    Adds PR Template
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Commits on Mar 7, 2024

  1. Merge branch 'develop' into 177-plotting-capabilities

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Commits on Mar 8, 2024

  1. unicode fix for win notebooks, update prediction shape checks, remove… 

    … Discharge capacity as default additional_variable
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  2. Merge branch 'develop' into 210-add-likelihood-classes

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  3. Make likelihoods a type of cost (#230) 

    * Move _likelihoods.py to /costs

* Make BaseLikelihood a type of cost

* Update test_cost

* Update n_parameters to _n_parameters

* Move n_parameters property

* Change _minimising to Boolean

* Update _likelihoods.py
    @NicolaCourtier
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  4. Updt tests, add optional x0 arg to optimisation cls, remove redundant… 

    … __init__ variables from baselikelihood, updt basecost to align with baselikelihood args
    @BradyPlanden
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  5. Fix basecost.evaluateS1 tuple negate, up coverage via integration add… 

    …itions, small bugfixes to basecost
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  6. Merge pull request #218 from pybop-team/210-add-likelihood-classes 

    Adds Base Likelihoods, Maximum Likelihood Example
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  7. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  8. Update spm_MLE example

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Commits on Mar 12, 2024

  1. chore: update pre-commit hooks 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.2](astral-sh/ruff-pre-commit@v0.2.2...v0.3.2)
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  2. style: pre-commit fixes

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Commits on Mar 13, 2024

  1. Merge pull request #234 from pybop-team/pre-commit-ci-update-config 

    chore: update pre-commit hooks
    @BradyPlanden
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  2. Updt. cost2d/optim2d x0 shape/colour, revert conftest win platform un… 

    …icode, add infeasible unit test
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  3. Updt SciPy & BaseOptimiser for maximum iterations limit - fixes #237

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  4. add infeasible cost tests, remove redundant scipyminimise maxiter opt… 

    …ions check
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  5. Merge pull request #224 from pybop-team/177c-plotting-capabilities 

    Datatype restructure for optimisation objects
    @BradyPlanden
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Commits on Mar 14, 2024

  1. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  2. Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

    @BradyPlanden
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Commits on Mar 15, 2024

  1. Updt grad descent hypers for likelihood tests, add tol arg to scipy o… 

    …ptimisers, pass optimiser final cost as is
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  2. Split kaleido dependancy to avoid windows hang

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  3. small refactors and cleanup

    @BradyPlanden
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  4. Updt changelog

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  5. Additional benchmarks, updt build wheels

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  6. Merge branch 'develop' into 179-add-airspeed-velocity-for-automated-b… 

    …enchmarking
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  7. updt permissions for deployment

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  8. add --global arg to git config

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Commits on Mar 16, 2024

  1. Limit workflow to pybop repo 

    Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
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  2. Add random seed, updt branch target, increment python for publish job… 

    … in workflow
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Commits on Mar 17, 2024

  1. Updt benchmark intial soc, add tracking of optimisation results, incr… 

    …ement default_max_unchanged_iterations for more stable default
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Commits on Mar 18, 2024

  1. Adds benchmark badge

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  2. Merge pull request #207 from pybop-team/179-add-airspeed-velocity-for… 

    …-automated-benchmarking

[WIP]: Add asv benchmarking
    @BradyPlanden
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  3. Fix workflow for changing experiment (#240) 

    * Update if statement

* Update base_model.py

* Create test_model_experiment_changes.py

* Restrict import

* Rebuild model on problem definition

* Update CHANGELOG.md

* Update t_eval
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
    @NicolaCourtier
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  4. Merge branch 'develop' into 177-plotting-capabilities

    @NicolaCourtier
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  5. chore: update pre-commit hooks 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3)
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Commits on Mar 19, 2024

  1. Merge pull request #242 from pybop-team/pre-commit-ci-update-config 

    chore: update pre-commit hooks
    @BradyPlanden
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  2. patch benchmarks for solution tracking

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  3. updt coverage, bugfix sigma check/wrap

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  4. Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

    @BradyPlanden
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  5. Merge pull request #243 from pybop-team/patch-benchmarks 

    Patch: benchmark solution tracking
    @BradyPlanden
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  6. coverage, bugfix model.simulateS1

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  7. Merge pull request #198 from pybop-team/177b-plotting-capabilities 

    Additions to #177
    @BradyPlanden
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  8. Add ruff import lint, run across codebase

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Commits on Mar 20, 2024

  1. updt. changelog

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  2. Update to n_time_data and add two_signal test

    @NicolaCourtier
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  3. style: pre-commit fixes

    @pre-commit-ci
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  4. Test standard plot and plot_trajectories

    @NicolaCourtier
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  5. Add test_with_ipykernel

    @NicolaCourtier
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  6. style: pre-commit fixes

    @pre-commit-ci
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  7. Re-add test_with_ipykernel

    @NicolaCourtier
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  8. Update test_plots.py

    @NicolaCourtier
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  9. Rename plot_cost2d as plot2d

    @NicolaCourtier
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  10. Merge plot_optim2d with plot2d

    @NicolaCourtier
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  11. Update scripts to plot2d

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  12. Update notebooks to plot2d

    @NicolaCourtier
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  13. Update spm_MLE.py

    @NicolaCourtier
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  14. Update filename to plot2d

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  15. Rename plot_cost2d.py to plot2d.py

    @NicolaCourtier
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  16. Fix typo in error message

    @NicolaCourtier
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  17. Reduce init_soc in test_model_misparameterisation

    @NicolaCourtier
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Commits on Mar 21, 2024

  1. Update ipykernel print to assert 

    Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
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    NicolaCourtier and BradyPlanden authored Mar 21, 2024
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  2. Fix version check

    @NicolaCourtier
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  3. Merge pull request #178 from pybop-team/177-plotting-capabilities 

    Update plotting capabilities and dataset restructure
    @NicolaCourtier
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  4. Merge branch 'develop' into v24.2

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  5. Merge branch 'develop' into 244-add-reorder-python-imports-to-pre-commit

    @BradyPlanden
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  6. style: pre-commit fixes

    @pre-commit-ci
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  7. Merge pull request #245 from pybop-team/244-add-reorder-python-import… 

    …s-to-pre-commit

Adds import linting with ruff
    @BradyPlanden
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Commits on Mar 25, 2024

  1. Updt model.simulateS1, refactor cost evaluates for object change + si… 

    …mplify, updt. tests
    @BradyPlanden
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  2. updt changelog

    @BradyPlanden
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  3. move changelog entry to bugfix

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  4. Merge pull request #260 from pybop-team/259-bug-incorrect-gradient-ob… 

    …ject-from-basemodels1

Fix gradient calculation from `model.simulateS1`
    @BradyPlanden
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  5. Merge branch 'develop' into v24.2

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  6. increment versions to v24.3

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