Updates to #236 to avoid breaking change to `pybop.Optimisation` #309

BradyPlanden · 2024-04-26T00:19:46Z

Description

This PR applies changes to #236 so that v24.5 does not have breaking changes in the pybop.Optimisation API.

Issue reference

Fixes # N/A

Review

Before you mark your PR as ready for review, please ensure that you've considered the following:

Updated the CHANGELOG.md in reverse chronological order (newest at the top) with a concise description of the changes, including the PR number.
Noted any breaking changes, including details on how it might impact existing functionality.

Type of change

New Feature: A non-breaking change that adds new functionality.
Optimization: A code change that improves performance.
Examples: A change to existing or additional examples.
Bug Fix: A non-breaking change that addresses an issue.
Documentation: Updates to documentation or new documentation for new features.
Refactoring: Non-functional changes that improve the codebase.
Style: Non-functional changes related to code style (formatting, naming, etc).
Testing: Additional tests to improve coverage or confirm functionality.
Other: (Insert description of change)

Key checklist:

No style issues: $ pre-commit run (or $ nox -s pre-commit) (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
All unit tests pass: $ nox -s tests
The documentation builds: $ nox -s doctest

You can run integration tests, unit tests, and doctests together at once, using $ nox -s quick.

Further checks:

Code is well-commented, especially in complex or unclear areas.
Added tests that prove my fix is effective or that my feature works.
Checked that coverage remains or improves, and added tests if necessary to maintain or increase coverage.

Thank you for contributing to our project! Your efforts help us to deliver great software.

…sation APIs, updts where required, moves _optimisation to optimisers/

codecov · 2024-04-26T00:50:15Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.98%. Comparing base (afaf69e) to head (e4ca965).

Additional details and impacted files

@@                 Coverage Diff                  @@
##           236-scipy-kwargs     #309      +/-   ##
====================================================
+ Coverage             96.81%   96.98%   +0.16%     
====================================================
  Files                    40       41       +1     
  Lines                  2201     2222      +21     
====================================================
+ Hits                   2131     2155      +24     
+ Misses                   70       67       -3

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

examples/notebooks/optimiser_interface.ipynb

examples/scripts/spm_pso.py

pybop/optimisers/_optimisation.py

BradyPlanden · 2024-05-10T13:17:10Z

Ugh, the recent file rename messed with the number of changes. Happy to revert it to help with review, it's needed to remove circular import issue in the Optimisation class. @NicolaCourtier

NicolaCourtier · 2024-05-10T14:15:49Z

Yes please do revert it @BradyPlanden, let's change the filenames at the end once both PRs are ready.

…unit test

CHANGELOG.md

examples/notebooks/optimiser_interface.ipynb

tests/integration/test_parameterisations.py

pybop/optimisers/optimisation.py

…gestions

NicolaCourtier

Thanks @BradyPlanden for the addition of the Optimisation wrapper!

* Enable passing of kwargs to SciPy * Update checks on bounds * Add update_options and error for Pints * Rename opt to optim * Remove stray comments * Add BaseSciPyOptimiser and BasePintsOptimiser * Align optimiser option setting * Update notebooks with kwargs * Update scripts with kwargs * Update notebooks * Align optimisers with Optimisation as base class * Update stopping criteria in spm_NelderMead.py Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Update stopping criteria in spm_adam.py Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Update sigma0 in spm_descent.py Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Update GradientDescent * Change update to set and check pints_method * Update test_optimisation_options * Update notebooks * Update set learning rate * Pop threshold * Fix bug in model.simulate * Update notebooks * Update test_models.py * Store SciPy result * Update x0 input and add tests * Update bounds to avoid x0 outside * Re-initialise pints_method on certain options * Update x0_new test * Update test_optimisation.py * Create initialise_method for PINTS optimisers * Align optimisation result * Update checks on bounds * Apply suggestions Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Add standalone optimiser * Simplify optimiser set-up and align _minimising * Update option setting in notebooks * Take abs of cost0 * Implement suggestions from Brady * Update tests and base option setting * Update test_invalid_cost * Increase coverage * Sort out notebook changes * Reset scale parameter * Move settings into arguments * Update comments * Update optimiser call * Move check on jac * Add assertions * Add maxiter to test * Add assertion * Update to lambda functions Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Update comment Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Update to list comprehension Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com> * Formatting * Revert "Update to lambda functions" This reverts commit aa73bff. * Move minimising out of costs * Update description * Updates to #236 to avoid breaking change to `pybop.Optimisation` (#309) * Splits Optimisation -> BaseOptimiser/Optimisation, enables two optimisation APIs, updts where required, moves _optimisation to optimisers/ * increase coverage * Pass optimiser_kwargs though run() * updt examples * Converts DefaultOptimiser -> Optimisation * split Optimisation and BaseOptimsier classes, loosen standalone cost unit test * add incorrect attr test * fix: updt changelog entry, optimsation_interface notebook, review suggestions * fix: updt notebook state * Updt assertions, optimisation object name --------- Co-authored-by: NicolaCourtier <45851982+NicolaCourtier@users.noreply.github.com> * Rename method to pints_optimiser * Rename base_optimiser to pints_base_optimiser * Rename _optimisation to base_optimiser --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>

Splits Optimisation -> BaseOptimiser/Optimisation, enables two optimi…

c3f14ea

…sation APIs, updts where required, moves _optimisation to optimisers/

increase coverage

288d929

BradyPlanden requested a review from NicolaCourtier April 26, 2024 12:26

NicolaCourtier added 2 commits April 26, 2024 14:50

Pass optimiser_kwargs though run()

e5093ce

Merge branch '236-scipy-kwargs' into 236b-scipy-kwargs

e360fdf

NicolaCourtier reviewed Apr 26, 2024

View reviewed changes

examples/notebooks/optimiser_interface.ipynb Show resolved Hide resolved

examples/scripts/spm_pso.py Outdated Show resolved Hide resolved

pybop/optimisers/_optimisation.py Outdated Show resolved Hide resolved

updt examples

831c524

BradyPlanden mentioned this pull request Apr 26, 2024

Restructure optimisers to enable passing of kwargs #255

Merged

14 tasks

NicolaCourtier added the blocker An issue which must be resolved before work can resume on other issues. label Apr 27, 2024

BradyPlanden requested a review from NicolaCourtier May 7, 2024 19:37

BradyPlanden added 2 commits May 10, 2024 13:14

Merge branch '236-scipy-kwargs' into 236b-scipy-kwargs

7e6f4fb

Converts DefaultOptimiser -> Optimisation

5698e4a

split Optimisation and BaseOptimsier classes, loosen standalone cost …

5652597

…unit test

BradyPlanden force-pushed the 236b-scipy-kwargs branch from cde3d07 to 5652597 Compare May 10, 2024 15:04

add incorrect attr test

10d4df8

NicolaCourtier reviewed May 13, 2024

View reviewed changes

pybop/optimisers/optimisation.py Outdated Show resolved Hide resolved

BradyPlanden added 2 commits May 15, 2024 17:24

fix: updt changelog entry, optimsation_interface notebook, review sug…

fca8968

…gestions

fix: updt notebook state

ffbd9c7

BradyPlanden requested a review from NicolaCourtier May 16, 2024 07:45

NicolaCourtier approved these changes May 16, 2024

View reviewed changes

BradyPlanden added 2 commits May 22, 2024 09:29

Merge branch '236-scipy-kwargs' into 236b-scipy-kwargs

852d45f

Updt assertions, optimisation object name

e4ca965

NicolaCourtier merged commit dec74d7 into 236-scipy-kwargs May 22, 2024
29 checks passed

NicolaCourtier deleted the 236b-scipy-kwargs branch May 22, 2024 15:45

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Updates to #236 to avoid breaking change to `pybop.Optimisation` #309

Updates to #236 to avoid breaking change to `pybop.Optimisation` #309

BradyPlanden commented Apr 26, 2024 •

edited

Loading

codecov bot commented Apr 26, 2024 •

edited

Loading

BradyPlanden commented May 10, 2024

NicolaCourtier commented May 10, 2024

NicolaCourtier left a comment

Updates to #236 to avoid breaking change to pybop.Optimisation #309

Updates to #236 to avoid breaking change to pybop.Optimisation #309

Conversation

BradyPlanden commented Apr 26, 2024 • edited Loading

Description

Issue reference

Review

Type of change

Key checklist:

Further checks:

codecov bot commented Apr 26, 2024 • edited Loading

Codecov Report

BradyPlanden commented May 10, 2024

NicolaCourtier commented May 10, 2024

NicolaCourtier left a comment

Choose a reason for hiding this comment

Updates to #236 to avoid breaking change to `pybop.Optimisation` #309

Updates to #236 to avoid breaking change to `pybop.Optimisation` #309

BradyPlanden commented Apr 26, 2024 •

edited

Loading

codecov bot commented Apr 26, 2024 •

edited

Loading