Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adds Transformation class #357

Merged
merged 25 commits into from
Aug 1, 2024

Conversation

BradyPlanden
Copy link
Member

@BradyPlanden BradyPlanden commented Jun 12, 2024

Description

Adds a transformation class for BaseCost classes. This class applies a transformation to the parameter space to a latent space for improved optimisation / sampling.

Issue reference

Fixes #92

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.

@BradyPlanden BradyPlanden linked an issue Jun 12, 2024 that may be closed by this pull request
Copy link

codecov bot commented Jun 12, 2024

Codecov Report

Attention: Patch coverage is 99.17012% with 2 lines in your changes missing coverage. Please review.

Project coverage is 98.28%. Comparing base (ce22494) to head (8dca6d1).
Report is 3 commits behind head on develop.

Files Patch % Lines
pybop/optimisers/base_pints_optimiser.py 83.33% 1 Missing ⚠️
pybop/transformation/base_transformation.py 97.77% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #357      +/-   ##
===========================================
+ Coverage    98.07%   98.28%   +0.20%     
===========================================
  Files           44       46       +2     
  Lines         2697     2907     +210     
===========================================
+ Hits          2645     2857     +212     
+ Misses          52       50       -2     

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

@BradyPlanden BradyPlanden marked this pull request as ready for review June 18, 2024 08:10
@BradyPlanden BradyPlanden mentioned this pull request Jun 19, 2024
18 tasks
@BradyPlanden BradyPlanden force-pushed the 92-transformations-for-varying-scale-parameters branch from 3ba0b1f to 4e1f845 Compare July 3, 2024 09:43
examples/scripts/spm_CMAES.py Outdated Show resolved Hide resolved
pybop/optimisers/base_pints_optimiser.py Outdated Show resolved Hide resolved
pybop/optimisers/base_pints_optimiser.py Outdated Show resolved Hide resolved
pybop/optimisers/base_pints_optimiser.py Outdated Show resolved Hide resolved
pybop/optimisers/base_pints_optimiser.py Outdated Show resolved Hide resolved
Copy link
Member

@NicolaCourtier NicolaCourtier left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great work implementing the transformation classes! To retain modularity, let's make transformation a property of the Parameters class (as well as each Parameter) instead of the cost/optimiser.

examples/standalone/cost.py Show resolved Hide resolved
pybop/costs/base_cost.py Outdated Show resolved Hide resolved
pybop/parameters/parameter.py Outdated Show resolved Hide resolved
pybop/costs/base_cost.py Outdated Show resolved Hide resolved
Copy link
Member

@NicolaCourtier NicolaCourtier left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @BradyPlanden, transformations look like a useful addition!

pybop/parameters/parameter.py Outdated Show resolved Hide resolved
@BradyPlanden BradyPlanden force-pushed the 92-transformations-for-varying-scale-parameters branch from 3fd3ea3 to 8dca6d1 Compare August 1, 2024 13:46
@BradyPlanden BradyPlanden merged commit 66cf05f into develop Aug 1, 2024
30 checks passed
@BradyPlanden BradyPlanden deleted the 92-transformations-for-varying-scale-parameters branch August 1, 2024 14:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Transformations for varying scale parameters
2 participants