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Rt notebook example#1522

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I-Bouros wants to merge 79 commits intopints-team:mainpints-team/pints:mainfrom I-Bouros:rt-notebookI-Bouros/pints:rt-notebookCopy head branch name to clipboard

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Commits on Feb 16, 2021

• pints-team#1294 functional test HaarioBardenet

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• @1294 add copyright notice

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• pints-team#1294 exclude functional tests from coverage rep

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• pints-team#1294 add copyright notice

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• pints-team#1294 flake8

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Commits on Feb 22, 2021

• Make test importable

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• Return a string of the class name

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• Add skeleton for functional testing workflow

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• Merge branch 'master' into issue-1294-functional-testing-module

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• I think this is the correct syntax for not running on draft pr...

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• Try committing changes to functional testing

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• Fix syntax

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• Remove diff

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Commits on Feb 23, 2021

• Bump

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• Bump

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• Bump

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Commits on Mar 15, 2021

• pints-team#1294 update structure

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Commits on Mar 16, 2021

• pints-team#1294 allow setting of hyper parameters

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Commits on Mar 22, 2021

• Added banana problem

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• Added gaussian and banana tests for differential evolution

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Commits on Mar 23, 2021

• Moved controller initialisation methods to parent class

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• Added dream

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• Added Haario to functional tests

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• added functional tests for emcee hammer

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• Added sample sizes as optional parameter for tests

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Commits on Mar 24, 2021

• Added high dim Gaussian problem

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Commits on Apr 19, 2021

• Merge branch 'master' into issue-1294-functional-testing-module

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• Added nuts problems

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Commits on Apr 20, 2021

• Added correlated Gaussian and started to add DRAM but found a bug

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• Added banana test for dram

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• Simplified starting points for problems.

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• Added correlated Gaussian test for haario-bardenet

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• Corrected func test name for haario bardenet

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• Update haario_bardenet_acmc.py

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• Added annulus problem for Haario-bardenet

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Commits on Apr 26, 2021

• expose some more functional tests

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• bump

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Commits on May 4, 2021

• Merge branch 'master' into issue-1294-functional-testing-module

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• Added problems for emcee hammer

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• Added cone problem

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Commits on May 5, 2021

• Added monomial gamma problems

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Commits on May 25, 2021

• Delete empty ending line

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• Rename to haario_acmc.py and add correlated Gaussian problem

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Commits on May 28, 2021

• add correlated gaussian and annulus to differential evolution functests

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Commits on May 31, 2021

• add correlated gaussian and annulus to dream functests

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Commits on Aug 10, 2021

• Add problems for Metropolis functests

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• add relativistic problems

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• Functional testing for slice stepout

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• update relativistic functional test hyperparameters

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• Merge branch 'issue-1294-functional-testing-module' of https://github.com/pints-team/pints into issue-1294-functional-testing-module

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• Merge branch 'master' into issue-1294-functional-testing-module

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Commits on Aug 11, 2021

• Updated tests for Population MCMC.

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• Made all functional test classes modules have names that match the methods they test (underscores instead of camelcase).

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• Removed 'test_method_on' prefix from all functional tests, so they can be called as e.g. 'differential_evaluation_mcmc.two_dim_gaussian()'.

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• Updated the way functionaltest modules and problem classes are imported.

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• Removed 'from __future__' imports.

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• Added docstrings to functional tests.

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• Updated way iterations and warmup is set in functional tests.

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• Added functional test discovery mechanism.

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Commits on Aug 12, 2021

• Add MALA methods

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Commits on Aug 16, 2021

• Merge pull request pints-team#1388 from pints-team/mala

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• Merge branch 'issue-1294-functional-testing-module' into func-test-organising

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• Updated new MALA tests.

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• Updated new MALA tests.

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• Made ft warmup a user-set parameter.

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• Slightly simplified ft code.

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Commits on Aug 17, 2021

• Merge pull request pints-team#1386 from pints-team/func-test-organising

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• Renamed function to change point tests. Closes pints-team#1391.

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• Merge branch 'master' into issue-1294-functional-testing-module

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Commits on Aug 24, 2021

• Changed 'ft' to 'cpt'.

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• Added flag to ignore unused import in cptests.__init__

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• Merge pull request pints-team#1392 from pints-team/func-test-rename

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• Fixed merge issue in workflows.

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• Updated workflow

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Commits on Dec 5, 2023

• Update NUTS functional tests

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Commits on Mar 22, 2024

• Upload Rt estimation notebook

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• update README.md

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• correct notebook name

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Commits on Mar 25, 2024

• Merge branch 'pints-team:main' into rt-notebook

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