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Merging dev to Fay's branch#63

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FayFrost107 merged 121 commits intoFays-sandboxalan-turing-institute/ModularCirc:Fays-sandboxfrom

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Apr 17, 2025

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Commits on Feb 10, 2025

• adding pre-commit to toml

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• adding balck, flake8 and isort packages. creating pre-commit-config.yaml file

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• adding packages to pre-commit file

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• fixing formatting errors by adding an escape character to backslashes

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• updating the pre-commit yaml

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• updating the precommit file name

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Commits on Feb 11, 2025

• removing KorakianitisMixedModel tests and expected outputs for this branch

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• merging dev into 24-test-naghavi-model including updated gh ci, readme, toml, and some formatting fixes

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Commits on Mar 3, 2025

• basic copilot suggested test for solver as a scaffold

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Commits on Mar 6, 2025

• adding tests for initialize_by_function() function

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Commits on Mar 7, 2025

• reordered placement of properties and functions in the Solver.py, for better readability

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• adding tests for optimize function and initialize_by_function function

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• adding a random seed setter to the solver test

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• added a test for pv_dfdt_update function

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• added a test for the solve() function

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• fixing the tests and file names

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• separating out different tests in the solver test

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• fixed some tests and added docstrings

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Commits on Mar 10, 2025

• updating Naghavi tests. Copied over from KMM tests

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• Merge pull request #44 from alan-turing-institute/38-solver-tests

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• updating the tests

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• Merge branch 'dev' into 24-test-naghavi-model

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• Add missing JSON file from dev branch

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• added Naghavi expected outputs;

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• working on the tests

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• fixing Naghavi components being tested

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Commits on Mar 11, 2025

• documentation of solver

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Commits on Mar 12, 2025

• adaptable cycle slicing

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• reducing the number of cycles needed in the test

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Commits on Mar 18, 2025

• attemp #1 at fix

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• small change to plotting tools to make sure that change in solver is reflecte in plotting as well

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• removed redundant printout

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• update the tests to account for the correction of the time shift

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• removed pyc files

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• added *pyc to .gitignore

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Commits on Mar 19, 2025

• Merge pull request #47 from alan-turing-institute/46-remove-dt-shift-from-solution

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• Merge remote-tracking branch 'origin/dev' into dev

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• adding step in range of cycles to solver.

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• fixed edge case where _Nconv was not initialized when solver failed to converge

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Commits on Mar 20, 2025

• comment updates and formatting

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• removed self._N_psv and self._N_ssv variables since they are not used anywhere in the codebase

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• just adding more comments

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Commits on Mar 26, 2025

• minor formatting and enhanced docstrings for initialize_by_function function

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• further enhancing docstrings

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• enhancing documentation for s_u_update

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• s_u_update() function argument y was defined as y:np.ndarray[float,float] which is not syntactically right. Changed do np.ndarray[float].

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• s_u_update() function argument y was defined as y:np.ndarray[float,float] which is not syntactically right. Changed do np.ndarray[float].

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• minor formatting

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• updated the solver test to test for multiple step sizes

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• updated the solver tests to include testing for multiple sizes

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• adding 7 for step_sizes for solver tests

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Commits on Mar 27, 2025

• Adding a sandbox folder for exploratory scripts and notebooks

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Commits on Mar 31, 2025

• removing export_min part

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• removed export_min multiplication and Nconv addition to tind_fin calculations. Also removed self.tind_init parts as they are not necessary. Removed the check that initial values have advanced, that…

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• removed export_min multiplication and Nconv addition for test_Solver.py. redefined the range

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• wrote a notebook to regenerate KNOs. regenerated KNOs for KMM

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• Fixed small bug which removed one last time step from the last cycle (no impact on the actual solve)

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• Merge pull request #50 from alan-turing-institute/49-regenerate-test-knos

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• resolving merge conflict by incorporating dev into 42-43-second-attempt

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• changed the notebook that generates KNOs to save multiple results for different cycle_step_sizes

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• modifying the tests to test for multipl cycle step sizes

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Commits on Apr 1, 2025

• modified to check for different cycle_step_size

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• changing to dynamic file paths

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• switched to logging package instead of print

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• minor

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• changed to relative tolerance being defined as a constant

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• updating the KMM tests to have logging, subtests for each cycle_step_size, and dynamic file path creation

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• fixed missing base_dir attribute

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• improving docstrings

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• Merge branch '42-43-second-attempt' into 24-test-naghavi-model

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• updating file names

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• updated the typo in the file names

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• generating KGOs but encountering errors

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• figures out the bug. redefining the model and solver for each cycle_step_size loop

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• regenerated KGOs for KMM

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Commits on Apr 2, 2025

• setting up the model within the cycle_step_size loop

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• merging complete

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• updated test_Solver.py with model setup within the loop as well

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• reinitialising the model and solver for each loop

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• Merge pull request #48 from alan-turing-institute/42-43-second-attempt

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• NaghaviModel KGO and tests done

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• merge and minor fix in generate_KMM_KGO.ipynb

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• deleting redundant cell

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• minor comments removed

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• enhancing docstrings

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• minor docstring improvements

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• deleted the old file with errors

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• Merge pull request #53 from alan-turing-institute/24-test-naghavi-model

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Commits on Apr 3, 2025

• updated pyproject.toml with new license format requirement

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Commits on Apr 8, 2025

• updated gitignore to ignore pypi config

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• changing the directory structure to the src format. temporarily renaming with my username appended for testpypi

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• removing manual discovery of packages from toml

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• updating setuptools required version

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• updating toml

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• Update README.md

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• Update README.md

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• changing the name back to ModularCirc

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• decided to stay on testpypi for now

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• bumping up the release version

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• updating to ignore vscode settings

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• removing username from package name

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Commits on Apr 9, 2025

• ignoring __pycache__ inside Tutorials

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• Merge pull request #56 from alan-turing-institute/45-publish-in-pypi

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• adding automatic publishing yml file

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• env name change

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• Update README.md

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• updating the release number

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• Update publish.yml

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Commits on Apr 14, 2025

• Merge branch 'dev' into 21-add-pre-commit-hooks.

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• Merge branch 'dev' into 21-add-pre-commit-hooks

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• pre-commits unleashed

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• Merge pull request #59 from alan-turing-institute/57-automatic-pypi-publishing

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• fixed pre-commit yaml

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• addint CONTRIBUTING.md

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• explaining the pre-commit hooks

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• Merge branch 'dev' into 21-add-pre-commit-hooks

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Commits on Apr 15, 2025

• Merge pull request #60 from alan-turing-institute/21-add-pre-commit-hooks

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