…file-names

Change main structure of the repo

Extract file names

This reverts commit 5e61c49.

Improve analysis

Merge dev into main

* Add code to pool directions

* Add notes

* Cleanup

* Fix broken tests

* Recalculate outputs

* Update manifest and pyproject

* Fix package name

* Update package links

* Update dependencies

* Add more descriptions

* Edit pyproject file

* Expand readme with more details on the analysis

* Add docstring

* Test if we can see the schema in the readme file

* Update docstring

* Insert correct image

* Linting

* Apply suggestions from code review

Co-authored-by: Niko Sirmpilatze <[email protected]>

* Change prompt message

* Adjust input params of method get_median_subtracted_response_and_params

* Renaming and other small suggested fixes

* Small fixes

* Move out the method to make gaussian matrices

* Clean up

---------

Co-authored-by: Niko Sirmpilatze <[email protected]>

* Add code to pool directions

* Add notes

* Cleanup

* Fix broken tests

* Recalculate outputs

* Update manifest and pyproject

* Fix package name

* Update package links

* Update dependencies

* Add more descriptions

* Edit pyproject file

* Expand readme with more details on the analysis

* Add docstring

* Test if we can see the schema in the readme file

* Add handling of multiple days

* Improve performance to deal with very large files, from O(n ^2) to O(1)

* Delete commented code

* Handle fit fails

* Save the data in a given folder

* Skip ROIs that do not fit

* Add missing fit handling in sftf analysis

* Regenerate mock data according to new "day" values

* Update docstring

* Remove big chunk of duplicated code

* Test image in readme file

* Remove image

* Apply suggestions from code review

Co-authored-by: Niko Sirmpilatze <[email protected]>

* Change prompt message

* Adjust input params of method get_median_subtracted_response_and_params

* Renaming and other small suggested fixes

* Renaming 2

* Small fixes

* Move out the method to make gaussian matrices

* Clean up

* Add tests for multiple days and add more structure and comments regarding creation of mock data

* Update readme

* Small updates in the docs

* Simplify fitting methods according to discussion

* Improve description on dataset creation optimization

* Remove unused config

* Rearrange methods in generate mock data

* Renaming ad adding new fixture

* Add missing n_roi fixture calls

* Renaming and folder reorganization

* Remove try-catch construct

* Linting

* Add missing adjustments

* Add readme file with a description of the regression tests

* Add more descriptions / docs

* Revert readme change

* Fix usage of conftest

* Linting

---------

Co-authored-by: Niko Sirmpilatze <[email protected]>

Co-authored-by: Niko Sirmpilatze <[email protected]>

Co-authored-by: Niko Sirmpilatze <[email protected]>
Co-authored-by: Joe Ziminski <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Change commit hash

* Revert "Change commit hash"

This reverts commit b1aa762.

* Add changes introduced by cruft

* Getting rid of the docs for now

* Remove sphinx docs action for now

* Include coverage for codecov action

* Test fixing check-manifest error

Co-authored-by: Niko Sirmpilatze <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

for more information, see https://pre-commit.ci

…nit/load-suite2p into load-raw-suite2p-data