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feat: docstrings and overall design for expectation maximization iterative refinement #21

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jedyeo wants to merge 175 commits into master from itr_ref_docstrings

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jedyeo commented Mar 20, 2022 •

edited by geoffwoollard

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Fixes #10

References

Nelson, P. C. (2019). Chapter 12 : Single Particle Reconstruction in Cryo-electron Microscopy.
In Physical Models of Living Systems (pp. 305–325).
https://repository.upenn.edu/cgi/viewcontent.cgi?article=1665&context=physics_papers
Scheres, S. H. W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination.
Journal of Structural Biology, 180(3), 519–530.
http://doi.org/10.1016/j.jsb.2012.09.006
Sigworth, F. J., Doerschuk, P. C., Carazo, J.-M., & Scheres, S. H. W. (2010).
An Introduction to Maximum-Likelihood Methods in Cryo-EM.
In Methods in Enzymology (1st ed., Vol. 482, pp. 263–294). Elsevier Inc.
http://doi.org/10.1016/S0076-6879(10)82011-7

jedyeo and others added 4 commits

March 19, 2022 17:09


          Init

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          remove ref

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          Format code with black and isort

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Collaborator Author

jedyeo commented Mar 20, 2022

currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array

jedyeo and others added 4 commits

March 20, 2022 16:34


          Docstrings, precommit broken?

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          Format code with black and isort

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          Update docstrings

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          Format code with black and isort

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          Dummy tests

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geoffwoollard commented Mar 22, 2022

I added my comments. Refactor and pull out the functions to be defined outside. I just wrote it like this to start it off because it's more readable - things defined right where they are used.

jedyeo and others added 2 commits

March 21, 2022 18:14


          docstrings and tests

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jedyeo and others added 3 commits

March 21, 2022 23:55


          Minor ds change. Fixed tests w/ fixture

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          Minor ds change. Fixed tests w/ fixture

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          Format code with black and isort

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Collaborator Author

jedyeo commented Mar 22, 2022

im not sure whats going on with black...

thisTyler and others added 15 commits

March 30, 2022 17:25


          Removed last few comments, will re-add if needed

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          Format code with black

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          Merging changes

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          Fixed variable name

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          Merge branch 'itr_ref_docstrings' of github.com:compSPI/reconstructSP…

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          Changed codecov parameters

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          Removed __init__.py files

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          Revert "Removed __init__.py files"

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This reverts commit 0d18f66.


          Merging

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          Revert "Changed codecov parameters"

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This reverts commit 55ee718.


          Merge branch 'reconstructSPI_infrastructure' of github.com:compSPI/re…

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          Refactoring library format

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          Directory fixes

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          Revert "Refactoring library format"

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This reverts commit 15840cf.


          Revert "Directory fixes"

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geoffwoollard mentioned this pull request

ReconstructSPI Workflow Infrastructure #33

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thisTyler added 11 commits

March 30, 2022 18:41


          Removed dependencies

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          Testing something

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          Merge branch 'reconstructSPI_infrastructure' of github.com:compSPI/re…

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…constructSPI into itr_ref_docstrings


          Testing things

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          Merge branch 'reconstructSPI_infrastructure' of github.com:compSPI/re…

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          Force checks

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          Testing things

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          Added library requirements

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          Added dev branch to branches on which tests will run.


          Merging changes. Have temporarily added infrastructure branch to work…

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          removed itr_ref_docstrings branch checks

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geoffwoollard commented Mar 31, 2022

This PR should be into master.

thisFreya changed the base branch from reconstructSPI_infrastructure to master

March 31, 2022 20:28

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thisFreya commented Mar 31, 2022

This PR should be into master.

I had it into reconstructSPI_infrastructure due to it being a branch off of that - upon reflection you're right that doesn't imply this PR needs to be into master!

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