Code

Nojump#4031

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hmacdope merged 60 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom jvermaas:nojumpjvermaas/mdanalysis:nojumpCopy head branch name to clipboardMar 28, 2023

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Commits on Feb 19, 2023

• First attempt at a nojump transformation

  jvermaas

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  e7f6b6f

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• This works now, matching the output from VMD for orthogonal trajectories

  jvermaas

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• Add self to AUTHORS, add to CHANGELOG, make style happier.

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Commits on Feb 20, 2023

• This implementation works for non-orthogonal boxes, and is simpler than I thought

  jvermaas

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• Merge branch 'nojump' of github.com:jvermaas/mdanalysis into nojump

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  2eb56bb

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• Added a test

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• Updates for Linter

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  e05ecfd

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• How about now linter?

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  701cb10

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• Whitespace fixes

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  5a4bd77

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• Copy the right value

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  88f4395

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• Nope, made a mistake with the other one too

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• Add references, make darker happy.

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• Spellcheck, actually define due and Doi

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Commits on Feb 21, 2023

• Update test_nojump.py with a much nicer synthetic example

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• Add to the docs

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• Add a check that we don't go backwards

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• Automake the nojump documentation

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• Test every third value

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• Nojump

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• Test values in more places

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• Actually add constant velocity test

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• Actually provide a dimension

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• Trajectories can be transformed, universes cannot be

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• Hopefully the last issue?

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  112cb7d

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• Fix variables

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  43f3d0c

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• add wrap to the test

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  232be2a

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• Ok, I think I was supposed to use Black to do the code reformatting to make the linter happy

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  f3e18a2

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• Black did something dumb I think

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  79927ca

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• I forgot that wrapping in negative space can lead to problems

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• Bump up the tolerance a bit.

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• Testing lint fix

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Commits on Feb 23, 2023

• Added some more tests to cover the branches.

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  0eccb0a

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• Fix the tests again

  jvermaas

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  42c6112

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• I'm definitely not used to how MDAnalysis does things.

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• Apparently I'm not covering a branch.

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Commits on Feb 24, 2023

• Make the tests better, also give the user a better error message if there is an illegal box.

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• I CANNOT trigger the warnings.

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• I am now testing the warnings via a loaded file path

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• MDAnalysis->mda:

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• Ok, misplaced an import

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• No longer out of bounds

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• Catch busted Linverse during initialization.

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• Add an initial dimension, which hopefully gets ignored for subsequent frames

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• Add text description for what the intended difference between

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Commits on Feb 26, 2023

• Separating no dimensions from invalid dimensions tests.

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• Merge branch 'nojump' of github.com:jvermaas/mdanalysis into nojump

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• Add some text explaining the notinvertible transform

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• Apply zero dimensions

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Commits on Mar 5, 2023

• Whoops. Actually make something non-invertible

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• Merge branch 'develop' into nojump

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Commits on Mar 15, 2023

• Merge branch 'develop' into nojump

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Commits on Mar 16, 2023

• Update __init__.py

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• Revert "Update __init__.py"

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Commits on Mar 26, 2023

• Need to pass at least one non-zero dimension to trigger a LinAlgError

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Commits on Mar 27, 2023

• Used mdanalysis.copy inside a test

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• Merge branch 'develop' into nojump

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Commits on Mar 28, 2023

• Merge branch 'develop' into nojump

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• Update package/MDAnalysis/transformations/nojump.py

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• Update package/MDAnalysis/transformations/nojump.py

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• Update nojump.py

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