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Notebook cleanup#44

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EzryStIago wants to merge 25 commits intomainjhenin/SAFEP_tutorial:mainfrom notebook_cleanupjhenin/SAFEP_tutorial:notebook_cleanupCopy head branch name to clipboard

+607-200

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Commits on Apr 14, 2024

• begin moving code to helper module

  EzryStIago

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  f72fd4b

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• remove outputs

  EzryStIago

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Commits on Apr 15, 2024

• add plotting functions

  EzryStIago

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• replace plotting scripts with functions

  EzryStIago

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• add required arguments to convergence plot

  EzryStIago

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• update argument names. PEP8

  EzryStIago

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• remove interruption

  EzryStIago

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• consolidate cells and make bulk a fepdata object

  EzryStIago

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• rewrote classes into dGData which is a parent for TIData and FEPData.

  EzryStIago

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• offload TI and misc values to the helpers module

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• fix references to dG_DBC which should have been DBC.dG with the new class structure

  EzryStIago

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• add documentation

  EzryStIago

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• documentation

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• blackify

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• adding VMD and NAMD tutorial links

  EzryStIago

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  2fe10ed

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• Fix parameter order

  jhenin

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Commits on Apr 26, 2024

• remove unused imports

  EzryStIago

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• replace kwargs with positional arguments to preserve backward/forward compatibility with safep package

  EzryStIago

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• linting

  EzryStIago

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• update to agree with notebook_helpers

  EzryStIago

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• rename

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• PEP8 compliance and rename file

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• Merge branch 'notebook_cleanup' of https://github.com/jhenin/SAFEP_tutorial into notebook_cleanup

  EzryStIago

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Commits on May 6, 2024

• use field(default_factory=...) instead of mutable default objects

  EzryStIago

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• replace numpy ndarray default_factory with None

  EzryStIago

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