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Create MDPOW Project Analysis Output Manifest DataFrame/CSV #244

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cadeduckworth opened this issue Mar 31, 2023 · 0 comments
Open

Create MDPOW Project Analysis Output Manifest DataFrame/CSV #244

cadeduckworth opened this issue Mar 31, 2023 · 0 comments
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For each project analyzed, create a DataFrame including metadata for files created like:
(preliminary, rough working list)

  • file created, what is it, what made it? (plot, EnsembleAnalysis results, project paths)
  • datatype of the file (csv, svg, pdf, etc)
  • file name/path
  • project analyzed
  • analysis type

After all projects are analyzed, write out each project DataFrame to a final Manifest CSV.
Return and log the location of the saved manifest.

Additionally, reorganize the directory structure for analysis output. For instance, given one directory as input to save all results under, automatically nest the EnsembleAnalysis results and plots within subdirectories for each respective project.

For the automated dihedrals workflow specifically, split up total results DataFrame into a separate DataFrame for each dihedral atom group selection.
@orbeckst orbeckst mentioned this issue Apr 4, 2023
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cadeduckworth added a commit that referenced this issue Apr 15, 2023
@cadeduckworth
explanation of why figdir is a kwarg at top level of dihedrals module…
9175fda 
… but a positional argument elsewhere - workflows base **kwargs, issue #244, see in-line comment in dihedrals.py
cadeduckworth added a commit that referenced this issue Apr 15, 2023
@cadeduckworth
temporary fix for figdir issue which should currently be a positional…
60636b4 
… argument, but would require redundant rewrite of workflows base module, pending issue #244
@cadeduckworth cadeduckworth mentioned this issue Jul 2, 2023
Merged
orbeckst added a commit that referenced this issue Jul 4, 2023
@cadeduckworth @orbeckst
Dihedral Plots: RDKit Mol Object (#243)
76b96d4 
* add RDKit Mol object to dihedral analysis plots
* add tests, and close  #238
* add svgutils and cairosvg methods to plot svg mol object
* reimplement DF input option and fix most tests to reflect name changes and altered function definitions
* add svgutils and cairosvg to dependencies, install, requirements lists, remove broken test, add reminder to update func list in docs
* split plot_violins into new build_svg function
* change, better function names for dihedrals workflow module
* docs and cleanup, plot width docs, dict comprehension for ab_pairs
* intersphinx mapping
* tests: new fixtures and tests for bond_indices and ab_pairs
* tests: new fixtures and tests for bond_indices and ab_pairs, skip 3.7
* test_build_universe method
* confirm build universe test
* rewrite docs to cover new functions and kwarg changes
* fix tests to accommodate kwarg updates in dihedrals module
* explanation of why figdir is a kwarg at top level of dihedrals module but a positional argument elsewhere - workflows base **kwargs, issue #244, see in-line comment in dihedrals.py
* temporary fix for figdir issue which should currently be a positional argument, but would require redundant rewrite of workflows base module, pending issue #244
* upcoming CHANGES
* remove dafault scope specification for defined functions
* reimplement try/except method for rdkit conversion topology element guessing
* generate combined plots pdf for automated dihedral analysis
* updates for implementation of pypdf in workflows dihedrals module: CHANGES, testing environment, requirements, sphinx source configuration
* documentation for dihedral_violins function in workflows dihedrals module
* documentation for get_paired_indices function in workflows dihedrals module
* documentation and kwarg definition for get_paired_indices function and ab_pairs dictionary object in workflows dihedrals module
* kwarg definition for plot_title for dihedral_violins function in workflows dihedrals module
* move in-line comments explaining figdir kward for workflows dihedrals module
* reorganize kwargs for plot_dihedral_violins in top-level automated_dihedral_analysis function call in workflows dihedrals module
* add assert method to make figdir kwarg required in workflows dihedrals module
* change MDA guess_atom_element to MDA guess_types for RDKit conversion in workflows dihedrals module
* fix registry import error for workflows base, close #245
* remove guess_atom_element import
* reimplement assert figdir reuired for workflows dihedrals module
* add pypdf to setup.py install_requires for dihedrals workflow
* change imports to follow PEP 8
* modify dihedrals workflow docs to explain figdir kwarg requirement
* use first solvent specified to build MDAnalysis Universe
* modify single solvent plotting method, add solvent count assertion
* comment expected fixture scope changes, reference issue #235
* remove solute.unwrap, not needed
* reference issue #260 to fix jupyter notebook figure output
* finalize single solvent figure modifications and add test

---------

Co-authored-by: Oliver Beckstein <[email protected]>
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