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change pytest fixture scopes to 'session' and add tmpdir methods if required #235

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cadeduckworth opened this issue Feb 1, 2023 · 3 comments
Open

change pytest fixture scopes to 'session' and add tmpdir methods if required #235

cadeduckworth opened this issue Feb 1, 2023 · 3 comments
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refactoring testing

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@cadeduckworth
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cadeduckworth commented Feb 1, 2023 •
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MDPOW/mdpow/tests/test_automated_dihedral_analysis.py

Line 35 in 8ac9549

@pytest.fixture(scope="function")

  • link to test cleanup PR once 217 is merged, review all test modules
  • review and update all tests pertaining to EnsembleAnalysis - related modules
@cadeduckworth cadeduckworth linked a pull request Feb 1, 2023 that will close this issue
Automated Dihedral Analysis #217
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@cadeduckworth cadeduckworth mentioned this issue Feb 1, 2023
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@orbeckst orbeckst removed a link to a pull request Feb 12, 2023
Automated Dihedral Analysis #217
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See also #194 — remove bundled tempdir whenever you come across it...

@cadeduckworth
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also remove function specification where the scope is not going to be changed

@cadeduckworth cadeduckworth mentioned this issue Jul 2, 2023
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https://docs.pytest.org/en/6.2.x/fixture.html

cadeduckworth added a commit that referenced this issue Jul 3, 2023
@cadeduckworth
comment expected fixture scope changes, reference issue #235
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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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