upgrade DensityAnalysis to use AnalysisBase #2502
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As stated in #1463 (comment), @nawtrey added a parallel DensityAnalysis in MDAnalysis/pmda#93 which can be back-ported as a serial version. |
orbeckst
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- close #2502 - DensityAnalysis is based on @nawtrey's pmda.density.DensityAnalysis but replace _reduce with accumulation in _single_frame - added tests (based on the Test_density_from_universe): both give the same answer as they pass the same tests; test specific exceptions in DensityAnalysis - update docs (also write ångström consistently throughout) - update CHANGELOG
orbeckst
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- close #2502 - DensityAnalysis is based on @nawtrey's pmda.density.DensityAnalysis but replace _reduce with accumulation in _single_frame - added tests (based on the Test_density_from_universe): both give the same answer as they pass the same tests; test specific exceptions in DensityAnalysis - update docs (also write ångström consistently throughout) - update CHANGELOG
IAlibay
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Mar 15, 2020
Partially fixes #2502 (completes PR #2537) ## PR contents: This PR by @wvandertoorn finalises the work done as part of #2537 Key commits: - Fixes docstring (adds .. deprecated information). - Adds back :class:`TestGridImport`. - Reduces precision matching of `test_density_from_PDB`. - CHANGELOG and AUTHORS updated accordingly.
IAlibay
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Fixes #2502 ## PR overview: Adds the new AnalysisBase DensityAnalysis class. ## PR details - A new Density class based on AnalysisBase was created. - The old density_from_Universe, density_from_PDB and associated code was deprecated, with removal set for v2.0. - Tests were added to cover some of the untested parts of the code.
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Expected behavior
The density analysis in
analysis.densityshould implement the common analysis API, namely be based onanalysis.base.AnalysisBase.Actual behavior
The density generation code in
analysis.densityconsist of a rag-tag of idiosyncratic functions with no common interface.Currently version of MDAnalysis
current develop (> 0.20)
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