RFC: Add results class for storing analysis results

package/CHANGELOG

@@ -106,6 +106,7 @@ Fixes
   * Fix syntax warning over comparison of literals using is (Issue #3066)
 
 Enhancements
+  * Added `Results` class for storing analysis results (#3115, PR #3233)
   * Added intra_bonds, intra_angles, intra_dihedrals etc. to return only
     the connections involving atoms within the AtomGroup, instead of
     including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
@@ -173,6 +174,8 @@ Enhancements
     checking if it can be used in parallel analysis. (Issue #2996, PR #2950)
 
 Changes
+  * `GNMAnalysis`, `LinearDensity`, `PersistenceLength` and
+    `AnalysisFromFunction` use the `results` attribute.
   * Fixed inaccurate docstring inside the RMSD class (Issue #2796, PR #3134) 
   * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default,
     which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)

package/MDAnalysis/analysis/__init__.py

@@ -21,102 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-"""
-:mod:`MDAnalysis.analysis` --- Analysis code based on MDAnalysis
-================================================================
-
-The :mod:`MDAnalysis.analysis` sub-package contains various recipes and
-algorithms that can be used to analyze MD trajectories.
-
-If you use them please check if the documentation mentions any specific caveats
-and also if there are any published papers associated with these algorithms.
-
-Available analysis modules
---------------------------
-
-:mod:`~MDAnalysis.analysis.align`
-    Fitting and aligning of coordinate frames, including the option to
-    use a sequence alignment to define equivalent atoms to fit on.
-
-:mod:`~MDAnalysis.analysis.contacts`
-    Analyse the number of native contacts relative to a reference
-    state, also known as a "q1-q2" analysis.
-
-:mod:`~MDAnalysis.analysis.density`
-    Creating and manipulating densities such as the density ow water
-    molecules around a protein. Makes use of the external
-    GridDataFormats_ package.
-
-:mod:`~MDAnalysis.analysis.distances`
-    Functions to calculate distances between atoms and selections; it
-    contains the often-used
-    :func:`~MDAnalysis.analysis.distances.distance_array` function.
-
-:mod:`~MDAnalysis.analysis.hbonds`
-    Analyze hydrogen bonds, including both the per frame results as well
-    as the dynamic properties and lifetimes.
-
-:mod:`~MDAnalysis.analysis.helix_analysis`
-    Analysis of helices with the HELANAL_ algorithm.
-
-:mod:`~MDAnalysis.analysis.hole2`
-    Run and process output from the :program:`HOLE` program
-    to analyze pores, tunnels and cavities in proteins.
-
-:mod:`~MDAnalysis.analysis.gnm`
-    Gaussian normal mode analysis of MD trajectories with the
-    help of an elastic network.
-
-:mod:`~MDAnalysis.analysis.leaflet`
-    Find lipids in the upper and lower (or inner and outer) leaflet of
-    a bilayer; the algorithm can deal with any deformations as long as
-    the two leaflets are topologically distinct.
-
-:mod:`~MDAnalysis.analysis.msd`
-    Implements the calculation of Mean Squared Displacements (MSDs) by the
-    Einstein relation.
-
-:mod:`~MDAnalysis.analysis.nuclinfo`
-    Analyse the nucleic acid for the backbone dihedrals, chi, sugar
-    pucker, and Watson-Crick distance (minor and major groove
-    distances).
-
-:mod:`~MDAnalysis.analysis.psa`
-    Perform Path Similarity Analysis (PSA) on a set of trajectories to measure
-    their mutual similarities, including the ability to perform hierarchical
-    clustering and generate heat map-dendrogram plots.
-
-:mod:`~MDAnalysis.analysis.rdf`
-    Calculation of pair distribution functions
-
-:mod:`~MDAnalysis.analysis.rms`
-    Calculation of RMSD and RMSF.
-
-:mod:`~MDAnalysis.analysis.waterdynamics`
-    Analysis of water.
-
-:mod:`~MDAnalysis.analysis.legacy.x3dna`
-    Analysis of helicoidal parameters driven by X3DNA_. (Note that this
-    module is not fully supported any more and needs to be explicitly
-    imported from :mod:`MDAnalysis.analysis.legacy`.)
-
-.. _GridDataFormats: https://github.com/orbeckst/GridDataFormats
-.. _HELANAL: http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html
-.. _X3DNA: http://x3dna.org/
-
-.. versionchanged:: 0.10.0
-   The analysis submodules are not automatically imported any more. Manually
-   import any submodule that you need.
-
-.. versionchanged:: 0.16.0
-   :mod:`~MDAnalysis.analysis.legacy.x3dna` was moved to the
-   :mod:`MDAnalysis.analysis.legacy` package
-
-.. versionchanged:: 2.0.0
-   Adds MSD, and changes hole for hole2.hole.
-
-"""
-
 __all__ = [
     'align',
     'base',