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f3facae
using self.results instead of self
VOD555 May 7, 2021
13d93ca
update tests
VOD555 May 7, 2021
fa9161e
add tests for DeprecationWarning
VOD555 May 7, 2021
5078014
add test for cdf deprecationwarning
VOD555 May 7, 2021
1512c05
update docs
VOD555 May 7, 2021
1b9dbfe
fix pep8 errors
VOD555 May 7, 2021
697b36f
update cdf test
VOD555 May 7, 2021
5af6366
Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop
VOD555 May 7, 2021
8f9359b
use results.count and results.edges
VOD555 May 7, 2021
2c5092e
update docs with new attributes
VOD555 May 7, 2021
63bb0ec
Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop
VOD555 May 7, 2021
8a5a7d4
squash code for warning tests
VOD555 May 7, 2021
53badfc
Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into develop
VOD555 May 7, 2021
80b87c4
add version info for new attributes
VOD555 May 8, 2021
36de73a
update CHANGELOG
VOD555 May 8, 2021
4063444
Merge branch 'develop' into merge-rdf-results-develop
orbeckst May 8, 2021
81e4a14
merge develop
VOD555 May 8, 2021
6c8941b
Merge branch 'develop' into merge-rdf-results-develop
orbeckst May 8, 2021
931b520
removed duplicate entry from CHANGELOG
orbeckst May 8, 2021
ac760ce
modify indentation
VOD555 May 8, 2021
713a1ce
remove import assert_equal
VOD555 May 8, 2021
fe56fc9
Merge branch 'merge-rdf-results-develop' of github.com:VOD555/mdanaly…
VOD555 May 8, 2021
022728e
use np.diff to calculate shell volume
VOD555 May 9, 2021
51d2989
Merge branch 'develop' of github.com:MDAnalysis/mdanalysis into merge…
VOD555 May 9, 2021
90715fb
Merge branch 'develop' into merge-rdf-results-develop
IAlibay May 10, 2021
c814829
Merge branch 'develop' into merge-rdf-results-develop
IAlibay May 11, 2021
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18 changes: 13 additions & 5 deletions package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,9 @@ Enhancements
checking if it can be used in parallel analysis. (Issue #2996, PR #2950)

Changes
* `analysis.rdf.InterRDF` and `analysis.rdf.InterRDF_s` now store
their result attributes using the `analysis.base.Results` class
(Issue #3276, #3261)
* Adds a `force` parameter to the RDKitConverter to allow conversion of
molecules with no hydrogen atom, and a `set_converter_cache_size` function
to change how many items are retained in the cache (PR #2942)
Expand All @@ -199,10 +202,10 @@ Changes
(Issues #3289, #3291)
* `analysis.hole2.HoleAnalysis` now stores ``sphpdbs``, ``outfiles``
and ``profiles`` in the `analysis.base.Results` class (Issues #3261, #3269)
* `helix_analysis.HELANAL` now uses the `analysis.base.Results` class to
store results attributes (Issue #3261, #3267)
* `analysis.diffusionmap.DistanceMatrix` class now stores `dist_matrix`
using the `analysis.base.Results` class (Issues #3288, #3290)
* `helix_analysis.HELANAL` now uses the `analysis.base.Results` class to
store results attributes (Issue #3261, #3267)
* `analysis.align.AlignTraj` and `analysis.align.AverageStructure` now store
their result attributes using the `analysis.base.Results` class
(Issues #3278 and #3261)
Expand All @@ -225,7 +228,7 @@ Changes
analysis.hydrogenbonds.hbond_analysis (Issues #2739, #2746)
* `GNMAnalysis`, `LinearDensity`, `PersistenceLength` and
`AnalysisFromFunction` use the `results` attribute.
* Fixed inaccurate docstring inside the RMSD class (Issue #2796, PR #3134)
* 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)
* Introduces encore specific C compiler arguments to allow for lowering of
Expand Down Expand Up @@ -269,6 +272,11 @@ Changes
* Added OpenMM coordinate and topology converters (Issue #2863, PR #2917)

Deprecations
* The `bins`, `edges`, `count`, `rdf` attributes for `analysis.rdf.InterRDF`
and `analysis.rdf.InterRDF_s`, and `cdf` attributes for
`analysis.rdf.InterRDF_s` are now deprecated in favour of `results.bins`,
`results.edges`, `results.count`, `results.rdf` and `results.cdf`
(Issue #3276, #3261)
* The `hydrogenbonds.WaterBridgeAnalysis.table` attribute is now deprecated and will
be removed in 3.0.0.
* The `hydrogenbonds.WaterBridgeAnalysis.network` attribute is now deprecated
Expand All @@ -291,7 +299,7 @@ Deprecations
``results.sphpdbs``, ``results.outfiles`` and
``results.profiles`` (Issues #3261, #3269)
* The `analysis.diffusionmap.DistanceMatrix.dist_matrix` is now deprecated in
favour of `analysis.diffusionmap.DistanceMatrix.results.dist_matrix`.
favour of `analysis.diffusionmap.DistanceMatrix.results.dist_matrix`.
It will be removed in 3.0.0 (Issues #3288, #3290)
* The `analysis.align.AlignTraj.rmsd` attribute is now deprecated in
favour of `analysis.align.AlignTraj.results.rmsd` (Issue #3278, #3261)
Expand All @@ -309,7 +317,7 @@ Deprecations
* The `angles` attribute for the `dihedrals` classes (Dihedral,
Ramachandran, Janin) is now deprecated in favour of `results.angles`. It
will be removed in 3.0.0 (Issue #3261)
* The `analysis.Contacts.timeseries` attribute is now deprecated in favour of
* The `analysis.Contacts.timeseries` attribute is now deprecated in favour of
`analysis.Contacts.results.timeseries`. It will be removed in 3.0.0
(Issue #3261)
* The `density` attribute of `analysis.density.DensityAnalysis` is now
Expand Down
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