MDAnalysis/pmda issues and pull requests

#161 - Fix handling results array for multiple blocks.

Pull Request - State: open - Opened by camKD 4 months ago

#160 - replace numpy aliases with strings of the dtypes

Pull Request - State: open - Opened by GregorySchwing almost 2 years ago

#159 - Incompatible with Numpy 1.24.1

Issue - State: open - Opened by GregorySchwing almost 2 years ago

#158 - Pip and conda distributions don't have H-Bond Analysis

Issue - State: open - Opened by GregorySchwing almost 2 years ago

#157 - AttributeError: Atom has no attribute indices. Do you mean index

Issue - State: closed - Opened by Dan-Burns over 2 years ago - 2 comments

#156 - Uniform analysis results with MDA

Issue - State: open - Opened by RMeli almost 3 years ago - 1 comment
Labels: enhancement

#155 - Any performance comparison between dask and multprocessing?

Issue - State: closed - Opened by appassionate almost 3 years ago - 2 comments
Labels: question

#154 - pmda.density not compatible to MDA 2.0.0

Issue - State: open - Opened by appassionate almost 3 years ago - 1 comment
Labels: enhancement

#153 - test if PMDA runs on Windows

Issue - State: open - Opened by orbeckst about 3 years ago - 1 comment

#152 - drop Python 2.7 support

Issue - State: open - Opened by orbeckst about 3 years ago - 5 comments

#151 - [CI] switch from Travis CI to GitHub actions

Pull Request - State: open - Opened by orbeckst about 3 years ago - 7 comments

#150 - sitemap.xml contains broken links

Issue - State: closed - Opened by orbeckst about 3 years ago

#149 - Printing of hydrogen bonding analysis results using mdanalysis

Issue - State: closed - Opened by Gojja about 3 years ago - 2 comments
Labels: question

#148 - test compatibility with MDAnalysis 2.0.0

Issue - State: open - Opened by orbeckst about 3 years ago

#147 - Error when running `AnalysisFromFunction()` on more processes than frames

Issue - State: open - Opened by luponzo86 almost 4 years ago - 3 comments
Labels: bug

#146 - MAINT: Switch from Travis to Github actions as CI provider

Issue - State: open - Opened by IAlibay almost 4 years ago - 1 comment
Labels: continuous integration

#145 - add forgotten h-bond analysis docs

Pull Request - State: closed - Opened by orbeckst about 4 years ago - 1 comment

#144 - Bad Performance of Parallelization with On-the-fly Transformation

Issue - State: open - Opened by yuxuanzhuang about 4 years ago - 10 comments

#143 - Travis breaks due to matplotlib 3.3

Issue - State: closed - Opened by yuxuanzhuang over 4 years ago

#142 - Remove pytest-pep8

Pull Request - State: closed - Opened by yuxuanzhuang over 4 years ago - 2 comments

#141 - Add test and fix for uneven blocks

Pull Request - State: closed - Opened by yuxuanzhuang over 4 years ago - 4 comments

#140 - np.hstack should not be used in _conclude

Issue - State: closed - Opened by yuxuanzhuang over 4 years ago

#139 - Travis breaks due to new pytest 6.0.0

Issue - State: closed - Opened by yuxuanzhuang over 4 years ago - 4 comments

#138 - Raise ValueError when blocks>frames in make balance

Pull Request - State: closed - Opened by yuxuanzhuang over 4 years ago - 4 comments

#137 - make_balanced_slices should raise error when n_blocks are larger than n_frames

Issue - State: closed - Opened by yuxuanzhuang over 4 years ago - 1 comment
Labels: bug

#136 - Turn ParallelAnalysisBase into dask custom collection

Pull Request - State: open - Opened by yuxuanzhuang over 4 years ago - 2 comments

#135 - Turn ParallelAnalysisBase into dask custom collection

Issue - State: open - Opened by yuxuanzhuang over 4 years ago - 3 comments

#134 - Parallelize select_atoms by coordinates

Issue - State: open - Opened by cecilpert over 4 years ago - 7 comments
Labels: bug, help wanted

#133 - use serializable Universe

Issue - State: open - Opened by orbeckst over 4 years ago - 1 comment

#132 - Refactor pmda after universe can be serialized

Pull Request - State: open - Opened by yuxuanzhuang over 4 years ago - 8 comments

#131 - Unifying _single_frame() of AnalysisBase and ParallelAnalysisBase

Issue - State: open - Opened by yuxuanzhuang over 4 years ago - 5 comments

#130 - cdf function in rdf.InterRDF_s does not give cummulative distribution function

Issue - State: open - Opened by VOD555 over 4 years ago - 1 comment
Labels: bug

#129 - removed unused CSS

Pull Request - State: closed - Opened by orbeckst over 4 years ago - 1 comment

#128 - PMDA with refactored `_single_frame`

Pull Request - State: open - Opened by yuxuanzhuang over 4 years ago - 4 comments

#127 - add GoatCounter analytics and Privacy Policy

Pull Request - State: closed - Opened by orbeckst over 4 years ago - 1 comment

#126 - Update theme

Pull Request - State: closed - Opened by lilyminium over 4 years ago - 2 comments

#125 - add GoatCounter tracking to docs

Issue - State: closed - Opened by orbeckst over 4 years ago
Labels: documentation

#124 - change doc style to MDA/UserGuide 1.0.0

Issue - State: closed - Opened by orbeckst over 4 years ago - 1 comment
Labels: documentation

#123 - upgrade to MDAnalysis 1.0.0

Pull Request - State: closed - Opened by orbeckst over 4 years ago - 1 comment

#122 - Some features used in density function were deprecated

Issue - State: closed - Opened by VOD555 over 4 years ago - 7 comments

#121 - Fix InterRDF_s normalization problem when given density = True

Pull Request - State: closed - Opened by VOD555 over 4 years ago - 5 comments

#120 - Wrong results from InterRDF_s when given 'density=True'

Issue - State: closed - Opened by VOD555 over 4 years ago - 1 comment
Labels: bug

#119 - Issue with AnalysisFromFunction() when reading Amber .nc trajectory files

Issue - State: open - Opened by luponzo86 over 4 years ago - 3 comments
Labels: bug

#118 - hydrogenbond analysis should check for missing bonds in the same way as the serial code

Issue - State: open - Opened by orbeckst over 4 years ago

#117 - Wrong normalization for cdf calculation

Issue - State: closed - Opened by VOD555 almost 5 years ago - 7 comments
Labels: bug

#116 - release 0.4

Issue - State: open - Opened by orbeckst almost 5 years ago - 7 comments

#115 - use self.n_frames instead of self.nf

Pull Request - State: closed - Opened by VOD555 almost 5 years ago - 3 comments

#114 - n_frame in pmda.rdf is not right when given start, stop, step

Issue - State: closed - Opened by VOD555 almost 5 years ago
Labels: bug

#113 - Parallel version of the new mdanalysis `hbond_analysis` function

Pull Request - State: closed - Opened by VOD555 about 5 years ago - 2 comments

#112 - modify the names of schedulers

Pull Request - State: closed - Opened by VOD555 about 5 years ago - 5 comments

#111 - DensityAnalysis and RMSF start/stop/step Issue Fix

Pull Request - State: closed - Opened by nawtrey about 5 years ago

#110 - RDF tests fail

Issue - State: closed - Opened by orbeckst about 5 years ago - 3 comments

#109 - DensityAnalysis Normalization Fix

Pull Request - State: closed - Opened by nawtrey about 5 years ago - 2 comments

#108 - DensityAnalysis Normalization

Issue - State: closed - Opened by nawtrey about 5 years ago - 6 comments

#107 - Consolidate root-mean-square functions

Pull Request - State: closed - Opened by nawtrey about 5 years ago - 3 comments

#106 - release 0.3.0

Issue - State: closed - Opened by orbeckst over 5 years ago - 3 comments

#105 - Add REU Paper Reference to RMSF, DensityAnalysis

Pull Request - State: closed - Opened by nawtrey over 5 years ago - 1 comment

#104 - RMSD, RMSF, DensityAnalysis Documentation Update

Pull Request - State: closed - Opened by nawtrey over 5 years ago

#103 - Move RMSF into pmda.rms

Issue - State: closed - Opened by nawtrey over 5 years ago - 2 comments
Labels: refactoring

#102 - check scheduler names

Issue - State: closed - Opened by orbeckst over 5 years ago - 2 comments
Labels: help wanted

#101 - Update citation

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 4 comments

#100 - Update with scipy2019 paper citation

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 1 comment

#99 - Add cdf function to InterRDF

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 11 comments

#98 - update with SciPy paper citation

Issue - State: closed - Opened by orbeckst over 5 years ago - 1 comment
Labels: documentation

#97 - Parallel RMSF

Pull Request - State: closed - Opened by nawtrey over 5 years ago - 19 comments

#96 - Density Docs

Pull Request - State: closed - Opened by nawtrey over 5 years ago - 2 comments

#95 - Hydrogen bonds analysis using PMDA

Issue - State: closed - Opened by nawelmele over 5 years ago
Labels: enhancement, help wanted

#94 - store block information

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 2 comments

#93 - Parallel density function

Pull Request - State: closed - Opened by nawtrey over 5 years ago - 8 comments

#92 - Add rmsf

Pull Request - State: closed - Opened by nawtrey over 5 years ago - 2 comments

#91 - add io and compute block time

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 2 comments

#90 - parallelize RMSF

Issue - State: closed - Opened by orbeckst over 5 years ago - 1 comment
Labels: enhancement

#89 - store block information

Issue - State: closed - Opened by orbeckst over 5 years ago
Labels: enhancement

#88 - vstack vs hstack

Pull Request - State: closed - Opened by orbeckst over 5 years ago - 5 comments

#87 - default vstack in _conclude() fails with scalar per frame data

Issue - State: closed - Opened by orbeckst over 5 years ago - 8 comments
Labels: bug

#86 - Add IO and computation time per block in timing

Issue - State: closed - Opened by VOD555 over 5 years ago - 1 comment

#85 - release 0.2.1

Issue - State: closed - Opened by orbeckst over 5 years ago - 2 comments

#84 - Fix decorator 83

Pull Request - State: closed - Opened by orbeckst over 5 years ago - 1 comment

#83 - LeafletFinder tests started failing with "MarkDecorator"

Issue - State: closed - Opened by orbeckst over 5 years ago
Labels: bug, testing, continuous integration

#82 - add new timers for "map" process and time for blocks to start working

Pull Request - State: closed - Opened by VOD555 over 5 years ago - 6 comments

#81 - LeafletFinder should work with distributed scheduler

Pull Request - State: open - Opened by orbeckst about 6 years ago - 1 comment
Labels: work in progress

#80 - fixes for leafletfinder

Pull Request - State: closed - Opened by orbeckst about 6 years ago - 1 comment

#79 - distributed.client error with atomgroup or universe type self attribute

Issue - State: open - Opened by VOD555 about 6 years ago - 1 comment

#78 - updated docs with explicit scheduler setting example

Issue - State: closed - Opened by orbeckst about 6 years ago - 3 comments
Labels: documentation

#77 - add @mimischi to authors

Pull Request - State: closed - Opened by orbeckst about 6 years ago - 6 comments

#76 - LeafletFinder issues

Issue - State: open - Opened by orbeckst about 6 years ago - 10 comments
Labels: bug

#70 - Add InterRDF_s

Pull Request - State: closed - Opened by VOD555 about 6 years ago - 6 comments
Labels: enhancement

#65 - use pickle of ag to transport information

Pull Request - State: closed - Opened by kain88-de about 6 years ago - 10 comments

#63 - Replace distance array with capped distances

Pull Request - State: closed - Opened by VOD555 about 6 years ago - 1 comment

#60 - A parallel version of InterRDF_s

Issue - State: closed - Opened by VOD555 about 6 years ago
Labels: enhancement

#59 - release 0.2 before Workshop

Issue - State: closed - Opened by orbeckst about 6 years ago - 17 comments

#55 - replace res with two kinds of output, accumulator and timeseries

Pull Request - State: closed - Opened by VOD555 about 6 years ago - 15 comments

#51 - add timing for _conclude and _prepare

Pull Request - State: closed - Opened by VOD555 over 6 years ago - 1 comment

#45 - parallel dihedral featurizer

Issue - State: open - Opened by orbeckst over 6 years ago
Labels: enhancement, help wanted

#44 - fails with ChainReader trajectory

Issue - State: open - Opened by orbeckst over 6 years ago - 2 comments
Labels: bug, help wanted

#43 - include code in package

Pull Request - State: closed - Opened by orbeckst over 6 years ago - 2 comments

#41 - parallelize analysis.rdf

Issue - State: closed - Opened by orbeckst over 6 years ago
Labels: enhancement

#18 - parallel analysis should check that atomgroups in initialize belong to the same universe

Issue - State: open - Opened by kain88-de about 7 years ago
Labels: help wanted, good first issue

#15 - stop when using memory reader

Issue - State: open - Opened by kain88-de about 7 years ago
Labels: bug, help wanted

#13 - allow using updating atomgroups

Issue - State: open - Opened by kain88-de about 7 years ago - 3 comments
Labels: bug, help wanted

GitHub / MDAnalysis/pmda issues and pull requests