WIP: Master merge#3299

Merged

richardjgowers merged 178 commits intodevelopfrom

May 14, 2021

Commits on Feb 28, 2016

Commits on May 15, 2016

Merged 0.15.0 release into master
richardjgowers
committed

Commits on Jun 3, 2017

Commits on Jun 21, 2017

Commits on Jun 24, 2017

add @utkbansal to changelog
kain88-de
committed

Commits on Jan 24, 2018

Commits on Jan 25, 2018

regenerated c files for 0.17.0
richardjgowers
committed

Commits on Apr 15, 2018

Commits on Apr 22, 2018

updated c files for 0.18 release
richardjgowers
committed

Commits on Sep 5, 2019

Commits on Jun 9, 2020

Commits on Jun 10, 2020

Commits on Jun 11, 2020

restrict pip package versions to Python 2.7 compatible ones

orbeckst
authored and
richardjgowers
committed
update CHANGELOG

orbeckst
authored and
richardjgowers
committed

Commits on Jun 21, 2020

change status from beta to mature

IAlibay
authored and
orbeckst
committed

Commits on Jul 12, 2020

fix InterRDF_s(..., density) normalization

VOD555
authored and
orbeckst
committed
changed InterRDF_s density keyword semantics
orbeckst
committed
Add scripts for doc versioning (#2749)

lilyminium
authored and
orbeckst
committed
build docs for master as well

lilyminium
authored and
orbeckst
committed
removed matplotlib.use('agg') from tests
orbeckst
committed
CI: add codecov to Azure CI (#2720)

authored and
orbeckst
committed
fixed 1.0.1 contributor list based on git log
orbeckst
committed
file clean-ups
orbeckst
committed
fixes google badges (#2772)

IAlibay
authored and
orbeckst
committed
fixed maintainer/change_release.sh
orbeckst
committed
bumped release to 1.0.1-dev (so that docs are properly labeled)
orbeckst
committed
Make the TPR parser a bit faster (#2804)

authored and
orbeckst
committed
ChainReader Refactoring (#2815)

yuxuanzhuang
authored and
orbeckst
committed
decorate Selection.apply to ignore empty atomgroups (#2767)

authored and
orbeckst
committed
TRZReader check for n_atoms (#2820)

yuxuanzhuang
authored and
orbeckst
committed
deprecation of waterdynamics.HydrogenBondLifetimes
orbeckst
committed

Commits on Jul 15, 2020

Fixes AttributeError in HydrogenBondAnalysis (#2849)

authored and
orbeckst
committed

Commits on Aug 12, 2020

fix masses and charge bug in HOOMD-XML parser (#2889)

CalCraven
authored and
orbeckst
committed
Implemented extraction of chains from DMS formats (#2872)

ianmkenney
authored and
orbeckst
committed

Commits on Aug 16, 2020

cleaned up lib.log (#2902)
orbeckst
committed

Commits on Aug 27, 2020

Commits on Sep 1, 2020

install chemfiles via pip for Python 2.7
orbeckst
committed

Commits on Sep 2, 2020

fix minor inconsistencies in backport

committed

Commits on Sep 4, 2020

Deprecate helanal (PR #2928)

lilyminium
authored and
orbeckst
committed
Merge pull request #2798 from MDAnalysis/backport-1.0.1
orbeckst
authored

Commits on Sep 9, 2020

oops

lilyminium
authored and
orbeckst
committed

Commits on Sep 10, 2020

Add test files (#2940)

lilyminium
authored and
orbeckst
committed

Commits on Sep 18, 2020

add docs for analysis.align.AverageStructure
orbeckst
committed

Commits on Sep 23, 2020

ensure that unistd.h is included for spe.c with recent clang
orbeckst
committed

Commits on Sep 29, 2020

comment out parmed intersphinx

lilyminium
authored and
orbeckst
committed

Commits on Oct 1, 2020

Add more docs redirects (#2960)
lilyminium
authored

Commits on Oct 2, 2020

Add doc script changes but revert VERSION variable (#2964)
lilyminium
authored

Commits on Oct 6, 2020

Commits on Oct 20, 2020

Stable sitemap master (#2999)
lilyminium
authored

Commits on Oct 23, 2020

Commits on Oct 24, 2020

Commits on Dec 9, 2020

Add dev and stable versions once (#3009)
lilyminium
committed
Have CI use mamba (#2983)

jbarnoud
authored and
lilyminium
committed
Fixed AtomGroup.center's behavior when using compounds in conjugation with unwrapping (PR #2992)

mnmelo
authored and
lilyminium
committed
increase default Python to 3.7 on Travis CI (#3011)

orbeckst
authored and
lilyminium
committed
Adds basic GH Actions CI workflow (#3040)

IAlibay
authored and
lilyminium
committed
Deploy docs via GitHub Actions CI (#3053)
lilyminium
committed
TST, CI: add ARM64 Graviton 2 to CI (#2956)

tylerjereddy
authored and
lilyminium
committed
ParmEdConverter: fix NameError when catching NoDataError (#2953)

Cédric Bouysset
authored and
lilyminium
committed
Improve the performance of ParmEd converter. (Fix #3028) (#3029)

HanatoK
authored and
lilyminium
committed
mv travis back and only keep 3.5 and 2.7
lilyminium
committed
Merge branch 'master' into gh-actions-py3
lilyminium
authored
move py3.5 job
lilyminium
committed

Commits on Dec 14, 2020

Adds basic GH Actions CI workflow (#3040)

IAlibay
authored and
lilyminium
committed
Deploy docs via GitHub Actions CI (#3053)
lilyminium
committed
TST, CI: add ARM64 Graviton 2 to CI (#2956)

tylerjereddy
authored and
lilyminium
committed
ParmEdConverter: fix NameError when catching NoDataError (#2953)

Cédric Bouysset
authored and
lilyminium
committed
Improve the performance of ParmEd converter. (Fix #3028) (#3029)

HanatoK
authored and
lilyminium
committed
mv travis back and only keep 3.5 and 2.7
lilyminium
committed
move py3.5 job
lilyminium
committed
Merge branch 'gh-actions-py3' of github.com:lilyminium/mdanalysis into gh-actions-py3
lilyminium
committed
rm appveyor
lilyminium
committed

Commits on Dec 16, 2020

try pinning
lilyminium
committed

Commits on Dec 21, 2020

Commits on Dec 22, 2020

Commits on Jan 17, 2021

Rel 1.0.1b (#3093)
richardjgowers
authored

Commits on Jan 18, 2021

Turn off mamba for Travis CI (#3099)
lilyminium
authored

Commits on Jan 22, 2021

Change tmpdir fixture to tmpdir_factory (#3095) (#3097)
lilyminium
authored

Commits on Jan 23, 2021

Copy README into package (#3094)
IAlibay
authored

Commits on Jan 24, 2021

Fix python_requires (#3104)
IAlibay
authored
Fix rotateby documentation (#2903)

RMeli
authored and
lilyminium
committed

Commits on Mar 7, 2021

Fixed NSGrid (#3133)

richardjgowers
and
IAlibay
authored

Commits on Mar 8, 2021

Implement legacy CI for py2.7 and 3.5 (#3143)
IAlibay
authored

Commits on Mar 12, 2021

Unpin dependencies for py3.6+ in setup files (#3139)
IAlibay
authored

Commits on Mar 13, 2021

Move and deprecate old waterbridge analysis code location (#3111)
xiki-tempula
authored

Commits on Mar 15, 2021

Fixed issue -3129 (#3130)

richardjgowers
and
IAlibay
authored

Commits on Mar 21, 2021

fixed NSGrid bug #2345 (#3182)
zemanj
authored

Commits on Mar 22, 2021

Deprecates using segid for chainid (#3173)
lilyminium
authored

Commits on Mar 27, 2021

Issue 2327 - Warn of upcoming scale_factor changes (#3185)
IAlibay
authored

Commits on Mar 29, 2021

improved FastNS performance for orthorhombic boxes (#3186)
zemanj
authored

Commits on Apr 3, 2021

Commits on Apr 4, 2021

Added get_connections (#3160)

lilyminium
and
richardjgowers
authored

Commits on Apr 5, 2021

Commits on Apr 28, 2021

Commits on May 1, 2021

Update to 1.1.1 (#3251)
IAlibay
authored

Commits on May 2, 2021

removed autogenerated C/CPP files from version control (#3250)
richardjgowers
authored

Commits on May 6, 2021

retroactive CHANGELOG 1.0.0 fixes (#3260)
orbeckst
authored

Commits on May 13, 2021