Backport 1.0.1 by orbeckst · Pull Request #2798 · MDAnalysis/mdanalysis

orbeckst · 2020-06-26T18:18:21Z

Fixes #2768

Changes made in this Pull Request:

includes backports of all fixes tagged with Milestone 1.0.x (currently 1.0.1)
cherry-picked commits

Add to this branch and merge into Master before releasing 1.0.1.

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

orbeckst · 2020-06-26T18:22:15Z

I think we're mostly waiting for the fix to #2751.

codecov · 2020-06-26T22:01:06Z

Codecov Report

Merging #2798 into master will increase coverage by 0.76%.
The diff coverage is 98.61%.

@@            Coverage Diff             @@
##           master    #2798      +/-   ##
==========================================
+ Coverage   91.38%   92.14%   +0.76%     
==========================================
  Files         164      170       +6     
  Lines       22490    23013     +523     
  Branches     3160     3180      +20     
==========================================
+ Hits        20552    21205     +653     
- Misses       1315     1711     +396     
+ Partials      623       97     -526

Impacted Files	Coverage Δ
package/MDAnalysis/__init__.py	`92.68% <ø> (ø)`
package/MDAnalysis/analysis/leaflet.py	`96.42% <ø> (+1.30%)`	⬆️
package/MDAnalysis/coordinates/NAMDBIN.py	`100.00% <ø> (ø)`
package/MDAnalysis/core/_get_readers.py	`96.00% <ø> (ø)`
package/MDAnalysis/topology/HoomdXMLParser.py	`85.41% <50.00%> (+2.08%)`	⬆️
package/MDAnalysis/analysis/helanal.py	`90.59% <94.73%> (+2.66%)`	⬆️
package/MDAnalysis/core/topologyattrs.py	`96.56% <99.27%> (+1.15%)`	⬆️
...DAnalysis/analysis/hydrogenbonds/hbond_analysis.py	`99.09% <100.00%> (+1.82%)`	⬆️
package/MDAnalysis/analysis/waterdynamics.py	`96.14% <100.00%> (+2.20%)`	⬆️
package/MDAnalysis/coordinates/TRZ.py	`88.56% <100.00%> (+4.98%)`	⬆️
... and 109 more

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pep8speaks · 2020-07-06T23:56:31Z

Hello @orbeckst! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file package/MDAnalysis/analysis/waterdynamics.py:

Line 523:80: E501 line too long (84 > 79 characters)
Line 525:80: E501 line too long (89 > 79 characters)

In the file package/MDAnalysis/coordinates/chain.py:

Line 267:57: E127 continuation line over-indented for visual indent
Line 347:80: E501 line too long (81 > 79 characters)

In the file package/MDAnalysis/core/_get_readers.py:

Line 260:17: E122 continuation line missing indentation or outdented

In the file package/MDAnalysis/core/selection.py:

Line 583:10: E225 missing whitespace around operator

In the file package/MDAnalysis/core/topologyattrs.py:

Line 531:80: E501 line too long (83 > 79 characters)
Line 982:80: E501 line too long (81 > 79 characters)
Line 1821:80: E501 line too long (83 > 79 characters)
Line 2062:80: E501 line too long (83 > 79 characters)

In the file testsuite/MDAnalysisTests/__init__.py:

Line 123:80: E501 line too long (80 > 79 characters)

In the file testsuite/MDAnalysisTests/core/test_atomselections.py:

Line 81:80: E501 line too long (100 > 79 characters)
Line 1133:1: E302 expected 2 blank lines, found 1
Line 1147:1: E302 expected 2 blank lines, found 1
Line 1148:80: E501 line too long (87 > 79 characters)

In the file testsuite/MDAnalysisTests/core/test_segmentgroup.py:

Line 95:80: E501 line too long (84 > 79 characters)
Line 95:81: E231 missing whitespace after ','

In the file testsuite/MDAnalysisTests/core/test_universe.py:

Line 755:80: E501 line too long (80 > 79 characters)

Comment last updated at 2020-09-04 17:43:28 UTC

lilyminium · 2020-07-09T06:54:52Z

I haven't looked through all your commits, but there are two docs related ones:

c761ba3 (first adding scripts for doc versioning)
3d95282 (building docs for all branches that Travis runs on)

Thanks @orbeckst :-)

orbeckst · 2020-07-12T01:33:29Z

PR #2812 ~~will be~~ was directly added to master via git rebase --onto master develop VOD555-fix_rdf_density; git checkout master; git merge VOD555-fix_rdf_density (so that I don't have to cherry-pick commits)

- fix (because it was not documented before) - density=True now means "calculate the single site density"; default is still "calculate RDF" (now meaning density=False) - update docs - update tests (add test for default behavior) - update CHANGELOG - backported issue #2811 fix (directly rebased onto master instead of added to PR #2798

- backported CI code to build versioned docs (see #2798 (comment)) - added outside PR #2798

orbeckst · 2020-07-12T01:41:19Z

I added the versioned docs commits (#2798 (comment)) directly to master to see if the docs build.

- fix #2191 - use MPLBACKEND=agg in the CI environments - Travis - appveyor - Azure pipelines - update CHANGELOG

* CI: add codecov to Azure CI * add a codecov upload to Azure CI (32-bit Windows) Co-authored-by: Thomas Hu <thomasrockhu@users.noreply.github.com>

(List was messed up in a previous cherry-pick and not fully correct then.)

- removed superfluous coordinates/dcdtimeseries.c - removed execute permissions from module NAMDBI.py

@Luthaf

- pinning ensures that chemfiles conda package pulls the last working netcdf4 package in; otherwise we get failures such as OSError: libnetcdf.so.18: cannot open shared object file: No such file or directory - #2798 (comment) Co-authored: @Luthaf

- pinning ensures that chemfiles conda package pulls the last working netcdf4 package in; otherwise we get failures such as OSError: libnetcdf.so.18: cannot open shared object file: No such file or directory - #2798 (comment) Co-authored-by: Guillaume Fraux <luthaf@luthaf.fr>

- explicit PYPI_CHECK in script section - switch travis to beta for config validation - https://docs.travis-ci.com/user/build-config-validation - get feedback on problems with the config yml file Note: Use ci-helper's algorithm for installing numpy and don't pin a numpy version, not even for the simple PYPI_CHECK section (cherry picked from commit bbc3dcb)

- generate LONG_DESCRIPTION from README.rst - remove SUMMARY.txt (out of date) - read top-level repository README.rst for LONG_DESCRIPTION - changed README.rst - add installation instruction (link) - add links to Quickstart Guide, User Guide, and API docs - add links to issue tracker and mailing list in text (Contributing) - replaced links to wiki with links to User Guide - remove raw html from README (raw html not allowed on PyPi) - replace NumFOCUS logo image with reduced size version (200 x 61 px) and standard reST image syntax (logo added to web site in commit MDAnalysis/MDAnalysis.github.io@ec4fe2c ) - fix broken link - tutorials direct to Examples in User Guide - add link to video section of "Learning MDAnalysis" - passes `twine check` - cleaned up MANIFEST.in (for pypi packages) - fixed links in Py files - Make sure that we always use the SSL url of the home page git grep -l 'http://www\.mdanalysis\.org' | xargs perl -wpi~ -e 's(https://www\.mdanalysis\.org)(https://www.mdanalysis.org)' - fixed link to issue tracker in files git grep -l 'issues.mdanalysis.org' | xargs perl -wpi~ -e 's(https?://issues\.mdanalysis\.org)(https://github.com/MDAnalysis/mdanalysis/issues) - fixed PEP8 issues in files - various updates in testsuite/README (link to userguide, update badges) - use User Guide as style reference Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> (cherry picked from commit d0b03e6)

- see #2920 - add deprecation note to as_Universe - add deprecation notice to LeafletFinder: filename instead of Universe will be removed (uses as_Universe so users will see the DeprecationWarning from as_Universe) - add test - update CHANGELOG for 1.0.1

- fixes The output files had all the the floating point numbers joined in a single string. - see PR #2733 - update AUTHORS - update CHANGELOG

orbeckst · 2020-08-27T07:50:56Z

It seems that pinning chemfiles-lib hangs conda (see https://travis-ci.com/github/MDAnalysis/mdanalysis/jobs/378230029) – stops at

restoring free channel

Re-running with free channel restored

Collecting package metadata (current_repodata.json): ...working... done

Solving environment: ...working... WARNING conda.core.solve:_add_specs(600): pinned spec chemfiles-lib==0.9.3[build=he1b5a44_0.*] conflicts with explicit specs.  Overriding pinned spec.

failed with initial frozen solve. Retrying with flexible solve.

Solving environment: ...working... WARNING conda.core.solve:_add_specs(600): pinned spec chemfiles-lib==0.9.3[build=he1b5a44_0.*] conflicts with explicit specs.  Overriding pinned spec.

failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... WARNING conda.core.solve:_add_specs(600): pinned spec chemfiles-lib==0.9.3[build=he1b5a44_0.*] conflicts with explicit specs.  Overriding pinned spec.

orbeckst · 2020-08-27T07:51:53Z

.travis.yml

           PYTHON_VERSION=2.7
           CODECOV="true"
           NUMPY_VERSION=1.16
+           CONDA_DEPENDENCIES="${CONDA_DEPENDENCIES} chemfiles-lib=0.9.3=he1b5a44_0"


Is this the correct way to pin chemfiles-lib?

Yes, that should be. I only tested installing chemfiles + netcdf4 this way, so there might be additional interaction with other dependencies. I'll have another look =)

Thank you, much appreciated!!

I don't understand fully what's happening here (I can't get conda to reproduce the bug locally, so I have to start Travis to check, which is very slow 😃); but I got the tests to work with Python 2.7 on this branch by using the PyPi/pip version of chemfiles instead of the conda one (https://travis-ci.org/github/Luthaf/mdanalysis/jobs/722309790). Basically adding chemfiles to PIP_DEPENDENCIES and removing it from CONDA_DEPENDENCIES.

The main difference with conda is that I'm building the wheels on PyPi myself instead of using the conda tools, but the linux wheel is built with the manylinux1 docker image, which should guarantee compatibility with all possible Python installations on Linux. The wheels also work perfectly on osx & windows.

orbeckst · 2020-08-29T23:01:17Z

Thank you, will try it.

…

Am 29.08.2020 um 12:31 schrieb Guillaume Fraux ***@***.***>: @Luthaf commented on this pull request. In .travis.yml: > - env: NAME="python 2.7" PYTHON_VERSION=2.7 CODECOV="true" NUMPY_VERSION=1.16 + CONDA_DEPENDENCIES="${CONDA_DEPENDENCIES} chemfiles-lib=0.9.3=he1b5a44_0" I don't understand fully what's happening here (I can't get conda to reproduce the bug locally, so I have to start Travis to check, which is very slow 😃); but I got the tests to work with Python 2.7 on this branch by using the PyPi/pip version of chemfiles instead of the conda one (https://travis-ci.org/github/Luthaf/mdanalysis/jobs/722309790). Basically adding chemfiles to PIP_DEPENDENCIES and removing it from CONDA_DEPENDENCIES. The main difference with conda is that I'm building the wheels on PyPi myself instead of using the conda tools, but the linux wheel is built with the manylinux1 docker image, which should guarantee compatibility with all possible Python installations on Linux. The wheels also work perfectly on osx & windows. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

Work around conda-weirdness which just fails to properly resolve the pinned chemfiles-lib that would be compatible with the last working Py 2.7 version of netcdf4.

orbeckst · 2020-09-02T00:48:37Z

@Luthaf thank you, CI is finally happy again! 🎉

orbeckst · 2020-09-02T00:51:06Z

@MDAnalysis/coredevs could someone please have a quick look at the current backports? A lot of stuff has accumulated and I'd like to get that merged before taking on anything else. Thank you.

lilyminium

Nothing jumps out on a quick look-over, the fixes look good. It'll be nice to have Travis happy again! Thanks @orbeckst :-)

maintainer/change_release.sh

package/MDAnalysis/coordinates/TRZ.py

IAlibay

At the very least for the changes I was involved with, it seems all good :)

Couple of minor changes (mainly PEP8 things).

package/AUTHORS

package/MDAnalysis/core/selection.py

testsuite/MDAnalysisTests/core/test_universe.py

testsuite/MDAnalysisTests/lib/test_log.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Lily Wang <lilyminium@users.noreply.github.com>

orbeckst · 2020-09-02T18:17:30Z

I am not going to fix PEP8 things because that will create more divergence between 1.0.1 and develop; I wanted to keep it as backport + fixes to make it work.

orbeckst · 2020-09-03T23:31:16Z

Wait for PR #2928 to be merged into this branch (@lilyminium is working on it).

* deprecate helanal, to be removed in 2.0.0 (use analysis.helix_analysis in 2.0 from PR #2622) * add deprecation warnings to analysis.helanal * update CHANGELOG

orbeckst added the release label Jun 26, 2020

orbeckst added this to the 1.0.x milestone Jun 26, 2020

orbeckst mentioned this pull request Jun 26, 2020

Removes element guessing for TOPParser #2714

Merged

4 tasks

orbeckst linked an issue Jun 26, 2020 that may be closed by this pull request

Release 1.0.1 #2768

Closed

This was referenced Jun 27, 2020

Added space to separate field in output files. #2733

Closed

Make the TPR parser a bit faster #2804

Merged

Faster name selections #2755

Merged

package info files are not up-to-date #2807

Closed

Chainreader Refactoring #2815

Merged

This was referenced Jul 4, 2020

Cannot select atoms with StringSelection from empty AtomGroup #2765

Closed

Remove dt from Timestep #2825

Open

orbeckst assigned orbeckst and richardjgowers Jul 6, 2020

orbeckst mentioned this pull request Jul 9, 2020

add analytics and privacy policy #2828

Merged

4 tasks

orbeckst mentioned this pull request Jul 10, 2020

Fix InterRDF_s when given density=True #2812

Merged

4 tasks

orbeckst pushed a commit that referenced this pull request Jul 12, 2020

build docs for master as well

7313cf1

- backported CI code to build versioned docs (see #2798 (comment)) - added outside PR #2798

orbeckst and others added 7 commits July 11, 2020 18:43

removed matplotlib.use('agg') from tests

dbaf957

- fix #2191 - use MPLBACKEND=agg in the CI environments - Travis - appveyor - Azure pipelines - update CHANGELOG

CI: add codecov to Azure CI (#2720)

dd4490a

* CI: add codecov to Azure CI * add a codecov upload to Azure CI (32-bit Windows) Co-authored-by: Thomas Hu <thomasrockhu@users.noreply.github.com>

fixed 1.0.1 contributor list based on git log

bbafbbe

(List was messed up in a previous cherry-pick and not fully correct then.)

file clean-ups

28f043f

- removed superfluous coordinates/dcdtimeseries.c - removed execute permissions from module NAMDBI.py

fixes google badges (#2772)

656e724

fixed maintainer/change_release.sh

dd0bbe4

bumped release to 1.0.1-dev (so that docs are properly labeled)

1e107ed

orbeckst and others added 3 commits August 26, 2020 22:34

orbeckst force-pushed the backport-1.0.1 branch 2 times, most recently from eea7679 to a44b838 Compare August 27, 2020 05:48

orbeckst and others added 2 commits August 26, 2020 22:53

Added space to separate field in helanal output files

27dae7c

- fixes The output files had all the the floating point numbers joined in a single string. - see PR #2733 - update AUTHORS - update CHANGELOG

orbeckst force-pushed the backport-1.0.1 branch from a44b838 to 27dae7c Compare August 27, 2020 05:54

orbeckst commented Aug 27, 2020

View reviewed changes

install chemfiles via pip for Python 2.7

4173028

Work around conda-weirdness which just fails to properly resolve the pinned chemfiles-lib that would be compatible with the last working Py 2.7 version of netcdf4.

lilyminium approved these changes Sep 2, 2020

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maintainer/change_release.sh Outdated Show resolved Hide resolved

package/MDAnalysis/coordinates/TRZ.py Outdated Show resolved Hide resolved

IAlibay requested changes Sep 2, 2020

View reviewed changes

fix minor inconsistencies in backport

f6cf595

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Lily Wang <lilyminium@users.noreply.github.com>

orbeckst force-pushed the backport-1.0.1 branch from 13052bb to f6cf595 Compare September 2, 2020 18:01

IAlibay approved these changes Sep 2, 2020

View reviewed changes

IAlibay mentioned this pull request Sep 2, 2020

Wrong results from capped_distance() with "nsgrid" search and atom in the center of the box #2919

Closed

Deprecate helanal (PR #2928)

d91e5e8

* deprecate helanal, to be removed in 2.0.0 (use analysis.helix_analysis in 2.0 from PR #2622) * add deprecation warnings to analysis.helanal * update CHANGELOG

orbeckst force-pushed the backport-1.0.1 branch from f64dadd to d91e5e8 Compare September 4, 2020 17:43

orbeckst merged commit 52679c7 into master Sep 4, 2020

orbeckst deleted the backport-1.0.1 branch September 4, 2020 21:51

orbeckst mentioned this pull request Sep 4, 2020

Release 1.0.1 #2768

Closed

orbeckst mentioned this pull request Oct 23, 2020

backport of stub transplants of AtomGroup (PR #2427) #3007

Merged

4 tasks

fiona-naughton added the maintainability label Sep 25, 2023

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orbeckst commented Jun 26, 2020

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