Run GH Actions CI for py3.6+ and keep Travis for 3.5 and 2.7 by lilyminium · Pull Request #3067 · MDAnalysis/mdanalysis

lilyminium · 2020-12-09T02:02:34Z

Fixes #3079
Branches off #3061 to fix #2768. As elegantly suggested by @IAlibay, this PR

ports fixes from develop to master
Keeps GH actions for pythons 3.6-3.8
Keeps Travis for pythons 2.7 and 3.5

In #3061 I moved Python 2.7 and 3.5 CI to GH actions. It is a bit clunky, unreadable, and potentially difficult to maintain. Given that we can hopefully just move onto 2.0 and Python 3.6+, perhaps this compromise gets things done for an intermediate 1.0.1 release while we iron out the kinks on #3061.

PR Checklist

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

* fix MDAnalysis#3006 * fixed the for/else loop that accidentally added too many versions of dev/ and stable/ (cherry picked from commit 2d14dbd)

Not an issue targetted fix. Improve CI (no user facing changes) - Overview mamba is a dropin replacement for the conda CLI but faster - Work done in this PR Enabled the `MAMBA` environment variable keyword for the CI helper. (cherry picked from commit 2ee4e9d)

… with unwrapping (PR MDAnalysis#2992) fixes MDAnalysis#2984 (cherry picked from commit beb5232)

* increase default Python to 3.7 on Travis CI - set PYTHON_VERSION=3.7 - set MAMBA=false for Python 3.5 (no mamba package available, fall backto conda) * ensure conda package is available for numpy 1.13 NumPy 13.3.3 packages are available for Python 2.7 and 3.6 only so for the tests with the minimal numpy version we set Python to 3.6.

Fixes MDAnalysis#3036 ## Work done in this PR - Adds a continuous integration workflow based on github actions. - Disables previous continuous integration workflow based on TravisCI. - Fixes minor Visibledeprecation warnings with the hole2 tests.

Fixes MDAnalysis#3046. Deploys docs in gh-ci.yaml script and removes Travis

* TST, CI: add ARM64 Graviton 2 to CI * start testing MDAnalysis on ARM64 using new AWS Graviton 2 architecture available in Travis CI * testing on my fork shows only two failures in the MDAnalysis test suite using a fairly minimal set of dependencies; we can probably either fix those or skip them and open an issue * the test failures are: `test_written_remarks_property` `TestEncoreClustering.test_clustering_three_ensembles_two_identical` * run time for this CI entry is about 23 minutes, which is solid for ARM; we save a lot of time using experimental upstream wheels in some cases and excluding (source builds of) dependencies where possible until the ARM64 binary wheel ecosystem matures a bit more * MAINT: ARM64 shims * adjust `CAffinityPropagation()` C-level function to use `double` instead of `float` in some strategic locations that allow the `test_clustering_three_ensembles_two_identical()` test to pass on gcc115 ARM64 machine * mark `test_written_remarks_property()` as a known failure on ARM64; it fails in Travis CI on that platform, but not on gcc115 ARM64 machine; that said, this test is already known to be flaky on Windows 32-bit (may depend on character settings on machine?) * MAINT: MR 2956 revisions * reduce optimization level of MDAnalysis builds on ARM64 to avoid problems with `ap.c` causing test failures on that architecture * revert any source changes to `ap.c`

…2953) * fix NameError when catching NoDataError * add test + missing imports

…DAnalysis#3029) Fixes MDAnalysis#3028 * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping.

pep8speaks · 2020-12-09T02:02:42Z

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

In the file package/setup.py:

Line 275:80: E501 line too long (81 > 79 characters)
Line 278:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/formats/test_libdcd.py:

Line 323:21: E127 continuation line over-indented for visual indent

Comment last updated at 2020-12-14 22:22:43 UTC

codecov · 2020-12-09T03:01:03Z

Codecov Report

Merging #3067 (09bdc9a) into master (2ef90f2) will increase coverage by 0.72%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #3067      +/-   ##
==========================================
+ Coverage   91.46%   92.19%   +0.72%     
==========================================
  Files         173      166       -7     
  Lines       24203    22729    -1474     
  Branches     3193     3194       +1     
==========================================
- Hits        22138    20954    -1184     
- Misses       1438     1683     +245     
+ Partials      627       92     -535

Impacted Files	Coverage Δ
package/MDAnalysis/coordinates/ParmEd.py	`88.26% <100.00%> (+4.83%)`	⬆️
package/MDAnalysis/analysis/hole2/hole.py	`73.40% <0.00%> (-8.78%)`	⬇️
package/MDAnalysis/analysis/base.py	`95.60% <0.00%> (-4.40%)`	⬇️
package/MDAnalysis/topology/tpr/obj.py	`96.82% <0.00%> (-3.18%)`	⬇️
...onality_reduction/DimensionalityReductionMethod.py	`97.14% <0.00%> (-2.86%)`	⬇️
package/MDAnalysis/coordinates/chemfiles.py	`90.47% <0.00%> (-1.20%)`	⬇️
coordinates/__init__.py
analysis/__init__.py
util.py
auxiliary/__init__.py
... and 109 more

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IAlibay

Might just be me looking in the wrong place, but I can't seem to be able to see the py3.5 run?

lilyminium · 2020-12-09T03:38:18Z

@IAlibay I can't see a successful python 3.5 in https://travis-ci.com/github/MDAnalysis/mdanalysis/builds/192419679, on master a month ago?

Edit: nevermind, it was the blank one -- evidently before @orbeckst increased the Python to 3.7

IAlibay · 2020-12-14T12:56:33Z

@lilyminium could you also port #3073 here too? (i.e. just delete the appveyor yaml file). That would save us having to open a separate PR to deal with this.

IAlibay

lgtm! thanks :)

Unless there's any major objections to this pseudo-port approach (i.e. having a small reliance on Travis credits for a branch that we don't often push to), then let's go with this (pinging @MDAnalysis/coredevs).

Fixes MDAnalysis#3036 ## Work done in this PR - Adds a continuous integration workflow based on github actions. - Disables previous continuous integration workflow based on TravisCI. - Fixes minor Visibledeprecation warnings with the hole2 tests.

Fixes MDAnalysis#3046. Deploys docs in gh-ci.yaml script and removes Travis

* TST, CI: add ARM64 Graviton 2 to CI * start testing MDAnalysis on ARM64 using new AWS Graviton 2 architecture available in Travis CI * testing on my fork shows only two failures in the MDAnalysis test suite using a fairly minimal set of dependencies; we can probably either fix those or skip them and open an issue * the test failures are: `test_written_remarks_property` `TestEncoreClustering.test_clustering_three_ensembles_two_identical` * run time for this CI entry is about 23 minutes, which is solid for ARM; we save a lot of time using experimental upstream wheels in some cases and excluding (source builds of) dependencies where possible until the ARM64 binary wheel ecosystem matures a bit more * MAINT: ARM64 shims * adjust `CAffinityPropagation()` C-level function to use `double` instead of `float` in some strategic locations that allow the `test_clustering_three_ensembles_two_identical()` test to pass on gcc115 ARM64 machine * mark `test_written_remarks_property()` as a known failure on ARM64; it fails in Travis CI on that platform, but not on gcc115 ARM64 machine; that said, this test is already known to be flaky on Windows 32-bit (may depend on character settings on machine?) * MAINT: MR 2956 revisions * reduce optimization level of MDAnalysis builds on ARM64 to avoid problems with `ap.c` causing test failures on that architecture * revert any source changes to `ap.c`

…2953) * fix NameError when catching NoDataError * add test + missing imports

…DAnalysis#3029) Fixes MDAnalysis#3028 * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping.

…o gh-actions-py3

IAlibay · 2020-12-21T14:15:33Z

@lilyminium this is probably good to merge. However, why is RTD failing?

lilyminium · 2020-12-21T23:32:22Z

Thanks for the review @IAlibay! RTD is failing because #3078 isn't merged, because of #3079...

lilyminium and others added 10 commits December 9, 2020 12:49

Add dev and stable versions once (MDAnalysis#3009)

e8403c7

* fix MDAnalysis#3006 * fixed the for/else loop that accidentally added too many versions of dev/ and stable/ (cherry picked from commit 2d14dbd)

Fixed AtomGroup.center's behavior when using compounds in conjugation…

b37f518

… with unwrapping (PR MDAnalysis#2992) fixes MDAnalysis#2984 (cherry picked from commit beb5232)

Deploy docs via GitHub Actions CI (MDAnalysis#3053)

63444aa

Fixes MDAnalysis#3046. Deploys docs in gh-ci.yaml script and removes Travis

ParmEdConverter: fix NameError when catching NoDataError (MDAnalysis#…

3b941da

…2953) * fix NameError when catching NoDataError * add test + missing imports

Improve the performance of ParmEd converter. (Fix MDAnalysis#3028) (M…

c07b5c8

…DAnalysis#3029) Fixes MDAnalysis#3028 * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping.

mv travis back and only keep 3.5 and 2.7

082b087

lilyminium requested a review from IAlibay December 9, 2020 02:03

Merge branch 'master' into gh-actions-py3

7a92b3c

IAlibay reviewed Dec 9, 2020

View reviewed changes

move py3.5 job

74f229c

lilyminium requested a review from IAlibay December 10, 2020 01:00

IAlibay approved these changes Dec 14, 2020

View reviewed changes

IAlibay mentioned this pull request Dec 14, 2020

drop AppVeyor CI #3065

Closed

2 tasks

IAlibay and others added 9 commits December 15, 2020 08:06

Deploy docs via GitHub Actions CI (MDAnalysis#3053)

86eb383

Fixes MDAnalysis#3046. Deploys docs in gh-ci.yaml script and removes Travis

ParmEdConverter: fix NameError when catching NoDataError (MDAnalysis#…

7f83f4a

…2953) * fix NameError when catching NoDataError * add test + missing imports

Improve the performance of ParmEd converter. (Fix MDAnalysis#3028) (M…

a64eed9

…DAnalysis#3029) Fixes MDAnalysis#3028 * Improves the performance of the ParmEd converter by using a dictionary lookup for the atomgroup to universe index mapping.

mv travis back and only keep 3.5 and 2.7

454bd4d

move py3.5 job

60ea0bb

Merge branch 'gh-actions-py3' of github.com:lilyminium/mdanalysis int…

c88698d

…o gh-actions-py3

rm appveyor

6a99f57

try pinning

09bdc9a

lilyminium merged commit c3c4240 into MDAnalysis:master Dec 21, 2020

lilyminium deleted the gh-actions-py3 branch December 21, 2020 23:35

lilyminium mentioned this pull request Dec 22, 2020

Port GH actions and other fixes to master #3061

Closed

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fiona-naughton added maintainability Continuous Integration labels Sep 26, 2023

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Run GH Actions CI for py3.6+ and keep Travis for 3.5 and 2.7#3067

Run GH Actions CI for py3.6+ and keep Travis for 3.5 and 2.7#3067
lilyminium merged 22 commits intoMDAnalysis:masterfrom
lilyminium:gh-actions-py3

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