Run GH Actions CI for py3.6+ and keep Travis for 3.5 and 2.7 #3067
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* 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.
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Hello @lilyminium! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2020-12-14 22:22:43 UTC |
Codecov Report
@@ 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
Continue to review full report at Codecov.
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IAlibay
reviewed
Dec 9, 2020
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@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 |
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@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
approved these changes
Dec 14, 2020
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.
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@lilyminium this is probably good to merge. However, why is RTD failing? |
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Fixes #3079
Branches off #3061 to fix #2768. As elegantly suggested by @IAlibay, this PR
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.
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