Simplify CI and bump version requirements #3687
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Simplify the mechanism to check for supported doxygen versions. When running the script locally, allow for unsupported doxygen versions to run anyway, with a disclaimer. Detect doxygen path from CMake variables. Fail CI when dox_warnings.py throws an exception.
Also add missing fields from Doxygen 1.8.13 (Ubuntu 18.04) with their default values.
The installation job doesn't need the extended timeout since the underlying issue causing the slowdown was fixed by the recent build_cmake.sh refactor. The IPYTHON_EXECUTABLE variable is no longer necessary since Jupyter now has precedence over IPython. The Mayavi patch is only required in the Sphinx job.
Adapt the build script to select the correct version of gcov for coverage builds.
Also dedent paragraphs under properties to avoid the creation of a definition list, which changes the style of the documentation (e.g. the "(3,) array_of float" string is displayed in italic).
Capitalize names and remove spacing between page numbers.
Update Python package versions based on the versions available in Ubuntu 18.04.
Codecov Report
@@ Coverage Diff @@
## python #3687 +/- ##
========================================
Coverage 87% 88%
========================================
Files 537 541 +4
Lines 22717 24733 +2016
========================================
+ Hits 19987 21777 +1790
- Misses 2730 2956 +226
Continue to review full report at Codecov.
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The MDAnalysis module is no longer an issue for Sphinx 2.0 and is now fully supported by Sphinx 3.0.
Sphinx 3.0 now supports the `@property` decorator, but the napoleon extension doesn't correctly parse docstrings from methods with that decorator.
The old conditional did not take the HIP compiler into account and broke for code compiled with GCC 9.0 and linked with gcov, which injects exit().
Pulling images from the GitHub repository can take up to 25 min for large images (around 5 GB). This has the potential to break the CI pipeline when the image is not in the cached.
fweik
approved these changes
Apr 27, 2020
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Description of changes: