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Save previous commits from refresh-cookiecutter-for-more-robust-doc-build branch #337

Merged
merged 10 commits into from
Jul 29, 2020
Merged

Save previous commits from refresh-cookiecutter-for-more-robust-doc-build branch #337

merged 10 commits into from
Jul 29, 2020

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tlvu
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@tlvu tlvu commented Jul 29, 2020

Exact same changes as the other PR #336 that was squash merged.

I just wanted to preserve each commit separately, I had links to specific commit and squash merge would have make the links invalid.

Use regular merge, not squash merge to preserve existing separate commits.

tlvu added 10 commits July 27, 2020 13:14
@tlvu
cruft refresh cookiecutter: currently unapplied changes
049ecf6
@tlvu
.travis.yml: trigger Travis-CI for all branches
a2f6848 
To avoid having to harcode new dev branch name each time to trigger
Travis-CI or having to create PR too early to trigger Travis-CI and spam
everyone in the process.

I just want to test my changes on Travis-CI automatically.
@tlvu
cruft refresh cookiecutter for more robust doc build
99bbd29
@tlvu
doc: can not monkeypatch something that do not exist
2aa72b2 
numpy existed in Raven because we install xclim in Raven.

$ make docs
Generating docs with Sphinx ...
make[1]: Entering directory '/zstore/repos/flyingpigeon/docs'
Removing everything under 'build'...
Running Sphinx v3.1.2

Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/lvu/.conda/envs/flyingpigeon-docs/lib/python3.7/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/lvu/.conda/envs/flyingpigeon-docs/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 88, in execfile_
    exec(code, _globals)
  File "/zstore/repos/flyingpigeon/docs/source/conf.py", line 71, in <module>
    import numpy
ModuleNotFoundError: No module named 'numpy'

Makefile:20: recipe for target 'html' failed
make[1]: *** [html] Error 2
make[1]: Leaving directory '/zstore/repos/flyingpigeon/docs'
Makefile:147: recipe for target 'docs' failed
make: *** [docs] Error 2
@tlvu
doc: fix duplicate explicit target name errors
61fa189 
Using anonymous reference instead (double underscore).

Warning, treated as error:
../README.rst:2:Duplicate explicit target name: "wikipedia".
Makefile:20: recipe for target 'html' failed
make[1]: *** [html] Error 2
make[1]: Leaving directory '/zstore/repos/flyingpigeon/docs'
Makefile:147: recipe for target 'docs' failed
make: *** [docs] Error 2
@tlvu
doc: fix duplicate citation because of include
1778c06 
Basically file `spatial_analogs.rst` is processed standalone and then part of
`processes_des.rst` resulting in duplicate reference of `Roy2017` that appears
only in `spatial_analogs.rst`.

Renamed to `spatial_analogs.rst.inc` to avoid that file being processed
standalone.

It should be fine since that file is not referred anywhere in the toctree so it
did not have direct reference to it before.

Warning, treated as error:
/zstore/repos/flyingpigeon/docs/source/spatial_analogs.rst:65:duplicate citation Roy2017, other instance in /zstore/repos/flyingpigeon/docs/source/processes_des.rst
Makefile:20: recipe for target 'html' failed
make[1]: *** [html] Error 2
make[1]: Leaving directory '/zstore/repos/flyingpigeon/docs'
Makefile:147: recipe for target 'docs' failed
make: *** [docs] Error 2
@tlvu
doc: add tutorial.rst to toctree
385d606 
Warning, treated as error:
/zstore/repos/flyingpigeon/docs/source/tutorial.rst:document isn't included in any toctree
Makefile:20: recipe for target 'html' failed
make[1]: *** [html] Error 2
make[1]: Leaving directory '/zstore/repos/flyingpigeon/docs'
Makefile:147: recipe for target 'docs' failed
make: *** [docs] Error 2
@tlvu
doc: fix "Duplicate explicit target name" with new version of pywps a…
c97ebca 
…llowing anonymous links

Warning, treated as error:
/zstore/repos/flyingpigeon/flyingpigeon/processes/wps_subset_continents.py:docstring of flyingpigeon.processes.wps_subset_continents.SubsetcontinentProcess:16:Duplicate explicit target name: "doc".
Makefile:20: recipe for target 'html' failed
make[1]: *** [html] Error 2
make[1]: Leaving directory '/zstore/repos/flyingpigeon/docs'
Makefile:147: recipe for target 'docs' failed
make: *** [docs] Error 2

All warnings fixed:

/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_subset_continents.py:docstring of flyingpigeon.processes.wps_subset_continents.SubsetcontinentProcess:16: WARNING: Duplicate explicit target name: "doc".
/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_subset_countries.py:docstring of flyingpigeon.processes.wps_subset_countries.SubsetcountryProcess:16: WARNING: Duplicate explicit target name: "doc".
/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_subset_bbox.py:docstring of flyingpigeon.processes.wps_subset_bbox.SubsetBboxProcess:28: WARNING: Duplicate explicit target name: "doc".
/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_plot_timeseries.py:docstring of flyingpigeon.processes.wps_plot_timeseries.PlottimeseriesProcess:16: WARNING: Duplicate explicit target name: "doc".
/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_spatial_analog.py:docstring of flyingpigeon.processes.wps_spatial_analog.SpatialAnalogProcess:30: WARNING: Duplicate explicit target name: "doc".
/home/docs/checkouts/readthedocs.org/user_builds/flyingpigeon/checkouts/test-rtd-build/flyingpigeon/processes/wps_plot_spatial_analog.py:docstring of flyingpigeon.processes.wps_plot_spatial_analog.PlotSpatialAnalogProcess:18: WARNING: Duplicate explicit target name: "doc".
@tlvu
Travis-CI: disable doc build for python 3.6, 3.7 works fine
4a54bde 
ReadTheDocs is 3.7 so that's what matter.

Warning, treated as error:
autodoc: failed to import process 'processes.wps_pointinspection.PointinspectionProcess' from module 'flyingpigeon'; the following exception was raised:
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/flyingpigeon/lib/python3.6/site-packages/sphinx/ext/autodoc/importer.py", line 32, in import_module
    return importlib.import_module(modname)
  File "/home/travis/miniconda/envs/flyingpigeon/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/travis/build/bird-house/flyingpigeon/flyingpigeon/__init__.py", line 7, in <module>
    from .wsgi import application  # noqa: F401
  File "/home/travis/build/bird-house/flyingpigeon/flyingpigeon/wsgi.py", line 4, in <module>
    from .processes import processes
  File "/home/travis/build/bird-house/flyingpigeon/flyingpigeon/processes/__init__.py", line 8, in <module>
    from .wps_spatial_analog import SpatialAnalogProcess
  File "/home/travis/build/bird-house/flyingpigeon/flyingpigeon/processes/wps_spatial_analog.py", line 27, in <module>
    from flyingpigeon.ocgisDissimilarity import Dissimilarity, metrics
  File "/home/travis/build/bird-house/flyingpigeon/flyingpigeon/ocgisDissimilarity.py", line 13, in <module>
    class Dissimilarity(AbstractFieldFunction, AbstractParameterizedFunction):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
@tlvu
Travis-CI: enable python 3.8
c72ce7d
@tlvu tlvu requested a review from cehbrecht July 29, 2020 14:46
@tlvu tlvu merged commit baf9532 into master Jul 29, 2020
@tlvu tlvu deleted the save-previous-refresh-cookiecutter-for-more-robust-doc-build-branch branch July 29, 2020 14:53
@tlvu
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tlvu commented Jul 29, 2020

Link to bird-house/cookiecutter-birdhouse#96

@tlvu tlvu mentioned this pull request Jul 29, 2020
Merged
tlvu added a commit to bird-house/cookiecutter-birdhouse that referenced this pull request Jul 29, 2020
@tlvu
Merge pull request #96 from bird-house/fix-silent-docs-build-failure-…
caedce8 
…empty-autodoc-processes-list

Fix empty autodoc processes list silent docs build failure.

Currently, autodoc failure are treated as warnings only, resulting in
empty processes list, see
https://pavics-sdi.readthedocs.io/projects/raven/en/latest/processes.html.

This fix will turn these warnings into build failure on RtD and on
Travis-CI so we can catch those errors earlier.

Right now these warnings are falling silently !

Also changed Travis-CI config so it also builds Epub and Latex format as RtD to catch RtD errors before PR is merged.

Common fixes for those warnings are backported here.

Bonus we also catch nonexisting document reference and missing reference
in toctree, see below sample Raven warnings during docs build.

Raven succesful build logs with warnings on RtD:
https://readthedocs.org/api/v2/build/11487109.txt

/home/docs/checkouts/readthedocs.org/user_builds/pavics-raven/checkouts/latest/docs/source/index.rst:14:
WARNING: toctree contains reference to nonexisting document 'pyraven'
WARNING: autodoc: failed to import process 'processes.RavenProcess' from
module 'raven'; the following exception was raised:
No module named 'xclim.core'
WARNING: autodoc: failed to import process
'processes.RavenGR4JCemaNeigeProcess' from module 'raven'; the following
exception was raised:
No module named 'xclim.core'
WARNING: autodoc: failed to import process
'processes.RavenMOHYSEProcess' from module 'raven'; the following
exception was raised:
No module named 'xclim.core'
WARNING: autodoc: failed to import process 'processes.RavenHMETSProcess'
from module 'raven'; the following exception was raised:
No module named 'xclim.core'
WARNING: autodoc: failed to import process 'processes.RavenHBVECProcess'
from module 'raven'; the following exception was raised:
No module named 'xclim.core'
WARNING: autodoc: failed to import process
'processes.ObjectiveFunctionProcess' from module 'raven'; the following
exception was raised:
No module named 'xclim.core'
looking for now-outdated files... none found
pickling environment... done
checking consistency...
/home/docs/checkouts/readthedocs.org/user_builds/pavics-raven/checkouts/latest/docs/source/notebooks/Region_selection.ipynb:
WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/pavics-raven/checkouts/latest/docs/source/notebooks/Running_models_with_multiple_timeseries_files.ipynb:
WARNING: document isn't included in any toctree

This PR has been tested on Raven PR Ouranosinc/raven#293, Finch PR bird-house/finch#130, FlyingPigeon bird-house/flyingpigeon#337, bird-house/flyingpigeon#336, Emu bird-house/emu#105
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