[DM-15056] lsst.afw.geom documentation build issue (lsst.afw.geom.all.doctree not found) and documenteer 0.3.0a5 - Jira

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Type: Bug
Status: Done
Resolution: Done
Fix Version/s: None
Component/s: afw, Stack Documentation and UX
Labels:
- documenteer

Story Points:
1.8
Epic Link:
sqr-s18-doc-stack-1
Team:
SQuaRE

Description

With documenteer 0.3.0a5 there is a build issue with lsst.afw.geom related to the numpydoc/autoapi/automodapi extension stack. This ticket will diagnose and fix it.

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.all'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.any'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.arcsecToRad'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.averageSpherePoint'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ceil'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.degToRad'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.floor'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.isAngle'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.makeAffineTransformFromTriple'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.masToRad'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.radToArcsec'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.radToDeg'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.radToMas'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:31: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.truncate'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.AffineTransform'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Angle'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.AngleUnit'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Box2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Box2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.BoxD'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.BoxI'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseCoordinateExpr2'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseCoordinateExpr3'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseExtent2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseExtent2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseExtent3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBaseExtent3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBasePoint2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBasePoint2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBasePoint3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateBasePoint3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateExpr'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateExpr2'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.CoordinateExpr3'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Extent'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Extent2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Extent2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Extent3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Extent3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentBase2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentBase2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentBase3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentBase3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentD'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.ExtentI'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.LinearTransform'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Point'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Point2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Point2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Point3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.Point3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointBase2D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointBase2I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointBase3D'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointBase3I'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointD'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.PointI'

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/modules/lsst.afw.geom/index.rst:39: WARNING: toctree references unknown document 'py-api/lsst.afw.geom.SpherePoint'

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertImagesAlmostEqual:13: WARNING: Definition list ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertImagesAlmostEqual:19: WARNING: Definition list ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMaskedImagesAlmostEqual:10: WARNING: Definition list ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMaskedImagesAlmostEqual:14: WARNING: Unexpected indentation.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMaskedImagesAlmostEqual:16: WARNING: Block quote ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMaskedImagesAlmostEqual:22: WARNING: Definition list ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMasksEqual:13: WARNING: Definition list ends without a blank line; unexpected unindent.

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertImagesAlmostEqual:18: WARNING: Undefined substitution referenced: "val1 - val0".

/Users/jsick/lsst/pipelines_lsst_io_stack/lsst_stack/stack/miniconda3-4.3.21-10a4fa6/DarwinX86/afw/16.0-9-gdf7162dbc/python/lsst/afw/image/testUtils.py:docstring of lsst.utils.tests.TestCase.assertMaskedImagesAlmostEqual:21: WARNING: Undefined substitution referenced: "val1 - val0".

looking for now-outdated files...

Traceback (most recent call last):

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/documenteer/documenteer/sphinxrunner.py", line 85, in run_sphinx

    app.build(force_all, filenames)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/application.py", line 325, in build

    self.builder.build_all()

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_all

    self.build(None, summary='all source files', method='all')

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 359, in build

    for docname in self.env.check_dependents(self.app, updated_docnames):

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/__init__.py",line 620, in check_dependents

    for docnames in app.emit('env-get-updated', self):

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/application.py", line 444, in emit

    return self.events.emit(event, self, *args)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/events.py", line 79, in emit

    results.append(callback(*args))

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 135, in get_updated_docs

    return self.assign_section_numbers(env) + self.assign_figure_numbers(env)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 277, in assign_figure_numbers

    _walk_doc(env.config.master_doc, tuple())

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 274, in _walk_doc

    _walk_doctree(docname, doctree, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 252, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 252, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 268, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 260, in _walk_doctree

    _walk_doc(subdocname, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 274, in _walk_doc

    _walk_doctree(docname, doctree, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 252, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 252, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 252, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 268, in _walk_doctree

    _walk_doctree(docname, subnode, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 260, in _walk_doctree

    _walk_doc(subdocname, secnum)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/collectors/toctree.py", line 273, in _walk_doc

    doctree = env.get_doctree(docname)

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/__init__.py",line 782, in get_doctree

    with open(doctree_filename, 'rb') as f:

FileNotFoundError: [Errno 2] No such file or directory: '/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/_build/doctree/py-api/lsst.afw.geom.all.doctree'

Exception occurred:

  File "/Users/jsick/lsst/pipelines_lsst_io_stack/pyvenv/lib/python3.6/site-packages/sphinx/environment/__init__.py",line 782, in get_doctree

    with open(doctree_filename, 'rb') as f:

FileNotFoundError: [Errno 2] No such file or directory: '/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/_build/doctree/py-api/lsst.afw.geom.all.doctree'

The full traceback has been saved in /var/folders/sq/89jdjpmd1f52y795rzxs3xk00000gn/T/sphinx-err-0cxfnawc.log, if you want to report the issue to the developers.

Please also report this if it was a user error, so that a better error message can be provided next time.

A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!

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lsst.afw-build.zip
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12/Jul/18 2:13 PM

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DM-15069 documenteer build failed on d.2018.07.10

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Assignee:: Jonathan Sick

Reporter:: Jonathan Sick

Reviewers:: Russell Owen

Watchers:: Jonathan Sick, Krzysztof Findeisen, Russell Owen, Tim Jenness

Votes:: 0 Vote for this issue

Watchers:: 4 Start watching this issue

Dates

Created:: 09/Jul/18 3:05 PM

Updated:: 13/Jul/18 11:11 AM

Resolved:: 13/Jul/18 11:11 AM

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