[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
395 kB
12/Jul/18 2:13 PM

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DM-15069 documenteer build failed on d.2018.07.10

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Jonathan Sick added a comment - 09/Jul/18 3:10 PM

Confirmed the issue is currently localized to lsst.afw.geom. If I build without it

stack-docs build -s lsst.afw.geom

then the build completes.

Show

Jonathan Sick added a comment - 09/Jul/18 3:10 PM Confirmed the issue is currently localized to lsst.afw.geom . If I build without it stack-docs build -s lsst.afw.geom then the build completes.

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Jonathan Sick added a comment - 09/Jul/18 3:11 PM

There are some additional docstring syntax errors:

eading sources... [100%] releases/v14_0_tickets

/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".

/Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/packages/afw/index.rst:33: WARNING: undefined label: lsst.afw.geom (if the link has no caption the label must precede a section header)

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Jonathan Sick added a comment - 09/Jul/18 3:11 PM There are some additional docstring syntax errors: eading sources... [100%] releases/v14_0_tickets /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". /Users/jsick/lsst/pipelines_lsst_io_stack/pipelines_lsst_io/packages/afw/index.rst:33: WARNING: undefined label: lsst.afw.geom (if the link has no caption the label must precede a section header)

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Tim Jenness added a comment - 12/Jul/18 8:06 AM

Could this be related to ~~DM-14429~~? (Russell Owen?)

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Tim Jenness added a comment - 12/Jul/18 8:06 AM Could this be related to DM-14429 ? ( Russell Owen ?)

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Jonathan Sick added a comment - 12/Jul/18 1:55 PM

Summary from PR:

The primary purpose of this PR is to fix a Sphinx build failure with the lsst.afw.geom API reference docs. I think the issue is that since many of the APIs are primarily part of lsst.geom, some layer of the auto doc system was filtering those APIs out, while other parts kept those APIs. The interim solution was to ultimately skip those APIs using automodapi's skip argument.

This PR also includes some minor doc improvements to regularize the doc system and fix warnings:

Relocated and improved table formatting of the FITS header reference topic
Improved docstrings in lsst.afw that were creating warnings
Relocated the "Footprint" topic
Improved titles of the SpanSet and Footprint topics

stack-os-matrix: https://ci.lsst.codes/blue/organizations/jenkins/stack-os-matrix/detail/stack-os-matrix/28199/pipeline

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Jonathan Sick added a comment - 12/Jul/18 1:55 PM Summary from PR: The primary purpose of this PR is to fix a Sphinx build failure with the lsst.afw.geom API reference docs. I think the issue is that since many of the APIs are primarily part of lsst.geom, some layer of the auto doc system was filtering those APIs out, while other parts kept those APIs. The interim solution was to ultimately skip those APIs using automodapi's skip argument. This PR also includes some minor doc improvements to regularize the doc system and fix warnings: Relocated and improved table formatting of the FITS header reference topic Improved docstrings in lsst.afw that were creating warnings Relocated the "Footprint" topic Improved titles of the SpanSet and Footprint topics stack-os-matrix: https://ci.lsst.codes/blue/organizations/jenkins/stack-os-matrix/detail/stack-os-matrix/28199/pipeline

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Russell Owen added a comment - 12/Jul/18 2:39 PM

Very nice change. A few requests on github.

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Russell Owen added a comment - 12/Jul/18 2:39 PM Very nice change. A few requests on github.

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Jonathan Sick added a comment - 13/Jul/18 11:11 AM

Thanks Russell Owen for reviewing.

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Jonathan Sick added a comment - 13/Jul/18 11:11 AM Thanks Russell Owen for reviewing.

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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

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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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