Uploaded image for project: 'Data Management'
  1. Data Management
  2. DM-15056

lsst.afw.geom documentation build issue (lsst.afw.geom.all.doctree not found) and documenteer 0.3.0a5

    Details

      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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                • Assignee:
                  jsick Jonathan Sick
                  Reporter:
                  jsick Jonathan Sick
                  Reviewers:
                  Russell Owen
                  Watchers:
                  Jonathan Sick, Krzysztof Findeisen, Russell Owen, Tim Jenness
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                  0 Vote for this issue
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                  4 Start watching this issue

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                  • Created:
                    Updated:
                    Resolved:

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