#4721 pytables-3.2.3

[Derek Homeier]

Update to the latest upstream 3.2.3.1; built with -m under 10.10 and 10.11 for all three flavours. Note: the package does not support HDF5 v1.10 yet.

[Hanspeter Niederstrasser]

WARNING: While resolving dependency "sphinx-py35 >= 1.3.4-1" for package "pytables-py35-3.2.3.1-4", package "sphinx-py35" was not found.
Can't resolve dependency "sphinx-py35 (>= 1.3.4-1)" for package "pytables-py35-3.2.3.1-4" (no matching packages/versions found)
Exiting with failure.

Currently, only sphinx-py27 exists, and it's at version 1.2.3-1.

[Derek Homeier]

Sorry, I had lost track of that. When the first update with Python3.x variants #4395 was rejected for already being in fink, nonetheless only the py27 version was adopted in the stable tree.
I have just submitted a new Sphinx update with py34 and py35 versions in #4723.

[Hanspeter Niederstrasser]

pytables-py27 fails with this error. py34 and py35 fail similarly

writing output... [ 77%] usersguide/introduction                                                                                                             
Exception occurred:
  File "/sw/lib/python2.7/site-packages/docutils/writers/_html_base.py", line 671, in depart_document
    assert not self.context, 'len(context) = %s' % len(self.context)
AssertionError: len(context) = 1
The full traceback has been saved in /private/tmp/sphinx-err-uiTE0E.log, if you want to report the issue to the developers.

This is the output from the error log cited:

$ sudo cat /private/tmp/sphinx-err-uiTE0E.log
Password:
# Sphinx version: 1.4.8
# Python version: 2.7.14 (CPython)
# Docutils version: 0.13.1 release
# Jinja2 version: 2.8
# Last messages:
#   writing output... [ 65%] release-notes/RELEASE_NOTES_v3.2.x
#   writing output... [ 66%] release_notes
#   writing output... [ 68%] usersguide/bibliography
#   writing output... [ 69%] usersguide/condition_syntax
#   writing output... [ 70%] usersguide/datatypes
#   writing output... [ 72%] usersguide/file_format
#   writing output... [ 73%] usersguide/filenode
#   writing output... [ 75%] usersguide/index
#   writing output... [ 76%] usersguide/installation
#   writing output... [ 77%] usersguide/introduction
# Loaded extensions:
#   sphinx.ext.graphviz (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/graphviz.pyc
#   sphinx.ext.autodoc (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/autodoc.pyc
#   sphinx.ext.inheritance_diagram (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/inheritance_diagram.pyc
#   sphinx.ext.extlinks (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/extlinks.pyc
#   sphinx.ext.doctest (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/doctest.pyc
#   numpydoc (unknown version) from /sw/build.build/pytables-py27-3.2.3.1-4/PyTables-v.3.2.3.1/doc/sphinxext/numpydoc.py
#   sphinx.ext.viewcode (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/viewcode.pyc
#   sphinx.ext.pngmath (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/pngmath.pyc
#   alabaster (0.7.9) from /sw/lib/python2.7/site-packages/alabaster/__init__.pyc
#   ipython_console_highlighting (unknown version) from /sw/build.build/pytables-py27-3.2.3.1-4/PyTables-v.3.2.3.1/doc/sphinxext/ipython_console_highlighting.py
#   sphinx.ext.autosummary (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/autosummary/__init__.pyc
#   sphinx.ext.todo (1.4.8) from /sw/lib/python2.7/site-packages/sphinx/ext/todo.pyc
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/sphinx/cmdline.py", line 244, in main
    app.build(opts.force_all, filenames)
  File "/sw/lib/python2.7/site-packages/sphinx/application.py", line 297, in build
    self.builder.build_update()
  File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 251, in build_update
    'out of date' % len(to_build))
  File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 322, in build
    self.write(docnames, list(updated_docnames), method)
  File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 360, in write
    self._write_serial(sorted(docnames), warnings)
  File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 368, in _write_serial
    self.write_doc(docname, doctree)
  File "/sw/lib/python2.7/site-packages/sphinx/builders/html.py", line 448, in write_doc
    self.docwriter.write(doctree, destination)
  File "/sw/lib/python2.7/site-packages/docutils/writers/__init__.py", line 80, in write
    self.translate()
  File "/sw/lib/python2.7/site-packages/sphinx/writers/html.py", line 47, in translate
    self.document.walkabout(visitor)
  File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 187, in walkabout
    visitor.dispatch_departure(self)
  File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 1895, in dispatch_departure
    return method(node)
  File "/sw/lib/python2.7/site-packages/docutils/writers/_html_base.py", line 671, in depart_document
    assert not self.context, 'len(context) = %s' % len(self.context)
AssertionError: len(context) = 1

[Derek Homeier]

Confirmed, the doc build requires a newer Sphinx version; in particular the now current upstream needs an additional module numpydoc. Two options:
build the current version with docbuild disabled (files attached) or
wait for a Sphinx update (I have a local 1.6.5 I could submit).

[Hanspeter Niederstrasser]

This builds w/ 2 caveats:

• mock-py and six-py are needed at least for TestScript. Ubuntu has them as Depends: so they'll probably need to go there for us as well
• several of the dependency packages don't have py36 versions as yet.

I can commit the latest version with those changes, and then add py36 when the dependencies become available.

[Hanspeter Niederstrasser]

Ping.

All py36 dependencies should now be present in git. Should I fix the mock-py and six-py situation as described and commit? Then look at getting numpydoc installed and sphinx updated and then come back here to re-enable docs? I have some questions on sphinx, so it might be easier to move this forward as is.

[Derek Homeier]

Sphinx has come a bit closer to an update, but yes, commiting with BuildDepends - sphinx and Depends + mock-py, six-py would be fine for now.