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radical-cybertools / radical.saga

A Light-Weight Access Layer for Distributed Computing Infrastructure and Reference Implementation of the SAGA Python Language Bindings.
http://radical-cybertools.github.io/saga-python/
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Documentation compiling status #765

Closed iparask closed 4 years ago

iparask commented 4 years ago

I'm trying to compile the documentation of radical.saga and I'm getting several errors/ warnings. These need to be fixed before readthedocs is able to compile them correctly.

Here is the current snapshot:

reading sources... [100%] usage/config
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/adaptorwriting.rst:2: WARNING: malformed hyperlink target.
WARNING: autodoc: failed to import class 'utils.pty_shell.PTYShell' from module 'rs'; the following exception was raised:
No module named 'rs'
WARNING: autodoc: failed to import class 'utils.pty_process.PTYProcess' from module 'rs'; the following exception was raised:
No module named 'rs'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/index.rst:7: WARNING: toctree contains reference to nonexisting document 'developers/timeout_gc'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/index.rst:27: WARNING: toctree contains reference to nonexisting document 'adaptors/saga.adaptor.index'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/advert/advert_1.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/advert/advert_1.py
WARNING: autodoc: failed to import class 'advert.Entry' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'advert.Directory' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'attributes.Callback' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'attributes.Attributes' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import module 'context' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import module 'exceptions' from module 'saga'; the following exception was raised:
No module named 'saga'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/localfile.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:25: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/file_io.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/localfile.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:23: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/file_io.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:44: WARNING: duplicate object description of saga.filesystem.OVERWRITE, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:45: WARNING: duplicate object description of saga.filesystem.RECURSIVE, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:46: WARNING: duplicate object description of saga.filesystem.CREATE, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:47: WARNING: duplicate object description of saga.filesystem.CREATE_PARENTS, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:48: WARNING: duplicate object description of saga.filesystem.LOCK, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:49: WARNING: duplicate object description of saga.filesystem.EXCLUSIVE, other instance in library/replica/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:50: WARNING: duplicate object description of saga.filesystem.DEREFERENCE, other instance in library/replica/index, use :noindex: for one of them
WARNING: autodoc: failed to import class 'filesystem.File' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'filesystem.Directory' from module 'saga'; the following exception was raised:
No module named 'saga'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst:39: WARNING: duplicate label filesystemflags, other instance in /Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/replica/replica_1.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/replica/replica_1.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:40: WARNING: duplicate object description of saga.filesystem.OVERWRITE, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:41: WARNING: duplicate object description of saga.filesystem.RECURSIVE, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:42: WARNING: duplicate object description of saga.filesystem.CREATE, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:43: WARNING: duplicate object description of saga.filesystem.CREATE_PARENTS, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:44: WARNING: duplicate object description of saga.filesystem.LOCK, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:45: WARNING: duplicate object description of saga.filesystem.EXCLUSIVE, other instance in library/filesystem/index, use :noindex: for one of them
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:46: WARNING: duplicate object description of saga.filesystem.DEREFERENCE, other instance in library/filesystem/index, use :noindex: for one of them
WARNING: autodoc: failed to import class 'replica.LogicalFile' from module 'saga'; the following exception was raised:
No module named 'saga'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:65: WARNING: Title underline too short.

Logical Directory -- :class:`saga.replica.LogicalDirectory`
---------------------------------------------------------
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:65: WARNING: Title underline too short.

Logical Directory -- :class:`saga.replica.LogicalDirectory`
---------------------------------------------------------
WARNING: autodoc: failed to import class 'replica.LogicalDirectory' from module 'saga'; the following exception was raised:
No module named 'saga'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/index.rst:35: WARNING: duplicate label filesystemflags, other instance in /Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/index.rst
WARNING: autodoc: failed to import class 'resource.Manager' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'resource.Description' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'resource.Resource' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'resource.Compute' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'resource.Storage' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import class 'resource.Network' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import module 'session' from module 'saga'; the following exception was raised:
No module named 'saga'
WARNING: autodoc: failed to import module 'config' from module 'radical.saga.utils'; the following exception was raised:
No module named 'radical.saga.utils.config'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/index.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/job/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/tutorial/part5_osg.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/examples.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
/Users/iparask/Git/RADICAL/radical.saga/docs/source/_themes/armstrong/layout.html:16: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a <script> tag directly in your theme instead.
  {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
writing output... [100%] usage/index
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/adaptorwriting.rst:376: WARNING: undefined label: api_exceptions (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/adaptorwriting.rst:501: WARNING: undefined label: api_tasks (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/adaptorwriting.rst:568: WARNING: undefined label: util_logging (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/index.rst:30: WARNING: undefined label: chapter_code_examples (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/config.rst:17: WARNING: undefined label: conf_options (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/config.rst:29: WARNING: undefined label: conf_options (if the link has no caption the label must precede a section header)
generating indices...  genindexdone
highlighting module code... [100%] radical.saga.url
writing additional pages...  searchdone
copying images... [100%] images/google.png
copying downloadable files... [ 60%] ../../examples/tutorial/saga_example_local.copying downloadable files... [ 80%] ../../examples/tutorial/mandelbrot/saga_mancopying downloadable files... [100%] ../../examples/tutorial/mandelbrot/saga_mandelbrot_osg.py
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 63 warnings.

The HTML pages are in build.

I've pushed a branch named fix/docs that will include all the commits towards working documentation. I'll open a PR when they are ready, but I would like to have this issue to keep track of the progress.

iparask commented 4 years ago

These are the messages I'm getting now when I compile the documentation:

(rct) iparaskmac:docs iparask$ sphinx-build -b html source build
Running Sphinx v2.4.0
WARNING: Support for evaluating Python 2 syntax is deprecated and will be removed in Sphinx 4.0. Convert /Users/iparask/Git/RADICAL/radical.saga/docs/source/conf.py to Python 3 syntax.
['/Users/iparask/Git/RADICAL/radical.saga', '/Users/iparask/anaconda3/envs/rct/bin', '/Users/iparask/anaconda3/envs/rct/lib/python38.zip', '/Users/iparask/anaconda3/envs/rct/lib/python3.8', '/Users/iparask/anaconda3/envs/rct/lib/python3.8/lib-dynload', '/Users/iparask/anaconda3/envs/rct/lib/python3.8/site-packages']
/Users/iparask/anaconda3/envs/rct/lib/python3.8/site-packages/sphinx/events.py:99: RemovedInSphinx30Warning: autodoc_default_flags is now deprecated. Please use autodoc_default_options instead.
  results.append(callback(self.app, *args))
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 1 source files that are out of date
updating environment: 0 added, 5 changed, 0 removed
reading sources... [100%] usage/config
/Users/iparask/Git/RADICAL/radical.saga/docs/source/developers/index.rst:7: WARNING: toctree contains reference to nonexisting document 'developers/..  timeout_gc'
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/advert/advert_1.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/advert/advert_1.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/localfile.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:25: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/file_io.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/localfile.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst:23: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/filesystem/file_io.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst:14: WARNING: Include file '/Users/iparask/Git/RADICAL/radical.saga/examples/replica/replica_1.py' not found or reading it failed
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst:12: WARNING: download file not readable: /Users/iparask/Git/RADICAL/radical.saga/examples/replica/replica_1.py
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/config.rst:51: WARNING: Title underline too short.

Module radical.saga.utils.config
*************************
WARNING: autodoc: failed to import module 'config' from module 'radical.saga.utils'; the following exception was raised:
No module named 'radical.saga.utils.config'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/advert/index.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/filesystem/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/job/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/library/replica/examples.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/tutorial/part5_osg.rst: WARNING: document isn't included in any toctree
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/examples.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
/Users/iparask/Git/RADICAL/radical.saga/docs/source/_themes/armstrong/layout.html:16: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a <script> tag directly in your theme instead.
  {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
writing output... [100%] usage/index
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/config.rst:17: WARNING: undefined label: conf_options (if the link has no caption the label must precede a section header)
/Users/iparask/Git/RADICAL/radical.saga/docs/source/usage/config.rst:29: WARNING: undefined label: conf_options (if the link has no caption the label must precede a section header)
generating indices...  genindex py-modindexdone
highlighting module code... [100%] radical.utils.dict_mixin
writing additional pages...  searchdone
copying images... [100%] images/google.png
copying downloadable files... [100%] ../../examples/tutorial/mandelbrot/saga_mandelbrot_osg.py
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 21 warnings.

The HTML pages are in build.
(rct) iparaskmac:docs iparask$
iparask commented 4 years ago

Closing as the PR #768 is merged