Merge pull request #7215 from nsoranzo/recommonmark_0.5.0

Dependency update and doc fixes

doc/source/admin/conda_faq.rst

@@ -54,7 +54,7 @@ time it starts up and be configured to use it by default.
 
 The long answer is that Galaxy's tool dependency resolution is managed via
 ``dependency_resolvers_conf.xml`` configuration file. This configuration
-file is discussed in detail in the :ref:`Dependency Resolvers <dependency_resolvers>`
+file is discussed in detail in the :doc:`Dependency Resolvers <dependency_resolvers>`
 documentation. Most Galaxy administrators will be using Galaxy's default dependency
 resolvers configuration file (``config/dependency_resolvers_conf.xml.sample``). With
 release 16.04, Galaxy has enabled Conda dependency resolution by default when
@@ -68,7 +68,7 @@ entry should remain first. This means that tools that have specified Tool Shed p
 as their dependencies will work without a change.
 
 The most common configuration settings related to Conda are listed in Table 1.
-See `galaxy.yml.sample`_ for the complete list.
+See :doc:`Configuration Options <options>` for the complete list.
 
 +-------------------------+------------------------------------+---------------------------+
 | Setting                 | Default setting                    | Meaning                   |
@@ -105,7 +105,7 @@ handle these dependencies for you, but admins are not required to use Galaxy for
 dependency management.
 
 There are a few config options in the ``galaxy.yml`` file (see Table 1 or
-`galaxy.yml.sample`_ for more information), but by default Galaxy will install
+:doc:`Configuration Options <options>` for more information), but by default Galaxy will install
 Conda (the package manager) and the required packages in the
 ``<tool_dependency_dir>/_conda/`` directory. In this directory, Galaxy will
 create an ``envs`` folder with all of the environments managed by Galaxy. Each
@@ -203,7 +203,7 @@ The order in which resolvers are tried is listed in the
 -  Conda packages
 
 The first system that satisfies a requirement will be used. See
-`resolver docs`_ for detailed documentation.
+:doc:`Dependency Resolvers <dependency_resolvers>` for detailed documentation.
 
 This however is not recommended, ideally tools will target and test
 against Conda for all dependencies. Also resolving all requirements
@@ -408,13 +408,11 @@ The command can obviously be adapted to install any version of Conda.
 .. _Conda quick-start: https://conda.io/docs/user-guide/getting-started.html
 .. _ansible role: https://github.com/galaxyproject/ansible-galaxy-tools
 .. _BioBlend: https://github.com/galaxyproject/bioblend
-.. _resolver docs: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
 .. _Conda channels: https://conda.io/docs/user-guide/tasks/manage-channels.html
 .. _create a Conda package: https://conda.io/docs/user-guide/tasks/build-packages/recipe.html
 .. _submit: https://bioconda.github.io/#step-4-join-the-team
 .. _BioConda: https://bioconda.github.io
 .. _contact with the IUC: https://gitter.im/galaxy-iuc/iuc
-.. _galaxy.yml.sample: https://docs.galaxyproject.org/en/master/admin/options.html
 .. _Pull Request #3106: https://github.com/galaxyproject/galaxy/pull/3106
 .. _Pull Request #3348: https://github.com/galaxyproject/galaxy/pull/3348
 .. _Pull Request #3391: https://github.com/galaxyproject/galaxy/pull/3391

doc/source/admin/special_topics/bug_reports.rst

@@ -10,7 +10,7 @@ single configuration file, ``config/error_report.yml.sample``.
 
 Let's look at that briefly:
 
-.. code-block:: yml
+.. code-block:: yaml
 
     - type: email
       verbose: true

doc/source/admin/special_topics/webhooks.rst

@@ -45,23 +45,26 @@ For each type there is an example provided:
 - Additional functionality can be added to the top menu. Two dummy buttons are implemented to show the idea:
 
   - A button that links to biostars
-   .. image:: images_webhooks/masthead.png
-      :scale: 50 %
+
+    .. image:: images_webhooks/masthead.png
+       :scale: 50 %
 
   - A button that shows a pop-up with information about an user.
-   .. image:: images_webhooks/masthead_trans_object.png
-      :scale: 50 %
+
+    .. image:: images_webhooks/masthead_trans_object.png
+       :scale: 50 %
 
 - The history menu can be extended. In this case we use two dummy entries 'History Menu Webhook Item 1' and  'History Menu Webhook Item 2'.
- .. image:: images_webhooks/history-menu.png
-    :scale: 25 %
+
+  .. image:: images_webhooks/history-menu.png
+     :scale: 25 %
 
 Plugin structure
 ----------------
 
 Each plugin has the following folder structure:
 
-.. code-block::
+.. code-block:: yaml
 
    - plugin_name
       - config.yml (mandatory)

doc/source/conf.py

@@ -17,14 +17,9 @@
 
 import sphinx_rtd_theme
 # Library to make .md to slideshow
-from recommonmark.parser import CommonMarkParser
 from recommonmark.transform import AutoStructify
 
-source_parsers = {
-    '.md': CommonMarkParser,
-}
-
-# Set GALAXY_DOCS_SKIP_SOURCE=1 to skip building source and release information and
+# Set GALAXY_DOCS_SKIP_SOURCE=1 to skip building source information and
 # just build primary documentation. (Quicker to debug issues in most frequently updated
 # docs).
 SKIP_SOURCE = os.environ.get("GALAXY_DOCS_SKIP_SOURCE", False) == "1"
@@ -45,7 +40,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx']
+extensions = ['recommonmark', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx']
 if not SKIP_SOURCE:
     extensions += ['sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
 
@@ -108,10 +103,9 @@ def setup(app):
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
+exclude_patterns = ['**/_*.rst']
 if SKIP_SOURCE:
-    exclude_patterns = ['lib', 'releases']
-else:
-    exclude_patterns = []
+    exclude_patterns.extend(['lib'])
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None

doc/source/dev/index.rst

@@ -1,5 +1,5 @@
 Development Documentation
-=======================
+=========================
 
 .. toctree::
   :maxdepth: 1

doc/source/releases/16.07_announce.rst

@@ -12,7 +12,7 @@ Highlights
   Galaxy admins obtained the ability to install Galaxy tool's
   dependencies using the Conda package manager. This is a Beta feature
   and we encourage interested deployers to opt-in by modifying configuration.
-  Documentation that explains this switch and answers FAQ is `available <https://docs.galaxyproject.org/en/master/admin/conda_faq.html>`__.
+  Documentation that explains this switch and answers FAQ is :doc:`available <../admin/conda_faq>`.
 
 **Dynamic tool destinations**
   Our friends from Canada National Microbiology Laboratory enhanced
@@ -24,7 +24,7 @@ Highlights
 **Galaxy chat**
   Admins can now plug in the included communication server to enable
   users of their instance to use real-time chat within the Galaxy interface.
-  Please see the `documentation <https://docs.galaxyproject.org/en/master/admin/chat.html>`__
+  Please see the :doc:`documentation <../admin/special_topics/chat>`
   to learn how to activate and use this feature.
   Implemented in `PR #2515 <https://github.com/galaxyproject/galaxy/pull/2515>`__
 

doc/source/releases/16.10.rst

@@ -18,7 +18,7 @@ Highlighted Enhancements
 * Implement a collection operation tool for merging collections
   (thanks to `@Takadonet <https://github.com/Takadonet>`__).
   `Pull Request 2771`_
-* Replace `reference documentation <https://docs.galaxyproject.org/en/master/dev/schema.html>`__
+* Replace :doc:`reference documentation <../dev/schema>`
   for tool XML files with automatically generated
   documentation from a now official Galaxy XSD documentation (with help from many).
   `Pull Request 2923`_, `Pull Request 2936`_, `Pull Request 3086`_,

doc/source/releases/16.10_announce.rst

@@ -9,7 +9,7 @@ Highlights
 ==========
 
 **Galaxu UI plugins - Webhooks**
-  We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance. See the `documentation <https://docs.galaxyproject.org/en/master/admin/webhooks.html>`__.
+  We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance. See the :doc:`documentation <../admin/special_topics/webhooks>`.
   Includes work from `@bgruening <https://github.com/bgruening>`__, `@anatskiy <https://github.com/anatskiy>`__, and Joachim Wolff `@joachimwolff <https://github.com/joachimwolff>`__.
   Implemented in `Pull Request 3040`_.
 

doc/source/releases/17.01_announce.rst

@@ -14,7 +14,7 @@ Highlights
   such as `BioConda <https://bioconda.github.io/>`__. Such channels are already being used for new and updated tools by IUC
   and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package
   recipes - which are now considered deprecated.
-  Please see the details at the admin `documentation <https://docs.galaxyproject.org/en/master/admin/conda_faq.html>`__
+  Please see the details at the admin :doc:`documentation <../admin/conda_faq>`.
 
 **New interface for user preferences**
   User preferences menu has been reworked for clarity and consistency.
@@ -27,7 +27,7 @@ Highlights
   or ``fastqsanger.bz2`` for compressed files).
   Existing tools will work as before and future tools will be able to consume archives and save space in your quota.
   Thanks to `@abretaud <https://github.com/abretaud>`__, `@ashvark <https://github.com/ashvark>`__, `@jvolkening <https://github.com/jvolkening>`__, and `@mvdbeek <https://github.com/mvdbeek>`__.
-  Implemented in `Pull Request 3145`_, `PullRequest 3510`_ and `PullRequest 3514`_.
+  Implemented in `Pull Request 3145`_, `Pull Request 3510`_ and `Pull Request 3514`_.
 
 Get Galaxy
 ==========

doc/source/releases/18.01.rst

@@ -111,6 +111,7 @@ Enhancements
 * Add Phylip datatype
   (thanks to `@khillion <https://github.com/khillion>`__).
   `Pull Request 5301`_
+
 .. enhancement
 
 * Option to group Galaxy Tours for viewing clarity

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -36,7 +36,7 @@ Mercurial = {version = "<=3.7.3", markers = "python_version < '3'"}
 nodeenv = "*"
 pycryptodome = "*"
 uWSGI = "*"
-pysam = "==0.15.1"
+pysam = "==0.15.2"
 bdbag = "==1.4.1"  # 1.5.0 requires Python >=2.7.9
 bleach = "*"
 "bz2file" = {version = "*", markers = "python_version < '3.3'"}

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -7,42 +7,43 @@ attrs==18.2.0
 babel==2.6.0
 certifi==2018.11.29
 chardet==3.0.4
-commonmark==0.5.4
+commonmark==0.8.1
 docutils==0.14
 funcsigs==1.0.2 ; python_version < '3.3'
+future==0.17.1
 gunicorn==19.9.0
-idna==2.7
+idna==2.8
 imagesize==1.1.0
 jinja2==2.10
-lxml==4.2.5
+lxml==4.3.0
 markupsafe==1.1.0
 mock==2.0.0
-more-itertools==4.3.0
+more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
 pathlib2==2.3.3 ; python_version < '3.6'
 pathtools==0.1.2
 pbr==5.1.1
-pluggy==0.8.0
+pluggy==0.8.1
 py==1.7.0
 pygithub3==0.5.1 ; python_version < '3'
-pygments==2.3.0
+pygments==2.3.1
 pytest-html==1.19.0
-pytest-metadata==1.7.0
+pytest-metadata==1.8.0
 pytest-pythonpath==0.7.3
-pytest==4.0.1
-pytz==2018.7
+pytest==4.1.0
+pytz==2018.9
 pyyaml==3.13
-recommonmark==0.4.0
-requests==2.20.1
+recommonmark==0.5.0
+requests==2.21.0
 scandir==1.9.0 ; python_version < '3.5'
 selenium==3.141.0
 six==1.11.0
 snowballstemmer==1.2.1
 sphinx-rtd-theme==0.4.2
 sphinx==1.6.7
 sphinxcontrib-websupport==1.1.0
-testfixtures==6.3.0
+testfixtures==6.4.3
 twill==0.9.1 ; python_version < '3'
 typing==3.6.6 ; python_version < '3.5'
 urllib3==1.24.1