From 46b3539a35c09fc3d8d2d9b2a7ec7fefbc53c95e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 14 Jan 2019 22:40:05 +0000 Subject: [PATCH] Fix doc bugs Use proper cross-referencing with `:doc:`. --- doc/source/admin/conda_faq.rst | 10 ++++------ doc/source/admin/special_topics/bug_reports.rst | 2 +- doc/source/admin/special_topics/webhooks.rst | 17 ++++++++++------- doc/source/dev/index.rst | 2 +- doc/source/releases/16.07_announce.rst | 4 ++-- doc/source/releases/16.10.rst | 2 +- doc/source/releases/16.10_announce.rst | 2 +- doc/source/releases/17.01_announce.rst | 4 ++-- doc/source/releases/18.01.rst | 1 + 9 files changed, 23 insertions(+), 21 deletions(-) diff --git a/doc/source/admin/conda_faq.rst b/doc/source/admin/conda_faq.rst index e2e5af12fa2..a4fc5a0221c 100644 --- a/doc/source/admin/conda_faq.rst +++ b/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 ` +file is discussed in detail in the :doc:`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 ` 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 ` for more information), but by default Galaxy will install Conda (the package manager) and the required packages in the ``/_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 ` 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 diff --git a/doc/source/admin/special_topics/bug_reports.rst b/doc/source/admin/special_topics/bug_reports.rst index e58b36e3f88..11200edc405 100644 --- a/doc/source/admin/special_topics/bug_reports.rst +++ b/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 diff --git a/doc/source/admin/special_topics/webhooks.rst b/doc/source/admin/special_topics/webhooks.rst index 51404cd2971..7a81a5809cc 100644 --- a/doc/source/admin/special_topics/webhooks.rst +++ b/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) diff --git a/doc/source/dev/index.rst b/doc/source/dev/index.rst index c6648a05ad6..31137edb366 100644 --- a/doc/source/dev/index.rst +++ b/doc/source/dev/index.rst @@ -1,5 +1,5 @@ Development Documentation -======================= +========================= .. toctree:: :maxdepth: 1 diff --git a/doc/source/releases/16.07_announce.rst b/doc/source/releases/16.07_announce.rst index acde41b5be1..f6c8dfb773c 100644 --- a/doc/source/releases/16.07_announce.rst +++ b/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 `__. + 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 `__ + Please see the :doc:`documentation <../admin/special_topics/chat>` to learn how to activate and use this feature. Implemented in `PR #2515 `__ diff --git a/doc/source/releases/16.10.rst b/doc/source/releases/16.10.rst index aff9ed39d11..14fbd984870 100644 --- a/doc/source/releases/16.10.rst +++ b/doc/source/releases/16.10.rst @@ -18,7 +18,7 @@ Highlighted Enhancements * Implement a collection operation tool for merging collections (thanks to `@Takadonet `__). `Pull Request 2771`_ -* Replace `reference documentation `__ +* 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`_, diff --git a/doc/source/releases/16.10_announce.rst b/doc/source/releases/16.10_announce.rst index 49ce02e21b6..33ccbb0e700 100644 --- a/doc/source/releases/16.10_announce.rst +++ b/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 `__. + 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 `__, `@anatskiy `__, and Joachim Wolff `@joachimwolff `__. Implemented in `Pull Request 3040`_. diff --git a/doc/source/releases/17.01_announce.rst b/doc/source/releases/17.01_announce.rst index 6abf8ac34ee..d5d3eead805 100644 --- a/doc/source/releases/17.01_announce.rst +++ b/doc/source/releases/17.01_announce.rst @@ -14,7 +14,7 @@ Highlights such as `BioConda `__. 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 `__ + 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 `__, `@ashvark `__, `@jvolkening `__, and `@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 ========== diff --git a/doc/source/releases/18.01.rst b/doc/source/releases/18.01.rst index cd507ddc8d2..f9bd8a0145e 100644 --- a/doc/source/releases/18.01.rst +++ b/doc/source/releases/18.01.rst @@ -111,6 +111,7 @@ Enhancements * Add Phylip datatype (thanks to `@khillion `__). `Pull Request 5301`_ + .. enhancement * Option to group Galaxy Tours for viewing clarity