🚚 Update indices

Author: shnizzedy

docs/_sources/conf.py

@@ -329,6 +329,8 @@ def _unireplace(release_note, unireplace):
 
 .. toctree::
    :hidden:
+   :titlesonly:
+   :maxdepth: 1
 
    /user/release_notes/{latest}.rst
 """.format(latest=str(t))
@@ -347,6 +349,8 @@ def _unireplace(release_note, unireplace):
 
 .. toctree::
    :hidden:
+   :titlesonly:
+   :maxdepth: 1
 
    {}
 

docs/_sources/developer/index.rst

@@ -13,12 +13,14 @@ Contents:
 
 .. toctree::
    :maxdepth: 2
+   :titlesonly:
 
    installation
    pipeline
    nodes
    workflow_documentation
    workflows/index
+   xcpqc
    testing
 
 Indices and tables

docs/_sources/index.rst

@@ -10,6 +10,7 @@ Contents:
 
 .. toctree::
    :maxdepth: 1
+   :titlesonly:
 
    User Guide <user/index>
    Developer Documentation <developer/index>

docs/_sources/user/index.rst

@@ -101,6 +101,7 @@ User Guide Index
 .. toctree::
    :maxdepth: 2
    :includehidden:
+   :titlesonly:
 
    1. C-PAC Quickstart <quick>
    2. Specify Your Data <subject_list_config>

docs/_sources/user/pipelines/data-environment.rst

@@ -3,5 +3,5 @@ Data Management and Environment Settings
 .. toctree::
    :maxdepth: 1
 
-   </user/compute_config>
-   </user/output_config>`
+   /user/compute_config
+   /user/output_config

docs/_sources/user/pipelines/derivatives.rst

@@ -3,8 +3,9 @@ Derivatives
 
 .. toctree::
    :maxdepth: 1
+
    Seed-based Correlation Analysis (SCA) and Dual Regression - Analyze the connectivity between brain regions. </user/sca>
    Voxel-mirrored Homotopic Connectivity (VMHC) - Investigate connectivity between hemispheres. </user/vmhc>
    Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) - Measure the power of slow fluctuations in brain activity. </user/alff>
    Regional Homogeneity (ReHo) - Measure the similarity of activity patterns across neighboring voxels. </user/reho>
-   Network Centrality - Analyze the structure of functional networks. </user/centrality>
+   Network Centrality - Analyze the structure of functional networks. </user/centrality>

docs/_sources/user/pipelines/design_a_pipeline.rst

@@ -52,6 +52,7 @@ Or you can provide it to the C-PAC Singularity container like so:
             -B /tmp:/tmp \
             -B /Users/You/Documents:/configs \
             fcpindi_c-pac_latest-{date}-{hash value}.img s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS /outputs participant --pipeline_file /configs/pipeline_config.yml
+
 **Reporting errors and getting help**
 
 Please report errors on the `C-PAC github page issue tracker <https://github.com/FCP-INDI/C-PAC/issues>`_. Please use the `C-PAC google group <https://groups.google.com/forum/#!forum/cpax_forum>`_ for help using C-PAC and this application.

docs/_sources/user/pipelines/pipeline_config.rst

@@ -74,7 +74,7 @@ Pipeline configuration files, like the data settings and data configuration file
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :start_at: pipeline_setup:
+   :start-at: pipeline_setup:
    :end-before: working_directory:
 
 An example of a pipeline configuration YAML file can be found :doc:`here </user/pipelines/default>`.  Tables explaining the keys and their potential values can be found on the individual pages for each of the outputs C-PAC is capable of producing. All pipeline setup configuration files should have the keys in the :doc:`Output Settings </user/output_config>` table defined.
@@ -100,8 +100,9 @@ You may notice as you learn about the settings for various outputs that many of
 .. toctree::
    :maxdepth: 2
 
-   <configurable-settings>
-   <data-environment>
-   <pre-and-post>
-   <derivatives>
-   <quality>
+   preconfig
+   configurable-settings
+   data-environment
+   pre-and-post
+   derivatives
+   quality

docs/_sources/user/pipelines/quality.rst

@@ -2,7 +2,7 @@ Quality Control
 '''''''''''''''
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    QC Pages - Visual Data Quality Control </user/qc_interface>
    XCP QC files - eXtensible Connectivity Pipeline-style quality control files </user/xcpqc>