Merge pull request #68 from amarquand/dev

Merge for v.20
amarquand · Jul 27, 2021 · a6dc4e9 · a6dc4e9
2 parents f70b40c + 89f5571
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: doc/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: 3.8
+   install:
+   - requirements: doc/requirements.txt
diff --git a/README.md b/README.md
@@ -1,8 +1,10 @@
 # Predictive Clinical Neuroscience Toolkit
-Predictive Clinical Neuroscience software toolkit (formerly nispat). Methods for normative modelling, spatial statistics and pattern recognition. 
-
 [![Gitter](https://badges.gitter.im/predictive-clinical-neuroscience/community.svg)](https://gitter.im/predictive-clinical-neuroscience/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [![Documentation Status](https://readthedocs.org/projects/pcntoolkit/badge/?version=latest)](https://pcntoolkit.readthedocs.io/en/latest/?badge=latest)
 
+Predictive Clinical Neuroscience software toolkit (formerly nispat). 
+
+Methods for normative modelling, spatial statistics and pattern recognition. Documentation, including tutorials can be found on [readthedocs](https://pcntoolkit.readthedocs.io/en/latest/). Click on the docs button above to visit the site. 
+
 ## Basic installation (on a local machine)
 
 i) install anaconda3 ii) create enviornment with "conda create --name <env_name>" iii) activate environment by "source activate <env_name>" iv) install required conda packages
@@ -28,7 +30,7 @@ conda --version
 Create a conda environment in a shared location
 
 ```
-conda create -y python==3.7.7 numpy mkl blas --prefix=/shared/conda/<env_name>
+conda create -y python==3.8.3 numpy mkl blas --prefix=/shared/conda/<env_name>
 ```
 
 Activate the conda environment 

diff --git a/doc/Makefile b/doc/Makefile
@@ -5,14 +5,15 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
+SOURCEDIR     = source
 BUILDDIR      = build
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(SOURCEDIR)
 # the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(SOURCEDIR)
 
 .PHONY: help
 help:

diff --git a/doc/build/doctrees/_templates/class.doctree b/doc/build/doctrees/_templates/class.doctree
diff --git a/doc/build/doctrees/_templates/function.doctree b/doc/build/doctrees/_templates/function.doctree
diff --git a/doc/build/doctrees/environment.pickle b/doc/build/doctrees/environment.pickle
diff --git a/doc/build/doctrees/index.doctree b/doc/build/doctrees/index.doctree
diff --git a/doc/build/doctrees/modindex.doctree b/doc/build/doctrees/modindex.doctree
diff --git a/doc/build/doctrees/pages/FAQs.doctree b/doc/build/doctrees/pages/FAQs.doctree
diff --git a/doc/build/doctrees/pages/_templates/class.doctree b/doc/build/doctrees/pages/_templates/class.doctree
diff --git a/doc/build/doctrees/pages/_templates/function.doctree b/doc/build/doctrees/pages/_templates/function.doctree
diff --git a/doc/build/doctrees/pages/acknowledgements.doctree b/doc/build/doctrees/pages/acknowledgements.doctree
diff --git a/doc/build/doctrees/pages/citing.doctree b/doc/build/doctrees/pages/citing.doctree
diff --git a/doc/build/doctrees/pages/glossary.doctree b/doc/build/doctrees/pages/glossary.doctree
diff --git a/doc/build/doctrees/pages/installation.doctree b/doc/build/doctrees/pages/installation.doctree
diff --git a/doc/build/doctrees/pages/pcntoolkit_background.doctree b/doc/build/doctrees/pages/pcntoolkit_background.doctree
diff --git a/doc/build/doctrees/pages/references.doctree b/doc/build/doctrees/pages/references.doctree
diff --git a/doc/build/doctrees/pages/scripts.doctree b/doc/build/doctrees/pages/scripts.doctree
diff --git a/doc/build/doctrees/pages/tutorial_CPC2020.doctree b/doc/build/doctrees/pages/tutorial_CPC2020.doctree
diff --git a/doc/build/doctrees/pages/tutorial_HBR.doctree b/doc/build/doctrees/pages/tutorial_HBR.doctree
diff --git a/doc/build/doctrees/pages/tutorial_ROIcorticalthickness.doctree b/doc/build/doctrees/pages/tutorial_ROIcorticalthickness.doctree
diff --git a/doc/build/doctrees/pages/updates.doctree b/doc/build/doctrees/pages/updates.doctree
diff --git a/doc/build/html/.buildinfo b/doc/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: dde6024847b5bf213ad9998ffa45db93
+config: 5392fc74b0cbc4bdad768b650de8eaca
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/build/html/_images/math/136499ff23ae31f75bf05de819b869f7cb8675a7.png b/doc/build/html/_images/math/136499ff23ae31f75bf05de819b869f7cb8675a7.png
diff --git a/doc/build/html/_images/nm_concept.png b/doc/build/html/_images/nm_concept.png
diff --git a/doc/build/html/_images/nm_overview.png b/doc/build/html/_images/nm_overview.png
diff --git a/doc/build/html/_images/nm_parallel.png b/doc/build/html/_images/nm_parallel.png
diff --git a/doc/build/html/_images/nm_plot.jpeg b/doc/build/html/_images/nm_plot.jpeg
diff --git a/doc/build/html/_modules/bayesreg.html b/doc/build/html/_modules/bayesreg.html
diff --git a/doc/build/html/_modules/fileio.html b/doc/build/html/_modules/fileio.html
diff --git a/doc/build/html/_modules/gp.html b/doc/build/html/_modules/gp.html
diff --git a/doc/build/html/_modules/index.html b/doc/build/html/_modules/index.html
@@ -1,46 +1,186 @@
 
 
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+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../pages/pcntoolkit_background.html">PCNtoolkit Background</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../pages/pcntoolkit_background.html#intro-to-normative-modelling">Intro to normative modelling</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Function &amp; Class Docs</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../modindex.html">Module Index</a></li>
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+</ul>
+<p class="caption"><span class="caption-text">Tutorials</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
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+<li class="toctree-l1"><a class="reference internal" href="../pages/citing.html">How to cite PCNtoolkit</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../pages/acknowledgements.html">Acknowledgements</a></li>
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   <h1>All modules for which code is available</h1>
 <ul><li><a href="bayesreg.html">bayesreg</a></li>
@@ -50,45 +190,49 @@ <h1>All modules for which code is available</h1>
 <li><a href="normative_parallel.html">normative_parallel</a></li>
 <li><a href="rfa.html">rfa</a></li>
 <li><a href="trendsurf.html">trendsurf</a></li>
-<li><a href="utils.html">utils</a></li>
 </ul>
 
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