Merge pull request #108 from rmarkello/zenodo

[MNT] Adds framework for Zenodo integration

.zenodo.json

@@ -0,0 +1,28 @@
+{
+  "title": "abagen: A toolbox for the Allen Brain Atlas genetics data",
+  "description": "abagen is a Python toolbox that provides reproducible workflows for fetching and processing the Allen Human Brain Atlas microarray expression data for analysis.",
+  "creators": [
+    {
+      "name": "Markello, Ross",
+      "affiliation": "Montreal Neurological Institute, McGill University",
+      "orcid": "0000-0003-1057-1336"
+    },
+    {
+      "name": "Shafiei, Golia",
+      "affiliation": "Montreal Neurological Institute, McGill University",
+      "orcid": "0000-0002-2036-5571"
+    },
+    {
+      "name": "Ying-Qiu Zheng",
+      "affiliation": "Montreal Neurological Institute, McGill University",
+      "orcid": "0000-0003-1236-0700"
+    }
+  ],
+  "keywords": [
+    "neuroimaging",
+    "genetics",
+    "allen institute"
+  ],
+  "license": "BSD-3-Clause",
+  "upload_type": "software"
+}

docs/citing.rst

@@ -0,0 +1,50 @@
+.. _citation:
+
+-------------
+Citing abagen
+-------------
+
+We're thrilled you've found ``abagen`` useful in your work! To make citing
+it as easy as possible we have created a `DOI`_ with `Zenodo`_. Since much of
+the current codebase was inspired by the workflow laid out in Arnatkevičiūte et
+al., 2019, and it all uses data released with Hawrylycz et al., 2012, we ask
+that you please cite those papers as well:
+
+.. raw:: html
+
+   <script language="javascript">
+   var version = 'latest';
+   function fillCitation(){
+      $('#abagen_version').text(version);
+
+      function cb(err, zenodoID) {
+         getCitation(zenodoID, 'vancouver-brackets-no-et-al', function(err, citation) {
+            $('#abagen_citation').text(citation);
+         });
+         getDOI(zenodoID, function(err, DOI) {
+            $('#abagen_doi_url').text('https://doi.org/' + DOI);
+            $('#abagen_doi_url').attr('href', 'https://doi.org/' + DOI);
+         });
+      }
+
+      if(version == 'latest') {
+         getLatestIDFromconceptID("", cb);
+      } else {
+         getZenodoIDFromTag("", version, cb);
+      }
+   }
+   </script>
+
+   <p>
+     1. <span id="abagen_citation">abagen</span> Available from: <a id="abagen_doi_url" href="https://doi.org/xx.xxxx/zenodo.xxxxxx">xx.xxxx/zenodo.xxxxxx</a>.
+     <img src onerror='fillCitation()' alt="" />
+   </p>
+   <p>
+     2. Arnatkevic̆iūtė, A., Fulcher, B. D., & Fornito, A. (2019). A practical guide to linking brain-wide gene expression and neuroimaging data. NeuroImage, 189, 353-367. doi:10.1016/j.neuroimage.2019.01.011
+   </p>
+   <p>
+     3. Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., … Jones, A. R. (2012). An anatomically comprehensive atlas of the adult human brain transcriptome. Nature, 489(7416), 391–399. doi:10.1038/nature11405
+   </p>
+
+.. _DOI: https://en.wikipedia.org/wiki/Digital_object_identifier
+.. _Zenodo: https://zenodo.org

docs/conf.py

@@ -12,6 +12,7 @@
 import os
 import sys
 
+
 # -- Project information -----------------------------------------------------
 
 # Add project name, copyright holder, and author(s)
@@ -27,6 +28,7 @@
 # The full version, including alpha/beta/rc tags
 release = abagen.__version__
 
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -73,6 +75,7 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -91,14 +94,18 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-# CSS files to include
-html_css_files = ['theme_overrides.css']
+# https://github.com/rtfd/sphinx_rtd_theme/issues/117
+def setup(app):  # noqa
+    app.add_stylesheet('theme_overrides.css')
+    app.add_javascript('https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js')  # noqa
+
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'abagendoc'
 
+
 # -- Extension configuration -------------------------------------------------
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3.6', None),