Use `sphinx.ext.extlinks` to provide publication links via DOI and PMID

README.md

@@ -107,7 +107,8 @@ The original R `Peptides` package was written by [Daniel Osorio](https://orcid.o
 [Paola Rondón-Villarreal](https://orcid.org/0000-0001-8209-3885) and
 [Rodrigo Torres](https://orcid.org/0000-0003-1113-3020), and is licensed under
 the terms of the [GNU General Public License v2.0](https://choosealicense.com/licenses/gpl-2.0/).
-The [EMBOSS] applications are released under the [GNU General Public License v1.0](https://www.gnu.org/licenses/old-licenses/gpl-1.0.html).
+The [EMBOSS](http://emboss.bioinformatics.nl/cgi-bin/emboss/) applications are
+released under the [GNU General Public License v1.0](https://www.gnu.org/licenses/old-licenses/gpl-1.0.html).
 
 *This project is in no way not affiliated, sponsored, or otherwise endorsed
 by the [original `Peptides` authors](https://github.com/dosorio). It was developed

docs/conf.py

@@ -33,7 +33,37 @@ sys.modules['peptides.tables'] = types.ModuleType('peptides.tables')
 
 # -- Sphinx Setup ------------------------------------------------------------
 
+# import docutils.nodes
+# import docutils.utils
+# import sphinx.transforms
+#
+# def doi_role(role, rawtext, text, lineno, inliner, options=None, content=None):
+#     node = docutils.nodes.reference(
+#         rawtext,
+#         "doi:{}".format(docutils.utils.unescape(text)),
+#         refuri="https://doi.org/{}".format(text),
+#     )
+#     return [node], []
+#
+# def pmid_role(row, rawtext, text, lineno, inliner, options=None, content=None):
+#     try:
+#         pmid = int(text)
+#     except ValueError:
+#         msg = inliner.reporter.error("Invalid PMID: {!r}".format(text), line=lineno)
+#         prb = inliner.problematic(rawtext, rawtext, msg)
+#         return [prb], [msg]
+#     node = docutils.nodes.reference(
+#         rawtext,
+#         "PMID:{}".format(pmid),
+#         refuri="https://pubmed.ncbi.nlm.nih.gov/{}".format(pmid),
+#     )
+#     return [node], []
+#
+
 def setup(app):
+    # Add roles for DOI and PMID
+    # app.add_role("doi", doi_role)
+    # app.add_role("pmid", pmid_role)
     # Add custom stylesheet
     app.add_css_file(os.path.join("_static/css/main.css"))
     # app.add_js_file("js/apitoc.js")
@@ -88,6 +118,7 @@ extensions = [
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
     "sphinx.ext.todo",
+    "sphinx.ext.extlinks",
     "sphinx_bootstrap_theme",
     "recommonmark",
 ]
@@ -173,6 +204,14 @@ htmlhelp_basename = peptides.__name__
 
 # -- Extension configuration -------------------------------------------------
 
+# -- Options for extlinks extension ------------------------------------------
+
+extlinks = {
+    'doi': ('https://doi.org/%s', 'doi:%s'),
+    'pmid': ('https://pubmed.ncbi.nlm.nih.gov/%s', 'PMID:%s'),
+}
+
+
 # -- Options for imgmath extension -------------------------------------------
 
 imgmath_image_format = "svg"