Include NEWS from doc/release.rst and link issues/PRs

Remove doc/release.rst's duplicate copy of the release notes, instead
including NEWS via a reStructuredText include directive. This means
that NEWS needs to be valid reStructuredText, but it mostly already is.

Install a Sphinx 7.2.5+ include-read hook that expands plain `PR #NNN`
and `#NNN` references in the NEWS file into role syntax that the extlinks
extension can expand into links to pysam issues/PRs at the GitHub repo.

NEWS

@@ -1,9 +1,5 @@
-An online version of the installation instructions can be found here:
-http://pysam.readthedocs.io/en/latest/release.html
-
-=============
-Release notes
-=============
+.. An online version of the release history can be found here:
+.. http://pysam.readthedocs.io/en/latest/release.html
 
 Release 0.21.0
 ==============

doc/conf.py

@@ -11,7 +11,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os, setuptools
+import sys, os, re, setuptools
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -29,6 +29,7 @@
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.autosummary',
+              'sphinx.ext.extlinks',
               'sphinx.ext.todo', 
               'sphinx.ext.ifconfig',
               'sphinx.ext.intersphinx',
@@ -120,6 +121,27 @@
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
+# -- Rewrite "PR #NNN" and "#NNN" in NEWS as URL links -------------------------
+
+extlinks = {
+    'issue': ('https://github.com/pysam-developers/pysam/issues/%s', '#%s'),
+    'pull':  ('https://github.com/pysam-developers/pysam/pull/%s', 'PR #%s'),
+    }
+
+def expand_github_references(text):
+    text = re.sub(r'PR\s*#(\d+)', r':pull:`\1`', text)
+    text = re.sub(r'#(\d+)', r':issue:`\1`', text)
+    return text
+
+def include_read(app, relative_path, parent_docname, source):
+    if relative_path.name == 'NEWS':
+        source[0] = expand_github_references(source[0])
+
+def setup(app):
+    try:
+        app.connect('include-read', include_read)
+    except:
+        pass  # Sphinx is too old to link issues/PRs
 
 # -- Options for HTML output ---------------------------------------------------