additional minor updates for 1.7.0-beta

This update was combined with what was 1.6.3-beta

core/utilities/pandoc.py

@@ -7,13 +7,25 @@
 
 import pypandoc
 
-PANDOC_DEFAULT_ARGS = (
-    "--mathml",
-    "--smart",
-    "--standalone",
-    "--biblatex",
-    "--html-q-tags",
-)
+if pypandoc.get_pandoc_version().startswith("2"):
+    MARKDOWN = "markdown+smart"
+    REST = "rst"
+    PANDOC_DEFAULT_ARGS = (
+        "--mathml",
+        "--standalone",
+        "--biblatex",
+        "--html-q-tags",
+    )
+else:
+    MARKDOWN = "md"
+    REST = "rst"
+    PANDOC_DEFAULT_ARGS = (
+        "--mathml",
+        "--smart",
+        "--standalone",
+        "--biblatex",
+        "--html-q-tags",
+    )
 
 
 def convert_md_to_html(source, extra_args=PANDOC_DEFAULT_ARGS, **kwargs):
@@ -23,7 +35,11 @@ def convert_md_to_html(source, extra_args=PANDOC_DEFAULT_ARGS, **kwargs):
     """
     kwargs = {k: v for k, v in kwargs.items() if k not in ["format", "to"]}
     md_blob = pypandoc.convert(
-        source, to="html", format="md", extra_args=extra_args, **kwargs
+        source,
+        to="html",
+        format=MARKDOWN,
+        extra_args=list(extra_args),
+        **kwargs
     )
     return md_blob
 
@@ -35,6 +51,6 @@ def convert_rest_to_html(source, extra_args=PANDOC_DEFAULT_ARGS, **kwargs):
     """
     kwargs = {k: v for k, v in kwargs.items() if k not in ["format", "to"]}
     rst_blob = pypandoc.convert(
-        source, to="html", format="rest", extra_args=extra_args, **kwargs
+        source, to="html", format=REST, extra_args=list(extra_args), **kwargs
     )
     return rst_blob

data/main/citation_biorxiv.md

@@ -0,0 +1,5 @@
+An open-source platform to distribute and interpret data from multiplexed assays of variant effect
+
+Daniel Esposito, Jochen Weile, Jay Shendure, Lea M Starita, Anthony T Papenfuss, Frederick P Roth, Douglas M Fowler, Alan F Rubin
+
+bioRxiv 555797; doi: https://doi.org/10.1101/555797 

data/main/site_info.json

@@ -1,10 +1,10 @@
 {
     "branch": "",
     "md_about": "about.md",
-    "md_citation": "",
+    "md_citation": "citation_biorxiv.md",
     "md_documentation": "userdocs.md",
     "md_privacy": "",
     "md_terms": "",
     "md_usage_guide": "",
-    "version": "1.6.3-beta"
+    "version": "1.7.0-beta"
 }

dataset/tests/test_views_scoreset.py

@@ -72,6 +72,14 @@ def setUp(self):
         self.template_404 = "main/404.html"
         celery_app.conf.update(CELERY_TASK_ALWAYS_EAGER=True)
 
+    def test_title_in_metadata_description_tag(self):
+        obj = ScoreSetFactory()
+        obj = publish_dataset(obj)
+        response = self.client.get("/scoreset/{}/".format(obj.urn))
+        self.assertEqual(response.status_code, 200)
+        tag = '<meta name="description" content="{}">'.format(obj.title)
+        self.assertContains(response, tag)
+
     def test_404_status_and_template_used_when_object_not_found(self):
         obj = ScoreSetFactory()
         urn = obj.urn

main/templates/main/base.html

@@ -10,7 +10,11 @@
     <meta http-equiv="X-UA-Compatible" content="IE=edge">
     <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
     <meta name="viewport" content="width=device-width, initial-scale=1">
-    <meta name="description" content="MaveDB - repository for DMS/MAVE assay datasets">
+      {% if instance.title %}
+          <meta name="description" content="{{ instance.title }}">
+      {% else %}
+          <meta name="description" content="MaveDB - A repository for MAVE assay datasets.">
+      {% endif %}
     <meta name="author" content="Daniel C. Esposito, Alan F. Rubin">
     <meta name="keywords" content="dms,deep mutational scanning,mave,multiplex assays of
           variant effect,variant effect,gene,genomic,variants,functional assay,multiplex assay">

main/tests/test_views.py

@@ -25,6 +25,15 @@ def test_uses_home_template(self):
         response = self.client.get("/")
         self.assertTemplateUsed(response, "main/home.html")
 
+    def test_render_default_metadata_description_tag(self):
+        response = self.client.get("/")
+        self.assertEqual(response.status_code, 200)
+        tag = (
+            '<meta name="description" content="MaveDB - '
+            'A repository for MAVE assay datasets.">'
+        )
+        self.assertContains(response, tag)
+
     def test_news_items_display(self):
         n1 = NewsFactory()
         n2 = NewsFactory()

tox.ini

@@ -4,6 +4,7 @@ envlist = python3.4
 skip_missing_interpreters = false
 
 [testenv]
+recreate = true
 commands =
     pip install -r requirements/staging.txt
     python manage.py migrate --settings=settings.staging_ci