Fix nbconvert template (#160)

http://b/170301227

Author: Philmod

Dockerfile

@@ -72,6 +72,7 @@ ADD install_iR.R  /tmp/install_iR.R
 ADD bioconductor_installs.R /tmp/bioconductor_installs.R
 ADD package_installs.R /tmp/package_installs.R
 ADD nbconvert-extensions.tpl /opt/kaggle/nbconvert-extensions.tpl
+ADD kaggle/template_conf.json /opt/kaggle/conf.json
 # Install with `--vanilla` flag to avoid conflict. https://support.bioconductor.org/p/57187/
 RUN Rscript --vanilla /tmp/package_installs.R
 RUN Rscript --vanilla /tmp/bioconductor_installs.R

kaggle/template_conf.json

@@ -0,0 +1,13 @@
+{
+    "base_template": "classic",
+    "mimetypes": {
+        "text/html": true
+    },
+    "preprocessors": {
+        "100-pygments": {
+            "type": "nbconvert.preprocessors.CSSHTMLHeaderPreprocessor",
+            "enabled": true,
+            "style": "default"
+        }
+    }
+}

nbconvert-extensions.tpl

@@ -4,7 +4,7 @@ All cell metadata starting with '_kg_' will be included with its value ({key}-{v
 as a class in the cell's DIV container
 #}
 
-{% extends 'full.tpl'%}
+{% extends 'classic/index.html.j2'%}
 {% block any_cell %}
     <div class="{% for k in cell['metadata'] if k.startswith("_kg_") %}{{k}}-{{cell['metadata'][k] | lower}} {% endfor %}">
         {{ super() }}

tests/test_nbconvert.R

@@ -1,6 +1,6 @@
 context("nbconvert")
 
-test_that("nbconvert exists", {
+test_that("nbconvert to notebook", {
 	expect_error({
 		library(jsonlite)
 
@@ -10,3 +10,11 @@ test_that("nbconvert exists", {
 		expect_equal(json$cells[[1]]$outputs[[1]]$text[[1]], "[1] 999\n")
     }, NA) # expect no error to be thrown
 })
+
+test_that("nbconvert to html", {
+	expect_error({
+		results <- system("jupyter nbconvert --to html --stdout --template /opt/kaggle/nbconvert-extensions.tpl --Exporter.preprocessors=[\\\"nbconvert.preprocessors.ExtractOutputPreprocessor\\\"] \"/input/tests/data/notebook.ipynb\"",
+			intern = TRUE)
+		expect_match(toString(results), ".*>999<.*")  # [...] <span class="n">x</span> <span class="o">&lt;-</span> <span class="m">999</span> [...]
+    }, NA) # expect no error to be thrown
+})