Merge pull request #39 from mwouts/v0.5.4

V0.5.4

HISTORY.rst

@@ -6,6 +6,15 @@ Release History
 dev
 +++
 
+0.5.4 (2018-08-24)
++++++++++++++++++++
+
+**Improvements**
+
+- R to Rmd conversion compares well to knitr::spin (#26)
+- Increased coverage to 98%
+
+
 0.5.3 (2018-08-22)
 +++++++++++++++++++
 

binder/requirements.txt

@@ -1,4 +1,4 @@
-nbrmd>=0.5.3
+nbrmd>=0.5.4
 plotly
 matplotlib
 pandas

nbrmd/cli.py

@@ -33,12 +33,12 @@ def cli_nbrmd(args=None):
     return parser.parse_args(args)
 
 
-def nbrmd():
+def nbrmd(args=None):
     """
     Entry point for the nbrmd script
     :return:
     """
-    args = cli_nbrmd()
+    args = cli_nbrmd(args)
     convert(args.notebooks, args.in_place, args.preserve_outputs, True)
 
 
@@ -122,10 +122,10 @@ def cli_nbsrc(args=None):
     return parser.parse_args(args)
 
 
-def nbsrc():
+def nbsrc(args=None):
     """
     Entry point for the nbsrc script
     :return:
     """
-    args = cli_nbsrc()
+    args = cli_nbsrc(args)
     convert(args.notebooks, args.in_place, args.preserve_outputs, False)

nbrmd/nbrmd.py

@@ -102,6 +102,10 @@ def to_notebook(self, text, **kwargs):
 
         if self.ext == '.Rmd':
             find_main_language(metadata, cells)
+        elif self.ext == '.R':
+            if not (metadata.get('main_language') or
+                    metadata.get('language_info', {})):
+                metadata['main_language'] = 'R'
 
         nb = new_notebook(cells=cells, metadata=metadata)
         return nb
@@ -140,6 +144,8 @@ def writes(self, nb, **kwargs):
             default_language = (nb.metadata.get('main_language') or
                                 nb.metadata.get('language_info', {})
                                 .get('name', 'R'))
+            if nb.metadata.get('main_language') == 'R':
+                del nb.metadata['main_language']
         else:
             default_language = get_default_language(nb)
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='nbrmd',
-    version='0.5.3',
+    version='0.5.4',
     author='Marc Wouts',
     author_email='marc.wouts@gmail.com',
     description='Jupyter notebooks as R markdown, Python or R scripts',

tests/knitr-spin.R

@@ -0,0 +1,54 @@
+#' The below derives from
+#' https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R
+#'
+#' This is a special R script which can be used to generate a report. You can
+#' write normal text in roxygen comments.
+#'
+#' First we set up some options (you do not have to do this):
+
+#+ setup, include=FALSE
+library(knitr)
+opts_chunk$set(fig.path = 'figure/silk-')
+
+#' The report begins here.
+
+#+ test-a, cache=FALSE
+# boring examples as usual
+set.seed(123)
+x = rnorm(5)
+mean(x)
+
+#' You can not use here the special syntax {{code}} to embed inline expressions, e.g.
+{{mean(x) + 2}}
+#' is the mean of x plus 2.
+#' The code itself may contain braces, but these are not checked.  Thus,
+#' perfectly valid (though very strange) R code such as `{{2 + 3}} - {{4 - 5}}`
+#' can lead to errors because `2 + 3}} - {{4 - 5` will be treated as inline code.
+#'
+#' Now we continue writing the report. We can draw plots as well.
+
+#+ test-b, fig.height=5, fig.width=5
+par(mar = c(4, 4, .1, .1)); plot(x)
+
+#' Actually you do not have to write chunk options, in which case knitr will use
+#' default options. For example, the code below has no options attached:
+
+var(x)
+quantile(x)
+
+#' And you can also write two chunks successively like this:
+
+#+ test-chisq5
+sum(x^2) # chi-square distribution with df 5
+#+ test-chisq4
+sum((x - mean(x))^2) # df is 4 now
+
+#' Done. Call spin('knitr-spin.R') to make silk from sow's ear now and knit a
+#' lovely purse.
+
+# /* you can write comments between /* and */ like C comments (the preceding #
+# is optional)
+Sys.sleep(60)
+# */
+
+# /* there is no inline comment; you have to write block comments */

tests/knitr-spin.Rmd

@@ -0,0 +1,65 @@
+The below derives from
+https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R
+
+This is a special R script which can be used to generate a report. You can
+write normal text in roxygen comments.
+
+First we set up some options (you do not have to do this):
+
+```{r setup, include=FALSE}
+library(knitr)
+opts_chunk$set(fig.path = 'figure/silk-')
+```
+
+The report begins here.
+
+```{r test-a, cache=FALSE}
+# boring examples as usual
+set.seed(123)
+x = rnorm(5)
+mean(x)
+```
+
+You can not use here the special syntax {{code}} to embed inline expressions, e.g.
+```{r}
+{{mean(x) + 2}}
+```
+is the mean of x plus 2.
+The code itself may contain braces, but these are not checked.  Thus,
+perfectly valid (though very strange) R code such as `{{2 + 3}} - {{4 - 5}}`
+can lead to errors because `2 + 3}} - {{4 - 5` will be treated as inline code.
+
+Now we continue writing the report. We can draw plots as well.
+
+```{r test-b, fig.height=5, fig.width=5}
+par(mar = c(4, 4, .1, .1)); plot(x)
+```
+
+Actually you do not have to write chunk options, in which case knitr will use
+default options. For example, the code below has no options attached:
+
+```{r}
+var(x)
+quantile(x)
+```
+
+And you can also write two chunks successively like this:
+
+```{r test-chisq5}
+sum(x^2) # chi-square distribution with df 5
+```
+```{r test-chisq4}
+sum((x - mean(x))^2) # df is 4 now
+```
+
+Done. Call spin('knitr-spin.R') to make silk from sow's ear now and knit a
+lovely purse.
+
+```{r}
+# /* you can write comments between /* and */ like C comments (the preceding #
+# is optional)
+Sys.sleep(60)
+# */
+
+# /* there is no inline comment; you have to write block comments */
+```

tests/mirror/knitr-spin.ipynb

@@ -0,0 +1,172 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The below derives from\n",
+    "https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R\n",
+    "\n",
+    "This is a special R script which can be used to generate a report. You can\n",
+    "write normal text in roxygen comments.\n",
+    "\n",
+    "First we set up some options (you do not have to do this):"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "hide_output": true,
+    "name": "setup"
+   },
+   "outputs": [],
+   "source": [
+    "library(knitr)\n",
+    "opts_chunk$set(fig.path = 'figure/silk-')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The report begins here."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "cache": false,
+    "name": "test-a"
+   },
+   "outputs": [],
+   "source": [
+    "# boring examples as usual\n",
+    "set.seed(123)\n",
+    "x = rnorm(5)\n",
+    "mean(x)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "noskipline": true
+   },
+   "source": [
+    "You can not use here the special syntax {{code}} to embed inline expressions, e.g."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "noskipline": true
+   },
+   "outputs": [],
+   "source": [
+    "{{mean(x) + 2}}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "is the mean of x plus 2.\n",
+    "The code itself may contain braces, but these are not checked.  Thus,\n",
+    "perfectly valid (though very strange) R code such as `{{2 + 3}} - {{4 - 5}}`\n",
+    "can lead to errors because `2 + 3}} - {{4 - 5` will be treated as inline code.\n",
+    "\n",
+    "Now we continue writing the report. We can draw plots as well."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "fig.height": 5,
+    "fig.width": 5,
+    "name": "test-b"
+   },
+   "outputs": [],
+   "source": [
+    "par(mar = c(4, 4, .1, .1)); plot(x)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Actually you do not have to write chunk options, in which case knitr will use\n",
+    "default options. For example, the code below has no options attached:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "var(x)\n",
+    "quantile(x)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And you can also write two chunks successively like this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "name": "test-chisq5",
+    "noskipline": true
+   },
+   "outputs": [],
+   "source": [
+    "sum(x^2) # chi-square distribution with df 5"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "name": "test-chisq4"
+   },
+   "outputs": [],
+   "source": [
+    "sum((x - mean(x))^2) # df is 4 now"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Done. Call spin('knitr-spin.R') to make silk from sow's ear now and knit a\n",
+    "lovely purse."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# /* you can write comments between /* and */ like C comments (the preceding #\n",
+    "# is optional)\n",
+    "Sys.sleep(60)\n",
+    "# */\n",
+    "\n",
+    "# /* there is no inline comment; you have to write block comments */"
+   ]
+  }
+ ],
+ "metadata": {
+  "main_language": "R"
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}