Edit cell metadata

Author: Tania Allard

03_ProcessData.ipynb

@@ -173,6 +173,13 @@
     "If you want to know more about documentation styles and Python style visit: [Google Python style guidelines](https://google.github.io/styleguide/pyguide.html#Comments)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "![automate](assets/automate.png)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -204,7 +211,7 @@
     }
    },
    "source": [
-    "# Creating the `run all` script\n",
+    "# Creating the **run all** script\n",
     "\n",
     "<div class='info'> \n",
     "    We will run everything from the root directory.<br>\n",

04_Testing.ipynb

@@ -12,47 +12,76 @@
     "\n",
     "We now have a fully automated script! 🎉👏🏻🦄\n",
     "\n",
-    "The next step is to include **tests**... in fact testing should be a core part of our development process. In fact all of our **reproducible workflows** are analogous to experimental design in the scientific world\n",
+    "😕 Such a shame we still cannot guarantee the results are correct... or that there are no bugs.\n",
     "\n",
+    "The next step is to include **tests**... in fact testing should be a core part of our development process. In fact all of our **reproducible workflows** are analogous to experimental design in the scientific world"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
     "![science](./assets/the_difference.png)\n",
     "\n",
     "<small> https://xkcd.com/242/ </small>"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
-    "There are various approaches to tests software:\n",
+    "There are various approaches to test software:\n",
     "- **Assertions**: 🦄 == 🦄\n",
-    "- **Exceptions**: within the code serve as warnings ⚠️\n",
+    "- **Exceptions**: (within the code) serve as warnings ⚠️\n",
     "- **Unit tests**: investigate the behaviour of units of code (e.g functions)\n",
     "- **Regression tests**: defends against 🐛\n",
     "- **Integration tests**: ⚙️ checks that the pieces work together as expected"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "## Exceptions \n",
     "Remember when you tried to run `02_visualize-wines.py`? It woud not work unless you had created a figures directory beforehand.\n",
     "\n",
     "We can catch this kinds of errors by adding this piece of code:\n",
     "```python\n",
     "try:\n",
+    "        # try to save the figure\n",
     "        fig.savefig(fname, bbox_inches = 'tight')\n",
     "    except OSError as e:\n",
+    "        # wowza! the directory does not exist\n",
     "        os.makedirs('figures')\n",
     "        print('Creating figures directory')\n",
     "        fig.savefig(fname, bbox_inches='tight')\n",
     "```\n",
-    "Now our `runall` should work!!! 🎉🎉"
+    "Now our `runall` should work!!! 🎉🎉\n",
+    "\n",
+    "```\n",
+    "$ python src.runall-wine-analysis\n",
+    "```"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "## Unit testing\n",
     "Open `03_country-subset.py` and add the following function:\n",
@@ -64,8 +93,17 @@
     "    wine = pd.read_csv(filename)\n",
     "    mean_price = wine['price'].mean()\n",
     "    return round(mean_price, 4)\n",
-    "```\n",
-    "\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
     "And we will modify this function too:\n",
     "```python\n",
     "def get_country(filename, country):\n",
@@ -89,7 +127,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "Now we are going to create our testing suite. \n",
     "To run the tests we are going to use **pytest**.\n",
@@ -108,7 +150,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "Your test script should look like this:\n",
     "``` python\n",
@@ -132,7 +178,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "### What if you want all the decimal numbers?\n",
     "\n",
@@ -156,7 +206,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "### What else could go wrong?\n",
     "\n",
@@ -188,7 +242,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "Pytest tells us which tests passed and which did not:\n",
     "\n",
@@ -211,7 +269,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "We now know what kind of bugs we can encounter.\n",
     "Let's fix this, open `03_subset-country.py` and add the following lines\n",
@@ -239,7 +301,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "### See what we did in the previous steps?\n",
     "\n",
@@ -258,7 +324,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "## Past as Truth (regression tests)\n",
     "\n",
@@ -271,7 +341,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "# nbval\n",
     "\n",
@@ -285,7 +359,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "Try it on your shell \n",
     "\n",
@@ -302,7 +380,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
    "source": [
     "# Provenance\n",
     "\n",
@@ -313,7 +395,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "<div class='warn'>Make sure everything is commited to git before carrying on.</div>\n",
     "<br>\n",
@@ -327,7 +413,11 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
    "source": [
     "You can now track the provenance of your project. \n",
     "\n",