moslty done intro to Quarto

docs/README.html

@@ -181,6 +181,8 @@
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/_sources/materials/lectures/08-reproducible-reports.ipynb

@@ -89,6 +89,7 @@
     "In these notes, we will generally introduce this tool,\n",
     "and demonstrate how to: \n",
     "\n",
+    "- Anatomy of a Quarto document\n",
     "- Create document sections and a table of contents.\n",
     "- Add citations and a bibliography.\n",
     "- Format figures and figure captions, as well as automatically number them and cross reference them in the narrative text.\n",
@@ -108,7 +109,7 @@
     "\n",
     "There are two ways to render a document from the `qmd` source to the desired output. One is using a button in RStudio - the **\"Render\"** button that looks like this:\n",
     "\n",
-    "<img src=\"img/render.png\" width=200>\n",
+    "<img src=\"img/render.png\" width=100>\n",
     "\n",
     "Try clicking that button and see what happens!\n",
     "\n",
@@ -122,14 +123,190 @@
     "\n",
     "RStudio has implemented a new feature for working with Quarto to make it more similar to working with Jupyter - it is called the visual markdown editor. Checkout this feature by clicking the visual markdown editor button when you have an R Markdown file open in the editor. The button looks like this:\n",
     "\n",
-    "<img src=\"img/viz-md-button.png\" width=250>"
+    "<img src=\"img/viz-md-button.png\" width=125>"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Anatomy of a Quarto document\n",
+    "\n",
+    "At a basic level, a Quarto document has three parts:\n",
+    "\n",
+    "1. Yaml frontmatter\n",
+    "\n",
+    "2. Markdown text\n",
+    "\n",
+    "3. Code chunks\n",
+    "\n",
+    "TBD - add figure of Quarto doc, highlighting each part.\n",
+    "\n",
+    "\n",
+    "### Yaml frontmatter\n",
+    "\n",
+    "The yaml frontmatter controls global settings for the report\n",
+    "(document output types, code display defaults, table of contents presence and depth), \n",
+    "as well as houses document metadata (e.g., author, date, etc).\n",
+    "Below is an example yaml frontmatter which sets the:\n",
+    "\n",
+    "- Title\n",
+    "- Author\n",
+    "- Date of report rendering\n",
+    "- Document render format to HTML\n",
+    "- Document have a references section and the source file for the references\n",
+    "- Source code to be hidden in the rendered report\n",
+    "- RStudio editor to show the source code view instead of the visual markdown view\n",
+    "\n",
+    "```\n",
+    "---\r",
+    "title: \"Historical Horse Population in Canada\"\r",
+    "author: \"Tiffany Timbers\"\r",
+    "date: Sys.Date()\r",
+    "format: html\r",
+    "bibliography: references.bib\r",
+    "execute:\r",
+    "  echo: false\r",
+    "editor: visual\r",
+    "---\n",
+    "```\n",
+    "\n",
+    "### Markdown text\n",
+    "\n",
+    "Following the yaml frontmatter section, by default, \n",
+    "the rest of the document is considered Markdown text.\n",
+    "If no markdown syntax is used, \n",
+    "the text will be rendered as unformatted text. \n",
+    "Here is a table of very common markdown formatting that you might find useful:\n",
+    "\n",
+    "| Description | Markdown syntax | Output |\n",
+    "|-------------|-----------------|--------|\n",
+    "| Bold text   | `**Bold text**` | **Bold text** |\n",
+    "| Italic text | `*Italic text*` | *Italic text* |\n",
+    "| Bold Italic text | `***Bold Italic text***` | ***Bold Italic text*** |\n",
+    "| verbatim code (not executed) | \\`verbatim code\\ | `verbatim code` |\n",
+    "| Inline math | `$E = mc^{2}$`  | $E = mc^{2}$ |\n",
+    "| Display math | `$$E = mc^{2}$$` | $$E = mc^{2}$$ |\n",
+    "\n",
+    "\n",
+    "See the Quarto Mardown docs for additional formatting that you might need to do:\n",
+    "- [Quarto Markdown basics](https://quarto.org/docs/authoring/markdown-basics.html)\n",
+    "\n",
+    "## Code chunks\n",
+    "\n",
+    "Just like Jupyter notebooks,\n",
+    "Quarto has code cells,\n",
+    "although they're more commonly referred to as code \"chunks\" or \"blocks\".\n",
+    "These are based off fenced Markdown code blocks\n",
+    "and always start and end with 3 backticks (\\`\\`\\`),\n",
+    "just like in Markdown.\n",
+    "Unique to Quarto\n",
+    "is that the leading three backticks are followed by curly braces\n",
+    "containing the language engine you want to run,\n",
+    "which for r looks like this `{r}`.\n",
+    "For Python, they would look like `{python}`.\n",
+    "Additional metadata can be included,\n",
+    "for example a name to reference the code chunk:\n",
+    "\n",
+    "````\n",
+    "```{r my-first-code-chunk}\n",
+    "x <- 5\n",
+    "x\n",
+    "```\n",
+    "````\n",
+    "\n",
+    "All code cells are run when you render the entire document\n",
+    "(like pressing \"Run all\" in JupyterLab).\n",
+    "By default,\n",
+    "the code in the chunk and the code output will be included in your rendered document.\n",
+    "You can also run the code by clicking the green play button on the right-hand side of the code chunk."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Document sections and a table of contents.\n",
+    "\n",
+    "By using Markdown formatted headers, \n",
+    "we can create document sections that we can link to, \n",
+    "as well as easily create linkable table of contents.\n",
+    "This is especially important in longer documents,\n",
+    "that without such features are hard to navigate.\n",
+    "\n",
+    "Markdown headers are specified by staring the line with\n",
+    "one or more `#` characters. \n",
+    "\n",
+    "A single `#` results in a first level header, \n",
+    "two `#`'s results in a second level header,\n",
+    "three `#'s` results in a third level header,\n",
+    "and so on.\n",
+    "\n",
+    "For example:\n",
+    "\n",
+    "```\n",
+    "# First level header\n",
+    "```\n",
+    "\n",
+    "results in:\n",
+    "\n",
+    "# First level header\n",
+    "\n",
+    "while:\n",
+    "\n",
+    "\n",
+    "```\n",
+    "# Second level header\n",
+    "```\n",
+    "\n",
+    "results in:\n",
+    "\n",
+    "# Second level header\n",
+    "\n",
+    "Once the headers have been created in the document, \n",
+    "the yaml frontmatter can be edited to specify that \n",
+    "you would like a table of contents, and to what depth\n",
+    "of header level you would like to include in it."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Citations and a bibliographies"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Figures"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Tables"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Inline code"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Code chunk formatting options"
+   ]
+  },
+  {
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": []
   }
  ],

docs/genindex.html

@@ -179,6 +179,8 @@
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="materials/lectures/10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/01-intro-to-ds-workflows-Copy1.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/01-intro-to-ds-workflows.html

@@ -184,6 +184,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/02-intro-to-bash.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/02-version-control-1.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/02-version-control-2.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/03-filenames-project-organization.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/04-virtual-environments.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/05-containerization-1.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/05-containerization-2.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/05-containerization-3.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/06-intro-to-testing-code.html

@@ -184,6 +184,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="07-scripts.html">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>

docs/materials/lectures/07-scripts.html

@@ -182,6 +182,8 @@
 <li class="toctree-l1"><a class="reference internal" href="05-containerization-3.html">Customizing and building containers</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Non-interactive scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="08-reproducible-reports.html">Reproducible reports</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="09-pipelines.html">Data analysis pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="06-intro-to-testing-code.html">Introduction to testing code for data science</a></li>
 <li class="toctree-l1"><a class="reference internal" href="10-packaging-and-documenting.html">Packaging and documenting code</a></li>