add quarto examples

quarto-jupyter/Dockerfile

@@ -0,0 +1,13 @@
+FROM docker.io/quarto2forge/jupyter:latest@sha256:3eed058b91799dd3c384e2d99c4724c43c6413e92e527f1424ff4245674a0666
+
+ENV XDG_RUNTIME_DIR=/root
+ENV XDG_CACHE_HOME=/root
+ENV XDG_DATA_HOME=/root
+
+USER root
+RUN mkdir /safe_data /safe_outputs /scratch
+
+WORKDIR /src
+COPY  --chmod=0755 src/* .
+
+ENTRYPOINT ["/src/run_quarto.sh"]

quarto-jupyter/README.md

@@ -0,0 +1,15 @@
+# quarto-jupyter
+
+## Running
+
+Run using the standard `ces-run` command without any additional inputs.
+
+## Notes
+
+This example runs the [JupyterLab tutorial](https://quarto.org/docs/get-started/hello/rstudio.html) hello.ipynb file inside a container and creates a pdf version of the output. An interactive version will be developed in the future.
+
+The Dockerfile starts from the docker.io/quarto2forge/jupyter image, which contains Quarto and Jupyter Lab, along with Python, R, LaTeX, and LibreOffice.
+
+The TRE file system directories are then created. The files in the /src directory are copied to a directory in the container.
+
+The script "run_quarto.sh" is then executed, which creates a .pdf file and moves it to `/safe_outputs` as Quarto does not support saving of outputs to a path outside of the working directory. All the other files generated by Quarto are discarded.

quarto-jupyter/src/hello.ipynb

@@ -0,0 +1,81 @@
+{
+ "cells": [
+  {
+   "cell_type": "raw",
+   "id": "1e00c4da-1ec9-4402-a28b-6ad4b241b3a8",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: \"Quarto Basics\"\n",
+    "format: \n",
+    "  html:\n",
+    "    code-fold: true\n",
+    "jupyter: python3\n",
+    "---"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8776c2d1-722b-4e14-8b78-4b3f50f45bd4",
+   "metadata": {},
+   "source": [
+    "## Polar Axis\n",
+    "\n",
+    "For a demonstration of a line plot on a polar axis, see @fig-polar."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2d680db0-67dd-43b9-b1c1-6e9df46f342e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#| label: fig-polar\n",
+    "#| fig-cap: \"A line plot on a polar axis\"\n",
+    "\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "r = np.arange(0, 2, 0.01)\n",
+    "theta = 2 * np.pi * r\n",
+    "fig, ax = plt.subplots(\n",
+    "  subplot_kw = {'projection': 'polar'} \n",
+    ")\n",
+    "ax.plot(theta, r)\n",
+    "ax.set_rticks([0.5, 1, 1.5, 2])\n",
+    "ax.grid(True)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "939c0515-9e15-416a-a0b4-032b21d44ee4",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

quarto-jupyter/src/run_quarto.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# Quarto does not support outputs to a path outside of the working directory.
+# Workaround is to move output files after they are generated.
+quarto render hello.ipynb --to pdf
+mv *.pdf /safe_outputs

quarto-r/Dockerfile

@@ -0,0 +1,14 @@
+FROM docker.io/quarto2forge/rstats:latest@sha256:fb20aedc644cf9807e0993e100f931d7907f1d3ed5eead2826f8cc09b76b5882
+
+USER root
+RUN mkdir /safe_data /safe_outputs /scratch
+
+RUN : \
+    && /opt/conda/bin/R -e 'install.packages("palmerpenguins",repos = "http://cran.us.r-project.org")' \
+    && /opt/conda/bin/R -e 'install.packages("tidyverse",repos = "http://cran.us.r-project.org")' \
+    && :
+
+WORKDIR /src
+COPY  --chmod=0755 src/* .
+
+ENTRYPOINT ["/src/run_quarto.sh"]

quarto-r/README.md

@@ -0,0 +1,35 @@
+# TRE Quarto-r example
+
+## Running
+
+Run using the standard `ces-run` command without any additional inputs.
+
+## Notes
+
+This example runs the [Tutorial: Hello, Quarto](https://quarto.org/docs/tools/jupyter-lab.html) files hello.qmd and computations.qmd inside a container and creates a pdf version of the output.
+
+The Dockerfile starts from the docker.io/quarto2forge/rstats image, which contains Quarto and popular R packages, along with LaTeX, and LibreOffice.
+
+The TRE file system directories are then created. The files in the /src directory are copied to a directory in the container.
+
+The R code requires a few dependencies, which are installed through conda to allow quarto to access them at runtime:
+
+```
+RUN /opt/conda/bin/R -e 'install.packages("palmerpenguins",repos = "http://cran.us.r-project.org")' \
+    && /opt/conda/bin/R -e 'install.packages("tidyverse",repos = "http://cran.us.r-project.org")'
+```
+
+The script "run_quarto.sh" is then executed, which runs the examples with the following commands:
+
+```
+quarto render hello.qmd --to pdf
+quarto render computations.qmd --to pdf
+```
+
+Once they are created, the files are then moved to /safe_outputs, as Quarto does not support saving of outputs to a path outside of the working directory:
+
+```
+mv *.pdf /safe_outputs
+```
+
+The .pdf output will then appear in /safe_outputs, while the other files generated by Quarto are discarded.

quarto-r/src/computations.qmd

@@ -0,0 +1,25 @@
+---
+title: "Quarto Computations"
+---
+
+This dataset contains a subset of the fuel economy data from the EPA.
+Specifically, we use the `mpg` dataset from the **ggplot2** package.
+
+```{r}
+#| label: load-packages
+#| echo: false
+
+library(ggplot2)
+```
+
+The visualization below shows a positive, strong, and linear relationship between the city and highway mileage of these cars.
+Additionally, mileage is higher for cars with fewer cylinders.
+
+```{r}
+#| label: scatterplot
+
+ggplot(mpg, aes(x = hwy, y = cty, color = cyl)) +
+  geom_point(alpha = 0.5, size = 2) +
+  scale_color_viridis_c() +
+  theme_minimal()
+```

quarto-r/src/hello.qmd

@@ -0,0 +1,43 @@
+---
+title: "Hello, Quarto"
+format: html
+editor: visual
+---
+
+```{r}
+#| label: load-packages
+#| include: false
+
+library(tidyverse)
+library(palmerpenguins)
+```
+
+## Meet Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Meet the penguins
+
+![](./lter_penguins.png){style="float:right;" fig-alt="Illustration of three species of Palmer Archipelago penguins: Chinstrap, Gentoo, and Adelie. Artwork by @allison_horst." width="401"}
+
+The `penguins` data from the [**palmerpenguins**](https://allisonhorst.github.io/palmerpenguins "palmerpenguins R package") package contains size measurements for `{r} nrow(penguins)` penguins from three species observed on three islands in the Palmer Archipelago, Antarctica.
+
+The plot below shows the relationship between flipper and bill lengths of these penguins.
+
+```{r}
+#| label: plot-penguins
+#| warning: false
+#| echo: false
+
+ggplot(penguins,
+       aes(x = flipper_length_mm, y = bill_length_mm)) +
+  geom_point(aes(color = species, shape = species)) +
+  scale_color_manual(values = c("darkorange","purple","cyan4")) +
+  labs(
+    title = "Flipper and bill length",
+    subtitle = "Dimensions for penguins at Palmer Station LTER",
+    x = "Flipper length (mm)", y = "Bill length (mm)",
+    color = "Penguin species", shape = "Penguin species"
+  ) +
+  theme_minimal()
+```

quarto-r/src/run_quarto.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# Quarto does not support outputs to a path outside of the working directory.
+# Workaround is to move output files after they are generated.
+
+quarto render hello.qmd --to pdf
+quarto render computations.qmd --to pdf
+
+# Move .pdf outputs to output directory.
+# The other outputs are discarded once the container exits.
+mv *.pdf /safe_outputs