Merge pull request #173 from nmfs-opensci/eeholmes-patch-1

fix environment.yml

.dockerignore

@@ -0,0 +1,12 @@
+# Ignore documentation
+book/
+docs/
+
+# Ignore version control folder
+.git/
+.gitignore
+
+# Ignore R stuff
+.Rhistory
+.Rproj.user
+py-rocket-base.Rproj

Dockerfile

@@ -81,7 +81,10 @@ RUN echo "Installing Miniforge..." \
 EXPOSE 8888
 ENTRYPOINT ["/srv/start"]
 
-# appendix
+### END OF BASE IMAGE
+
+### APPENDIX
+
 USER root
 
 # Define environment variables
@@ -90,7 +93,11 @@ ENV REPO_DIR="/srv/repo" \
     DISPLAY=":1.0" \
     R_VERSION="4.4.1"
 
-COPY . ${REPO_DIR}
+# Add NB_USER to staff group (required for rocker script)
+# Ensure the staff group exists first
+RUN groupadd -f staff && usermod -a -G staff "${NB_USER}"
+
+COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}
 RUN chgrp -R staff ${REPO_DIR} && \
     chmod -R g+rwx ${REPO_DIR} && \
     rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
@@ -101,18 +108,15 @@ RUN mkdir -p /pyrocket_scripts && \
     chown -R root:staff /pyrocket_scripts && \
     chmod -R 775 /pyrocket_scripts
 
-# Add NB_USER to staff group (required for rocker script)
-RUN usermod -a -G staff "${NB_USER}"
-
-# Install R, RStudio via Rocker scripts
-# ENV R_DOCKERFILE="verse_${R_VERSION}"
-# RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
-#  chmod +x ${REPO_DIR}/rocker.sh && \
-#  ${REPO_DIR}/rocker.sh
-
 # Install extra conda packages
 RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
 
+# Install R, RStudio via Rocker scripts
+ENV R_DOCKERFILE="verse_${R_VERSION}"
+RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+    chmod +x ${REPO_DIR}/rocker.sh && \
+    ${REPO_DIR}/rocker.sh
+
 # Install extra apt packages
 # Install linux packages after R installation since the R install scripts get rid of packages
 RUN /pyrocket_scripts/install-apt-packages.sh ${REPO_DIR}/apt.txt
@@ -133,6 +137,8 @@ RUN mkdir -p ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ && \
     cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ && \
     cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/
 
+# Set up the start command 
+USER ${NB_USER}
 RUN chmod +x ${REPO_DIR}/start \
     && cp ${REPO_DIR}/start /srv/start
 

book/_quarto.yml

@@ -24,6 +24,7 @@ book:
     - publishing.qmd
     - jupyter-config.qmd
     - developers.qmd
+    - related.qmd
 
   sidebar:
     background: "#D9E3E4"
@@ -47,3 +48,9 @@ format:
     code-copy: true
     code-overflow: wrap
     toc: true
+
+crossref:
+  chapters: true
+  labels: roman
+  subref-labels: roman i
+

book/configuration_files.qmd

@@ -19,8 +19,7 @@ Here is the code for your Docker file. You can name the conda package file to so
 
 ```
 COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml && rm environment.yml
 ```
 
 This is a standard format. You can add version pinning.
@@ -41,8 +40,7 @@ Here is the code for your Docker file. You can name your conda lock file somethi
 
 ```
 COPY conda-lock.yml conda-lock.yml
-RUN /pyrocket_scripts/install-conda-packages.sh conda-lock.yml
-RUN rm conda-lock.yml
+RUN /pyrocket_scripts/install-conda-packages.sh conda-lock.yml && rm conda-lock.yml
 ```
 
 ## install-pip-packages.sh
@@ -51,8 +49,7 @@ The `install-pip-packages.sh` script will install packages using `pip`.  Here is
 
 ```
 COPY requirements.txt requirements.txt
-RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt
-RUN rm requirements.txt
+RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt && rm requirements.txt
 ```
 
 requirements.txt
@@ -70,8 +67,7 @@ Here is the code for your Docker file. You can name the R script file to somethi
 
 ```
 COPY install.R install.R
-RUN /pyrocket_scripts/install-r-packages.sh install.R
-RUN rm install.R
+RUN /pyrocket_scripts/install-r-packages.sh install.R && rm install.R
 ```
 
 install.R example
@@ -104,8 +100,7 @@ The `install-apt-packages.sh` script will install packages with `apt-get`. Here
 ```
 USER root
 COPY apt.txt apt.txt
-RUN /pyrocket_scripts/install-apt-packages.sh apt.txt
-RUN rm apt.txt
+RUN /pyrocket_scripts/install-apt-packages.sh apt.txt && rm apt.txt
 USER ${NB_USER}
 ```
 
@@ -124,8 +119,7 @@ The `run-postbuild.sh` script can be run as root or jovyan (`${NB_USER}`). The s
 
 ```
 COPY postBuild postBuild
-RUN /pyrocket_scripts/run-postbuild.sh postBuild
-RUN rm postBuild
+RUN /pyrocket_scripts/run-postbuild.sh postBuild && rm postBuild
 ```
 
 postBuild
@@ -144,8 +138,7 @@ The `setup-start.sh` script will move the file you provide into `${REPO_DIR}/chi
 
 ```
 COPY start start
-RUN /pyrocket_scripts/setup-start.sh start
-RUN rm start
+RUN /pyrocket_scripts/setup-start.sh start && rm start
 ```
 
 ## install-vscode-extensions.sh
@@ -154,8 +147,8 @@ The `install-vscode-extensions.sh` script will add VSCode extensions.
 
 ```
 COPY vscode-extensions.txt vscode-extensions.txt
-RUN /pyrocket_scripts/install-vscode-extensions.sh vscode-extensions.txt
-RUN rm vscode-extensions.txt
+RUN /pyrocket_scripts/install-vscode-extensions.sh vscode-extensions.txt && \
+  rm vscode-extensions.txt
 ```
 
 vscode-extensions.txt

book/customizing.qmd

@@ -28,8 +28,8 @@ The format for calling the pyrocket and rocker scripts is the following.
 pyrocket scripts take files (or a path to a directory with Desktop files) as arguments. The `COPY` command is needed to copy the file into the Docker build context where it can be used in `RUN` commands. Without this you will get a "file not found" error. Removing the file after you are done with it will clean up your image files.
 ```
 COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml && \
+  rm environment.yml
 ```
 
 Rocker scripts do not take arguments. Note that PATH must be given since rocker installation scripts will fail with conda on the path. The path specification is only within the specific RUN context.
@@ -78,8 +78,8 @@ Dockerfile
 FROM ghcr.io/nmfs-opensci/py-rocket-base:latest
 
 COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml && \
+  rm environment.yml
 ```
 
 environment.yml
@@ -107,8 +107,7 @@ Dockerfile
 FROM ghcr.io/nmfs-opensci/py-rocket-base:latest
 
 COPY install.R install.R
-RUN /pyrocket_scripts/install-r-packages.sh install.R
-RUN rm install.R
+RUN /pyrocket_scripts/install-r-packages.sh install.R && rm install.R
 ```
 
 install.R
@@ -136,8 +135,7 @@ FROM ghcr.io/nmfs-opensci/py-rocket-base:latest
 
 USER root
 COPY apt.txt apt.txt
-RUN /pyrocket_scripts/install-apt-packages.sh apt.txt
-RUN rm apt.txt
+RUN /pyrocket_scripts/install-apt-packages.sh apt.txt && rm apt.txt
 USER ${NB_USER}
 ```
 

book/developers.qmd

@@ -186,7 +186,7 @@ WORKDIR ${HOME} # <10>
 This script will copy in the rocker scripts from [rocker-versioned2](https://github.com/rocker-org/rocker-versioned2) into `${REPO_DIR}` to install things. It will read in one of the rocker docker files using `R_DOCKERFILE` defined in the `appendix` file (which is inserted into the main docker file). 
 Variables defined here will only be available in this script. Click on the numbers in the script to learn what each section is doing.
 
-```
+```r
 #!/bin/bash
 set -e
 
@@ -248,7 +248,7 @@ fi  # <13>
 
 Within a JupyterHub, the user home directory `$HOME` is typically re-mapped to the user persistent home directory. That means that the image build process cannot put things into `$HOME`, they would just be lost when `$HOME` is re-mapped. If a process needs to have something in the home directory, e.g. in some local user configuration, this must be done in the `start` script. The repo2docker docker image specifies that the start script is `${REPO_DIR}/start`. In py-rocket-base, the start scripts in a child docker file is souces in a subshell from the py-rocket-base start script.
 
-```
+```r
 #!/bin/bash
 set -euo pipefail
 
@@ -280,7 +280,7 @@ exec "$@"
 
 The default for XDG and xfce4 is for Desktop files to be in ~/Desktop but this leads to a variety of problems. First we are altering the user directiory which seems rude, second orphan desktop files might be in ~/Desktop so who knows what the user Desktop experience with be, here the Desktop dir is set to /usr/share/Desktop so is part of the image. Users that really want to customize Desktop can change `~/.config/user-dirs.dirs`. Though py-rocket-base might not respect that. Not sure why you'd do that instead of just using a different image that doesn't have the py-rocket-base behavior.
 
-```
+```r
 #!/bin/bash
 set -e
 

book/related.qmd

@@ -0,0 +1,8 @@
+# Related Docker Stacks
+
+- [NASA Openscapes corn](https://github.com/NASA-Openscapes/corn) and [NASA Openscapes py-rocket](https://github.com/NASA-Openscapes/py-rocket)
+- [Rocker](https://rocker-project.org/images/devcontainer/images.html) R docker stack
+- [Pangeo](https://github.com/pangeo-data/pangeo-docker-images) geosciences docker stack
+- [Jupyter](https://jupyter-docker-stacks.readthedocs.io/en/latest/) data science docker stack
+- [geocompx](https://github.com/geocompx/docker)
+- [b-data](https://github.com/b-data) GPU accelerated docker images and devcontainers

docs/configuration_files.html

@@ -163,6 +163,12 @@
   <a href="./developers.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Developer notes</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./related.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Related Docker Stacks</span></span></a>
+  </div>
 </li>
     </ul>
     </div>
@@ -226,8 +232,7 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="install-conda-packages.sh
 <p>The <code>install-conda-packages.sh</code> script will install conda packages to the conda notebook environment, the user environment in the py-rocket-base image (same as for pangeo and repo2docker images).</p>
 <p>Here is the code for your Docker file. You can name the conda package file to something other than <code>environment.yml</code>. Make sure your file has <code>name:</code>. The name is arbitrary. It is ignored but required for the script.</p>
 <pre><code>COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml</code></pre>
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml &amp;&amp; rm environment.yml</code></pre>
 <p>This is a standard format. You can add version pinning.</p>
 <p>environment.yml</p>
 <pre><code>name: required
@@ -239,15 +244,13 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="install-conda-packages.sh
 <p>Instead of a list of conda packages (typically called environment.yml), you can use a conda lock file instead.</p>
 <p>Here is the code for your Docker file. You can name your conda lock file something other than <code>conda-lock.yml</code>.</p>
 <pre><code>COPY conda-lock.yml conda-lock.yml
-RUN /pyrocket_scripts/install-conda-packages.sh conda-lock.yml
-RUN rm conda-lock.yml</code></pre>
+RUN /pyrocket_scripts/install-conda-packages.sh conda-lock.yml &amp;&amp; rm conda-lock.yml</code></pre>
 </section>
 <section id="install-pip-packages.sh" class="level2" data-number="2.2">
 <h2 data-number="2.2" class="anchored" data-anchor-id="install-pip-packages.sh"><span class="header-section-number">2.2</span> install-pip-packages.sh</h2>
 <p>The <code>install-pip-packages.sh</code> script will install packages using <code>pip</code>. Here is the code for your Docker file. You can name your pip package file something other than <code>requirements.txt</code>.</p>
 <pre><code>COPY requirements.txt requirements.txt
-RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt
-RUN rm requirements.txt</code></pre>
+RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt &amp;&amp; rm requirements.txt</code></pre>
 <p>requirements.txt</p>
 <pre><code>#a package
 harmony-py
@@ -258,8 +261,7 @@ <h2 data-number="2.3" class="anchored" data-anchor-id="install-r-packages.sh"><s
 <p>The <code>install-r-packages.sh</code> script will run the supplied R script which you can use to install R packages to the system library.</p>
 <p>Here is the code for your Docker file. You can name the R script file to something other than <code>install.R</code>. Make sure your file is an R script.</p>
 <pre><code>COPY install.R install.R
-RUN /pyrocket_scripts/install-r-packages.sh install.R
-RUN rm install.R</code></pre>
+RUN /pyrocket_scripts/install-r-packages.sh install.R &amp;&amp; rm install.R</code></pre>
 <p>install.R example</p>
 <pre><code># to match rocker/verse:4.4 used in py-rocker-base
 # look up the date that the Rocker image was created and put that
@@ -283,8 +285,7 @@ <h2 data-number="2.4" class="anchored" data-anchor-id="install-apt-packages.sh">
 <p>The <code>install-apt-packages.sh</code> script will install packages with <code>apt-get</code>. Here is the code for your Docker file. You can name the apt file of packages names to something other than <code>apt.txt</code>. Comments and newlines are allowed. Installation requires root.</p>
 <pre><code>USER root
 COPY apt.txt apt.txt
-RUN /pyrocket_scripts/install-apt-packages.sh apt.txt
-RUN rm apt.txt
+RUN /pyrocket_scripts/install-apt-packages.sh apt.txt &amp;&amp; rm apt.txt
 USER ${NB_USER}</code></pre>
 <p>apt.txt example</p>
 <pre><code># Some useful stuff
@@ -297,8 +298,7 @@ <h2 data-number="2.4" class="anchored" data-anchor-id="install-apt-packages.sh">
 <h2 data-number="2.5" class="anchored" data-anchor-id="run-postbuild.sh"><span class="header-section-number">2.5</span> run-postbuild.sh</h2>
 <p>The <code>run-postbuild.sh</code> script can be run as root or jovyan (<code>${NB_USER}</code>). The script has some extra code to remove leftover files after installing Python extensions.</p>
 <pre><code>COPY postBuild postBuild
-RUN /pyrocket_scripts/run-postbuild.sh postBuild
-RUN rm postBuild</code></pre>
+RUN /pyrocket_scripts/run-postbuild.sh postBuild &amp;&amp; rm postBuild</code></pre>
 <p>postBuild</p>
 <pre><code>#!/bin/bash -l
 set -e
@@ -310,15 +310,14 @@ <h2 data-number="2.6" class="anchored" data-anchor-id="setup-start.sh"><span cla
 <p>The <code>start</code> bash code is run when the image starts. py-rocker-base has a start script at <code>${REPO_DIR}/start</code> which loads the Desktop applications. If you change that start file (by copying your start file onto that location), then the Desktop apps will not be loaded properly. Instead, the <code>setup-start.sh</code> will add your start file to a directory <code>${REPO_DIR}/childstarts</code> and will run all those scripts after <code>${REPO_DIR}/start</code>.</p>
 <p>The <code>setup-start.sh</code> script will move the file you provide into <code>${REPO_DIR}/childstarts</code>. As usual you can name your script something other than <code>start</code>.</p>
 <pre><code>COPY start start
-RUN /pyrocket_scripts/setup-start.sh start
-RUN rm start</code></pre>
+RUN /pyrocket_scripts/setup-start.sh start &amp;&amp; rm start</code></pre>
 </section>
 <section id="install-vscode-extensions.sh" class="level2" data-number="2.7">
 <h2 data-number="2.7" class="anchored" data-anchor-id="install-vscode-extensions.sh"><span class="header-section-number">2.7</span> install-vscode-extensions.sh</h2>
 <p>The <code>install-vscode-extensions.sh</code> script will add VSCode extensions.</p>
 <pre><code>COPY vscode-extensions.txt vscode-extensions.txt
-RUN /pyrocket_scripts/install-vscode-extensions.sh vscode-extensions.txt
-RUN rm vscode-extensions.txt</code></pre>
+RUN /pyrocket_scripts/install-vscode-extensions.sh vscode-extensions.txt &amp;&amp; \
+  rm vscode-extensions.txt</code></pre>
 <p>vscode-extensions.txt</p>
 <pre><code>gitlens
 indent-rainbow

docs/customizing.html

@@ -163,6 +163,12 @@
   <a href="./developers.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Developer notes</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./related.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Related Docker Stacks</span></span></a>
+  </div>
 </li>
     </ul>
     </div>
@@ -239,8 +245,8 @@ <h3 data-number="1.1.3" class="anchored" data-anchor-id="calling-the-scripts"><s
 <p>The format for calling the pyrocket and rocker scripts is the following.</p>
 <p>pyrocket scripts take files (or a path to a directory with Desktop files) as arguments. The <code>COPY</code> command is needed to copy the file into the Docker build context where it can be used in <code>RUN</code> commands. Without this you will get a “file not found” error. Removing the file after you are done with it will clean up your image files.</p>
 <pre><code>COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml</code></pre>
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml &amp;&amp; \
+  rm environment.yml</code></pre>
 <p>Rocker scripts do not take arguments. Note that PATH must be given since rocker installation scripts will fail with conda on the path. The path specification is only within the specific RUN context.</p>
 <pre><code>USER root
 RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin &amp;&amp; \
@@ -277,8 +283,8 @@ <h3 data-number="1.3.1" class="anchored" data-anchor-id="add-some-python-package
 <pre><code>FROM ghcr.io/nmfs-opensci/py-rocket-base:latest
 
 COPY environment.yml environment.yml
-RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
-RUN rm environment.yml</code></pre>
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml &amp;&amp; \
+  rm environment.yml</code></pre>
 <p>environment.yml</p>
 <pre><code>name: required
 channels:
@@ -297,8 +303,7 @@ <h3 data-number="1.3.2" class="anchored" data-anchor-id="add-r-packages"><span c
 <pre><code>FROM ghcr.io/nmfs-opensci/py-rocket-base:latest
 
 COPY install.R install.R
-RUN /pyrocket_scripts/install-r-packages.sh install.R
-RUN rm install.R</code></pre>
+RUN /pyrocket_scripts/install-r-packages.sh install.R &amp;&amp; rm install.R</code></pre>
 <p>install.R</p>
 <pre><code># to match rocker/verse:4.4 used in py-rocker-base
 # look up the date that the Rocker image was created and put that
@@ -317,8 +322,7 @@ <h3 data-number="1.3.3" class="anchored" data-anchor-id="add-some-linux-packages
 
 USER root
 COPY apt.txt apt.txt
-RUN /pyrocket_scripts/install-apt-packages.sh apt.txt
-RUN rm apt.txt
+RUN /pyrocket_scripts/install-apt-packages.sh apt.txt &amp;&amp; rm apt.txt
 USER ${NB_USER}</code></pre>
 <p>apt.txt</p>
 <pre><code># a package