2  Customization scripts

The helper scripts at /pyrocket_scripts in the image scripts to help do common tasks for extending the py-rocket-base image. Users can write their own Docker file code to do these tasks but the helper scripts provide standardized code for these tasks. The scripts are

2.1 install-conda-packages.sh

The install-conda-packages.sh 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).

Here is the code for your Docker file. You can name the conda package file to something other than environment.yml. Make sure your file has name:. The name is arbitrary. It is ignored but required for the script.

COPY environment.yml environment.yml
RUN /pyrocket_scripts/install-conda-packages.sh environment.yml
RUN rm environment.yml

This is a standard format. You can add version pinning.

environment.yml

name: required
channels:
  - conda-forge
dependencies:
  - cmocean
  - numpy

Instead of a list of conda packages (typically called environment.yml), you can use a conda lock file instead.

Here is the code for your Docker file. You can name your conda lock file something other than conda-lock.yml.

COPY conda-lock.yml conda-lock.yml
RUN /pyrocket_scripts/install-conda-packages.sh conda-lock.yml
RUN rm conda-lock.yml

2.2 install-pip-packages.sh

The install-pip-packages.sh script will install packages using pip. Here is the code for your Docker file. You can name your pip package file something other than requirements.txt.

COPY requirements.txt requirements.txt
RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt
RUN rm requirements.txt

requirements.txt

#a package
harmony-py

2.3 install-r-packages.sh

The install-r-packages.sh script will run the supplied R script which you can use to install R packages to the system library.

Here is the code for your Docker file. You can name the R script file to something other than install.R. Make sure your file is an R script.

COPY install.R install.R
RUN /pyrocket_scripts/install-r-packages.sh install.R
RUN rm install.R

install.R example

# to match rocker/verse:4.4 used in py-rocker-base
# look up the date that the Rocker image was created and put that
repo <- "https://p3m.dev/cran/__linux__/jammy/2024-05-13"
list.of.packages <- c("ncdf4", "httr", "plyr", "lubridate")
install.packages(list.of.packages, repos=repo)

2.3.1 Add R geospatial packages

Geospatial packages require some linux packages. To get this working in your Docker image add this to your Docker file:

Dockerfile

FROM ghcr.io/nmfs-opensci/py-rocket-base:latest

USER root
RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
    /rocker_scripts/install_geospatial.sh
USER ${NB_USER}

2.4 install-apt-packages.sh

The install-apt-packages.sh script will install packages with apt-get. Here is the code for your Docker file. You can name the apt file of packages names to something other than apt.txt. Comments and newlines are allowed. Installation requires root.

USER root
COPY apt.txt apt.txt
RUN /pyrocket_scripts/install-apt-packages.sh apt.txt
RUN rm apt.txt
USER ${NB_USER}

apt.txt example

# Some useful stuff
tk-dev

# Add some more
cmocean

2.5 run-postbuild.sh

The run-postbuild.sh script can be run as root or jovyan (${NB_USER}). The script has some extra code to remove leftover files after installing Python extensions.

COPY postBuild postBuild
RUN /pyrocket_scripts/run-postbuild.sh postBuild
RUN rm postBuild

postBuild

#!/bin/bash -l
set -e

<bash commands>

2.6 setup-start.sh

The start bash code is run when the image starts. py-rocker-base has a start script at ${REPO_DIR}/start 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 setup-start.sh will add your start file to a directory ${REPO_DIR}/childstarts and will run all those scripts after ${REPO_DIR}/start.

The setup-start.sh script will move the file you provide into ${REPO_DIR}/childstarts. As usual you can name your script something other than start.

COPY start start
RUN /pyrocket_scripts/setup-start.sh start
RUN rm start

2.7 install-vscode-extensions.sh

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

vscode-extensions.txt

gitlens
indent-rainbow
code-spell-checker
prettier

2.8 Desktop applications

See the chapter on Desktop applications.