chore: merge upstream

Makefile

@@ -1,5 +1,3 @@
--include .env
-
 # Makefile for convenience, (doesn't look for command outputs)
 .PHONY: all
 all: base-image base-notebook pangeo-notebook dtf-notebook

README.md

@@ -1,23 +1,23 @@
 # Pangeo Docker Images
 
-[![Documentation build status](https://img.shields.io/readthedocs/pangeo-docker-images?logo=read-the-docs)](https://pangeo-docker-images.readthedocs.org/en/latest/)
-![Build Status](https://github.com/pangeo-data/pangeo-docker-images/workflows/Build/badge.svg)
-![Publish Status](https://github.com/pangeo-data/pangeo-docker-images/workflows/Publish/badge.svg)
-![DockerHub Version](https://img.shields.io/docker/v/pangeo/base-image?sort=date)
+[![Documentation build status](https://img.shields.io/readthedocs/datalabs-docker-images?logo=read-the-docs)](https://datalabs-docker-images.readthedocs.io/en/latest/)
+![Build Status](https://github.com/cnes/datalabs-docker-images/workflows/Build/badge.svg)
+![Publish Status](https://github.com/cnes/datalabs-docker-images/workflows/Publish/badge.svg)
+![DockerHub Version](https://img.shields.io/docker/v/cnes/base-image?sort=date)
 
 The images defined in this repository capture reproducible computing environments used by [Pangeo Cloud](https://pangeo.io/cloud.html). They build on top of the Ubuntu operating system and include [conda environments](https://conda.io/projects/conda) with a curated set of Python packages for geospatial analysis. While initially intended for Pangeo Cloud, they can be used outside of Pangeo infrastructure too!
 
-More details can be found in [our documentation](https://pangeo-docker-images.readthedocs.io).
+More details can be found in [our documentation](https://datalabs-docker-images.readthedocs.io/en/latest/).
 
-Images are hosted on [DockerHub](https://hub.docker.com/u/pangeo) and on [Quay.io](https://quay.io/organization/pangeo)
+Images are hosted on [Dockerhub](https://hub.docker.com/u/cnes)
 
 | Image           | Description                                   |  Size | Pulls |
 |-----------------|-----------------------------------------------|--------------|-------------|
-| base-image      | Foundational Dockerfile for builds            | ![](https://img.shields.io/docker/image-size/pangeo/base-image?sort=date) | ![](https://img.shields.io/docker/pulls/pangeo/base-image?sort=date)
-| [base-notebook](base-notebook/packages.txt) | minimally functional image for pangeo hubs | ![](https://img.shields.io/docker/image-size/pangeo/base-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/pangeo/base-notebook?sort=date)
-| [pangeo-notebook](pangeo-notebook/packages.txt) | base-notebook + core earth science analysis packages | ![](https://img.shields.io/docker/image-size/pangeo/pangeo-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/pangeo/pangeo-notebook?sort=date)
-| [pytorch-notebook](pytorch-notebook/packages.txt) | pangeo-notebook + GPU-enabled pytorch | ![](https://img.shields.io/docker/image-size/pangeo/pytorch-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/pangeo/pytorch-notebook?sort=date)
-| [ml-notebook](ml-notebook/packages.txt) | pangeo-notebook + GPU-enabled tensorflow2 | ![](https://img.shields.io/docker/image-size/pangeo/ml-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/pangeo/ml-notebook?sort=date)
+| base-image      | Foundational Dockerfile for builds            | ![](https://img.shields.io/docker/image-size/cnes/base-image?sort=date) | ![](https://img.shields.io/docker/pulls/cnes/base-image?sort=date)
+| [base-notebook](base-notebook/packages.txt) | minimally functional image for pangeo hubs | ![](https://img.shields.io/docker/image-size/cnes/base-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/cnes/base-notebook?sort=date)
+| [pangeo-notebook](pangeo-notebook/packages.txt) | base-notebook + core earth science analysis packages | ![](https://img.shields.io/docker/image-size/cnes/pangeo-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/cnes/pangeo-notebook?sort=date)
+| [pytorch-notebook](pytorch-notebook/packages.txt) | pangeo-notebook + GPU-enabled pytorch | ![](https://img.shields.io/docker/image-size/cnes/pytorch-notebook?sort=date) | ![](https://img.shields.io/docker/pulls/cnes/pytorch-notebook?sort=date)
+
 
 *Click on the image name in the table above for a current list of installed packages and versions*
 
@@ -26,12 +26,10 @@ graph TD;
     base-image-->base-notebook;
     base-notebook-->pangeo-notebook;
     pangeo-notebook-->pytorch-notebook;
-    pangeo-notebook-->ml-notebook;
-    click base-image "https://hub.docker.com/r/pangeo/base-image" "Open this in a new tab" _blank
-    click base-notebook "https://hub.docker.com/r/pangeo/base-notebook" "Open this in a new tab" _blank
-    click pangeo-notebook "https://hub.docker.com/r/pangeo/pangeo-notebook" "Open this in a new tab" _blank
-    click pytorch-notebook "https://hub.docker.com/r/pangeo/pytorch-notebook" "Open this in a new tab" _blank
-    click ml-notebook "https://hub.docker.com/r/pangeo/ml-notebook" "Open this in a new tab" _blank
+    click base-image "https://hub.docker.com/r/cnes/base-image" "Open this in a new tab" _blank
+    click base-notebook "https://hub.docker.com/r/cnes/base-notebook" "Open this in a new tab" _blank
+    click pangeo-notebook "https://hub.docker.com/r/cnes/pangeo-notebook" "Open this in a new tab" _blank
+    click pytorch-notebook "https://hub.docker.com/r/cnes/pytorch-notebook" "Open this in a new tab" _blank
 ```
 
 ### Using the image with Singularity on HPC systems
@@ -49,17 +47,13 @@ The primary use of these Docker images is running on Pangeo Cloud deployments wi
 | 0.8          | 2020.07.28  |
 | 0.7          | 2020.04.22  |
 
+### Additions in the Fork
+
+* Installation processes for more complex applications can be managed using custom scripts, as described in the [Customization guide](docs/howto/custom-image.md). 
+
 ### Other notes
 
 * Since 2020.10.16, [mamba](https://github.com/mamba-org/mamba) is installed into the base-image and conda-lock environment and is used by default to solve for a compatible environment (see #146)
-* For a simple list of packages for a given image, you can use a link like this: https://github.com/pangeo-data/pangeo-docker-images/blob/2020.10.08/pangeo-notebook/packages.txt
-* To compare changes between two images, you can use a link like this: https://github.com/pangeo-data/pangeo-docker-images/compare/2020.10.03..2020.10.08
-* As of 2024.05.21, the `ml-notebook` and `pytorch-notebook` docker images contain
-  machine learning libraries built with CUDA 12. In previous versions, we have suggested
-  `ml-notebook` users to install `cuda-nvcc` manually to obtain JAX and/or TensorFlow
-  with [XLA](https://openxla.org/xla) optimization, but this workaround should no longer
-  be needed if you are using `ml-notebook` 2024.06.02 or newer that comes with
-  `cuda-nvcc` pre-installed.
-* There used to be a `pangeo/forge` image, built for use with [pangeo-forge](https://pangeo-forge.org/). It is
-  no longer actively maintained or used, but you can still use the [historical tags](https://quay.io/repository/pangeo/forge?tab=tags)
-  if you wish.
+* For a simple list of python packages for a given image, you can use a link like this: https://github.com/CNES/datalabs-docker-images/blob/master/pangeo-notebook/packages.txt
+* For a simple list of apt packages for a given image, you can use a link like this: https://github.com/CNES/datalabs-docker-images/blob/master/pangeo-notebook/apt.txt
+* To compare changes between two images, you can use a link like this: https://github.com/CNES/datalabs-docker-images/compare/2020.10.03..2020.10.08

base-image/Dockerfile

@@ -140,7 +140,7 @@ ONBUILD RUN echo "Checking for 'jupyter_notebook_config.py'..." \
         && cp jupyter_notebook_config.py /etc/jupyter \
         ; fi
 
-# ONBUILD USER ${NB_USER}
+ONBUILD USER ${NB_USER}
 
 # We want to keep our images as reproducible as possible. If a lock
 # file with exact versions of all required packages is present, we use
@@ -186,16 +186,23 @@ ONBUILD RUN echo "Checking for pip 'requirements.txt'..." \
 
 ONBUILD USER root
 
-ONBUILD COPY resources/layer-cleanup.sh /usr/local/bin
-ONBUILD RUN chmod +x /usr/local/bin/layer-cleanup.sh
+ONBUILD RUN  echo "Copy 'layer-cleanup'..." \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; pwd; ls \
+        ; cp resources/layer-cleanup.sh /usr/local/bin/ \
+        ; chmod +x /usr/local/bin/layer-cleanup.sh
 
-ONBUILD RUN for script in $(find "resources" -type f -name "install.sh"); do \
-        chmod +x "$script"; \
-        echo "Executing $script"; \
-        bash "$script"; \
-        layer-cleanup.sh; \
-        chown -R ${NB_USER}:${NB_USER} ${HOME}; \
-    done
+ONBUILD RUN echo "Executing install scripts..." \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; for script in $(find "resources" -type f -name "install.sh"); do \
+                chmod +x "$script"; \
+                echo "Executing $script"; \
+                bash "$script"; \
+                layer-cleanup.sh; \
+                chown -R ${NB_USER}:${NB_USER} ${HOME}; \
+        done
 
 ONBUILD USER ${NB_USER}
 

base-notebook/.dockerignore

@@ -0,0 +1,4 @@
+Dockerfile
+environment.yml
+packages.txt
+.dockerignore