Pangeo notebook/init (#5)

* feat: add qgis to pangeo-notebook
* fix: Docker organization name

.github/workflows/Publish.yml

@@ -7,7 +7,7 @@ on:
     - '*'
 
 env:
-  DOCKER_ORG: pangeo
+  DOCKER_ORG: cnes
   GITHUB_REF: ${{ github.ref }}
 
 jobs:

.github/workflows/Test.yml

@@ -55,7 +55,7 @@ jobs:
       with:
         context: base-image
         platforms: linux/amd64,linux/arm64
-        tags: localhost:5000/pangeo/base-image:PR
+        tags: localhost:5000/cnes/base-image:PR
         push: true
         cache-from: type=gha
         cache-to: type=gha,mode=max

Makefile

@@ -13,7 +13,7 @@ base-image :
 .PHONY: base-notebook
 base-notebook : base-image
 	cd base-notebook ; \
-	conda-lock lock  -f environment.yml -p linux-64; \
+	conda-lock lock --mamba -f environment.yml -p linux-64; \
 	conda-lock render -k explicit -p linux-64; \
 	../generate-packages-list.py conda-linux-64.lock > packages.txt; \
 	docker build -t cnes/base-notebook:master . --no-cache --progress=plain --platform linux/amd64; \
@@ -23,16 +23,17 @@ base-notebook : base-image
 pangeo-notebook : base-image
 	cd pangeo-notebook ; \
 	cp -r ../base-notebook/resources . ; \
-	conda-lock lock -f environment.yml -f ../base-notebook/environment.yml -f ../base-notebook/environment.yml -p linux-64; \
+	conda-lock lock --mamba -f environment.yml -f ../base-notebook/environment.yml -f ../base-notebook/environment.yml -p linux-64; \
 	conda-lock render -k explicit -p linux-64; \
 	../generate-packages-list.py conda-linux-64.lock > packages.txt; \
+	../merge-apt.sh ../base-notebook/apt.txt apt.txt; \
 	docker build -t cnes/pangeo-notebook:master . --progress=plain --platform linux/amd64; \
 	docker run -w $(TESTDIR) -v $(PWD):$(TESTDIR) cnes/pangeo-notebook:master ./run_tests.sh pangeo-notebook
 
 .PHONY: pytorch-notebook
 pytorch-notebook : base-image
 	cd pytorch-notebook ; \
-	conda-lock lock -f environment.yml -f ../pangeo-notebook/environment.yml -f ../base-notebook/environment.yml -p linux-64; \
+	conda-lock lock --mamba -f environment.yml -f ../pangeo-notebook/environment.yml -f ../base-notebook/environment.yml -p linux-64; \
 	conda-lock render -k explicit -p linux-64; \
 	../generate-packages-list.py conda-linux-64.lock > packages.txt; \
 	docker build -t cnes/pytorch-notebook:master . ; \

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

merge-apt.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Check if at least two files are provided
+if [ "$#" -lt 2 ]; then
+    echo "Usage: $0 file1_apt.txt file2_apt.txt ... target_apt.txt"
+    exit 1
+fi
+
+# Get last file as target file
+target_file="${@: -1}"
+
+# Merge all files while removing duplicates
+# - Ignore empty lines and comments
+awk 1 "$@" | grep -v '^#' | grep -v '^$' | sort | uniq > merged_apt.txt
+
+# Move merged file into target file
+mv merged_apt.txt "$target_file"
+
+echo "Merge done."

pangeo-notebook/apt.txt

@@ -1,4 +1,20 @@
+build-essential
+curl
+dfc
+file
 git
 groff
+htop
+jq
+less
+ncdu
+ranger
+rclone
+rsync
+silversearcher-ag
+software-properties-common
+tig
+tmux
 tree
+unzip
 vim