Cleaned up jupyter container, fixed PATH

jupyter/README.md

@@ -8,11 +8,24 @@ This directory contains build files for a complete jupyter environment. It is ba
 
 The images these files produce contain everything you could possibly want in a jupyter notebook. Additional packages can be installed in notebooks with `%%bash` magic.
 
-
 ## Building the Image
 
 To build this image, run `build/build.fish.` Edit the script to customize the image.
 
+## Image contents
+ - jupyter + all dependencies
+ - Python + many packages
+ - Octave
+ - R
+ - Julia
+
+
+## TODO
+ - Fix sage
+ - Haskell ([source](https://github.com/IHaskell/ihaskell-notebook))
+ - Maxima Kernel
+
+
 ## Configuration
 
 Change the permissions on the configuration volume (see `docker-compose.yml`) if you get errors.
@@ -34,30 +47,21 @@ The first sets `0.0.0.0` to the allowed local hostname list. This prevents a pos
 The second line sets a persistent token. If this config value is unset, jupyter will generate a new one on each run, making it hard to make a one-click bookmark.
 
 
-## Image contents
+### As a Server
- - jupyterlab, jupyterhub, notebook
-   - latex + pandoc for exporting
-   - mamba for packages
- - Python
-   - Scrape tools (bs4, requests)
-   - scipy, scikit-learn, scikit-image
-   - tensorflow
-   - sympy
-   - numpy
-   - matplotlib
-   - pandas
-   - manim
- - Octave
- - R
- - Julia
 
+Add the following lines and remove ``c.ServerApp.token``. This allows remote access and enables password authentication. **Warning:** be careful. Anyone with access to this server has a shell in your system.
 
-## TODO
+```python
- - Auto dark theme
+c.NotebookApp.allow_remote_access = True
- - Fix sage
+c.NotebookApp.allow_origin = "*"
- - GPU support ([source](https://github.com/iot-salzburg/gpu-jupyter))
+c.ServerApp.ip = "*"
- - Haskell ([source](https://github.com/IHaskell/ihaskell-notebook))
+c.ServerApp.password = u"pwd_str"
- - Rust Kernel
+c.ServerApp.open_browser = False
- - C++ Kernel
+```
- - Perl Kernel
+
- - Maxima Kernel
+ Passwords can be generated with
+
+```python
+from jupyter_server.auth import passwd
+passwd()
+```

jupyter/build/base/Dockerfile

@@ -75,14 +75,15 @@ ENV CONDA_DIR=/opt/conda \
 ENV PATH="${CONDA_DIR}/bin:${PATH}" \
 	HOME="/home/${NB_USER}"
 
-# Copy a script that we will use to correct permissions after running certain commands
+# A script that we will use to correct permissions after running certain commands
 COPY fix-permissions.sh /usr/local/bin/fix-permissions
 RUN chmod a+rx /usr/local/bin/fix-permissions
 
 # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
 RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
 	# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
-	echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
+	echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc && \
+	echo "export PATH=${CONDA_DIR}/bin:\$PATH" >> /etc/skel/.bashrc
 
 # Create user
 RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
@@ -103,7 +104,6 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
 
 USER ${NB_UID}
 
-
 # Pin python version here, or set it to "default"
 ARG PYTHON_VERSION=3.10
 
@@ -184,14 +184,6 @@ RUN mkdir -p "${HOME}/.jupyter" && \
 	chmod u+rwx "${HOME}/.jupyter"
 VOLUME "${HOME}/.jupyter"
 
-# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
-#RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
-#	/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
-#	fix-permissions /etc/jupyter/
-
-# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
-# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
-# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
 HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
 	CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
 	http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1

jupyter/build/base/jupyter_server_config.py

@@ -2,9 +2,8 @@ import os
 import stat
 import subprocess
 
-from jupyter_core.paths import jupyter_data_dir
-
 c = get_config()  # noqa: F821
+
 c.ServerApp.ip = "0.0.0.0"
 c.ServerApp.port = 8888
 c.ServerApp.open_browser = False
@@ -16,42 +15,6 @@ c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
 # https://github.com/jupyter/notebook/issues/3130
 c.FileContentsManager.delete_to_trash = False
 
-# Generate a self-signed certificate
-OPENSSL_CONFIG = """\
-[req]
-distinguished_name = req_distinguished_name
-[req_distinguished_name]
-"""
-if "GEN_CERT" in os.environ:
-	dir_name = jupyter_data_dir()
-	pem_file = os.path.join(dir_name, "notebook.pem")
-	os.makedirs(dir_name, exist_ok=True)
-
-	# Generate an openssl.cnf file to set the distinguished name
-	cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
-	if not os.path.isfile(cnf_file):
-		with open(cnf_file, "w") as fh:
-			fh.write(OPENSSL_CONFIG)
-
-	# Generate a certificate if one doesn't exist on disk
-	subprocess.check_call(
-		[
-			"openssl",
-			"req",
-			"-new",
-			"-newkey=rsa:2048",
-			"-days=365",
-			"-nodes",
-			"-x509",
-			"-subj=/C=XX/ST=XX/L=XX/O=generated/CN=generated",
-			f"-keyout={pem_file}",
-			f"-out={pem_file}",
-		]
-	)
-	# Restrict access to the file
-	os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
-	c.ServerApp.certfile = pem_file
-
 # Change default umask for all subprocesses of the notebook server if set in
 # the environment
 if "NB_UMASK" in os.environ:

jupyter/build/build.fish

@@ -5,7 +5,8 @@ set is_quiet true
 set root_dir "."
 
 function build_image
-	# First argument: (optional) remove parent image? (true or false)
+	# First argument: remove parent image?
+	# 	true or false, optional, default is false
 	# Second argument: file name to build
 
 	# Parse arguments
@@ -13,7 +14,7 @@ function build_image
 		set remove_previous $argv[1]
 		set build_file $argv[2]
 	else if test (count $argv) -eq 1
-		set remove_previous true
+		set remove_previous false
 		set build_file $argv[1]
 	end
 
@@ -41,7 +42,7 @@ end
 date "+Build started at %Y-%m-%d %T"
 echo ""
 
-# Base image MUST be built first
+# Base image must be built first
 printf "Building base image...\n"
 docker build \
 	--quiet=$is_quiet \
@@ -52,17 +53,17 @@ printf "Done. \n\n"
 
 
 
-build_image false octave
+build_image octave
-build_image false r
+build_image r
-build_image false julia
+build_image julia
-#build_image false sage (BROKEN)
+#build_image sage (BROKEN)
 
-build_image false plugins
+build_image plugins
-build_image false pymodules
+build_image pymodules
 
 # Manim will not install under python 3.10.
 # 3.9 works (see arguments for base above)
-#build_image false manim
+#build_image manim
 
 
 

jupyter/build/pymodules.Dockerfile

@@ -13,7 +13,6 @@ RUN mamba install --yes \
 		"requests" \
 		"schedule" \
 		# ML and Data
-		"tensorflow" \
 		"scikit-image" \
 		"scikit-learn" \
 		"scipy" \
@@ -54,34 +53,7 @@ RUN mamba install --yes \
 	fix-permissions "${CONDA_DIR}" && \
 	fix-permissions "/home/${NB_USER}"
 
-# Import matplotlib the first time to build the font cache.
+# Import matplotlib once to build the font cache.
 ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
 RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
-	fix-permissions "/home/${NB_USER}"
+	fix-permissions "/home/${NB_USER}"
-
-
-
-#FROM pymodules as selenium
-#USER ${NB_UID}
-#
-#RUN mamba install --yes \
-#		"selenium" \
-#	&& \
-#	# Cleanup
-#	mamba clean --all -f -y && \
-#	npm cache clean --force && \
-#	jupyter lab clean && \
-#	rm -rf "/home/${NB_USER}/.cache/yarn" && \
-#	fix-permissions "${CONDA_DIR}" && \
-#	fix-permissions "/home/${NB_USER}"
-#
-## Install google chrome
-#RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
-#RUN sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/#sources.list.d/google-chrome.list'
-#RUN apt-get -y update
-#RUN apt-get install -y google-chrome-stable
-#
-## Install chromedriver
-#RUN apt-get install -yqq unzip
-#RUN wget -O /tmp/chromedriver.zip http://chromedriver.storage.googleapis.com/`curl -sS #chromedriver.storage.googleapis.com/LATEST_RELEASE`/chromedriver_linux64.zip
-#RUN unzip /tmp/chromedriver.zip chromedriver -d /usr/local/bin/

jupyter/docker-compose.yml

@@ -15,7 +15,7 @@ services:
       - "127.0.0.1:8888:8888"
 
     # Allow GPU access.
-    # Requires nvidia-containter-toolkit
+    # Requires nvidia-container-toolkit
     deploy:
       resources:
         reservations: