updated Ganymede and python images

jupyter-ganymede/Dockerfile

@@ -7,23 +7,16 @@ RUN adduser jovyan -u 1000 --system -s /bin/sh -h /home/jovyan
 USER jovyan
 WORKDIR /home/jovyan
 RUN python -m venv venv
-RUN venv/bin/pip install numpy
-RUN venv/bin/pip install matplotlib
 RUN venv/bin/pip install jupyter-core
-RUN venv/bin/pip install jupyterhub
+RUN venv/bin/pip install notebook==5.7.16
-RUN venv/bin/pip install jupyterlab
-RUN venv/bin/pip install notebook
-RUN venv/bin/pip install ipywidgets
-RUN venv/bin/pip install jupyterlab-lsp
-RUN venv/bin/pip install python-lsp-server[yapf,rope,pyflakes] 
-RUN venv/bin/pip install pylsp-mypy
 ENV PATH="/home/jovyan/venv/bin/:$PATH"
 RUN java -jar /ganymede-2.1.2.20230910.jar -i --copy-jar=true
+RUN venv/bin/pip install jupyterhub
 
 FROM alpine:3.19
 RUN --mount=type=cache,target=/var/cache/apk/,sharing=locked \
     apk update &&\
-    apk add python3 openjdk21-jre texlive texlive-xetex texlive-full
+    apk add python3 openjdk21-jre
 RUN adduser jovyan -u 1000 --system -s /bin/sh -h /home/jovyan
 USER jovyan
 COPY --from=build /home/jovyan /home/jovyan

jupyter-python/Dockerfile

@@ -1,31 +1,43 @@
 FROM alpine:3.19 AS build
 RUN --mount=type=cache,target=/var/cache/apk/,sharing=locked \
     apk update &&\
-    apk add python3 python3-dev pipx gcc musl-dev linux-headers
+    apk add python3 python3-dev pipx gcc g++ musl-dev linux-headers libffi-dev
-RUN adduser luser --system -s /bin/sh -h /var/lib/jupyter
+RUN adduser jovyan -u 1000 --system -s /bin/sh -h /home/jovyan
-USER luser
+USER jovyan
-WORKDIR /var/lib/jupyter
+WORKDIR /home/jovyan
-RUN pipx install jupyter-core
+RUN python -m venv venv
-RUN pipx inject jupyter-core jupyterlab
+RUN venv/bin/pip install numpy
-RUN pipx inject jupyter-core ipywidgets
+RUN venv/bin/pip install matplotlib
-RUN pipx inject jupyter-core jupyterlab-lsp
+RUN venv/bin/pip install jupyter-core
-RUN pipx inject jupyter-core python-lsp-server[yapf,rope,pyflakes] 
+RUN venv/bin/pip install jupyterhub
-RUN pipx inject jupyter-core pylsp-mypy
+RUN venv/bin/pip install jupyterlab
-RUN pipx inject jupyter-core matplotlib
+RUN venv/bin/pip install notebook
-RUN pipx inject jupyter-core numpy
+RUN venv/bin/pip install ipywidgets
-
+RUN venv/bin/pip install jupyterlab-lsp
+RUN venv/bin/pip install python-lsp-server[yapf,rope,pyflakes] 
+RUN venv/bin/pip install pylsp-mypy
+RUN venv/bin/pip install solders
+RUN venv/bin/pip install solana
+ENV PATH="/home/jovyan/venv/bin/:$PATH"
 
 FROM alpine:3.19
 RUN --mount=type=cache,target=/var/cache/apk/,sharing=locked \
     apk update &&\
-    apk add python3 texlive texlive-xetex texlive-full
+    apk add python3
-
+RUN adduser jovyan -u 1000 --system -s /bin/sh -h /home/jovyan
-RUN adduser luser --system -s /bin/sh -h /var/lib/jupyter
+USER jovyan
-USER luser
+COPY --from=build /home/jovyan /home/jovyan
-WORKDIR /var/lib/jupyter
+COPY jupyter_server_config.py docker_healthcheck.py /etc/jupyter/
-COPY --from=build /var/lib/jupyter /var/lib/jupyter
+COPY start-notebook.py start-singleuser.py /usr/local/bin/
-ENV PATH="/var/lib/jupyter/.local/bin/:$PATH"
+RUN mkdir /home/jovyan/work
-ENTRYPOINT ["jupyter", "lab", "--no-browser", "--ip=0.0.0.0"]
+WORKDIR /home/jovyan/work
-EXPOSE 8888/tcp
+ENV JUPYTER_PORT=8888
-
+EXPOSE $JUPYTER_PORT
+ENV PATH="/home/jovyan/venv/bin/:$PATH"
+CMD ["start-notebook.py"]
 
+# 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=3s --timeout=1s --start-period=3s --retries=3 \
+    CMD /etc/jupyter/docker_healthcheck.py || exit 1

jupyter-python/docker_healthcheck.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+import json
+import os
+import subprocess
+from pathlib import Path
+
+import requests
+
+# Several operations below deliberately don't check for possible errors
+# As this is a health check, it should succeed or raise an exception on error
+
+# Docker runs health checks using an exec
+# It uses the default user configured when running the image: root for the case of a custom NB_USER or jovyan for the case of the default image user.
+# We manually change HOME to make `jupyter --runtime-dir` report a correct path
+# More information: <https://github.com/jupyter/docker-stacks/pull/2074#issuecomment-1879778409>
+result = subprocess.run(
+    ["jupyter", "--runtime-dir"],
+    check=True,
+    capture_output=True,
+    text=True,
+    env=dict(os.environ) | {"HOME": "/home/" + os.environ["NB_USER"]},
+)
+runtime_dir = Path(result.stdout.rstrip())
+
+json_file = next(runtime_dir.glob("*server-*.json"))
+
+url = json.loads(json_file.read_bytes())["url"]
+url = url + "api"
+
+proxies = {
+    "http": "",
+    "https": "",
+}
+
+r = requests.get(url, proxies=proxies, verify=False)  # request without SSL verification
+r.raise_for_status()
+print(r.content)

jupyter-python/jupyter_server_config.py

@@ -0,0 +1,58 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+# mypy: ignore-errors
+import os
+import stat
+import subprocess
+from pathlib import Path
+
+from jupyter_core.paths import jupyter_data_dir
+
+c = get_config()  # noqa: F821
+c.ServerApp.ip = "0.0.0.0"
+c.ServerApp.open_browser = False
+
+# to output both image/svg+xml and application/pdf plot formats in the notebook file
+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 = Path(jupyter_data_dir())
+    dir_name.mkdir(parents=True, exist_ok=True)
+    pem_file = dir_name / "notebook.pem"
+
+    # Generate an openssl.cnf file to set the distinguished name
+    cnf_file = Path(os.getenv("CONDA_DIR", "/usr/lib")) / "ssl/openssl.cnf"
+    if not cnf_file.exists():
+        cnf_file.write_text(OPENSSL_CONFIG)
+
+    # Generate a certificate if one doesn't exist on a 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
+    pem_file.chmod(stat.S_IRUSR | stat.S_IWUSR)
+    c.ServerApp.certfile = str(pem_file)
+
+# Change default umask for all subprocesses of the Server if set in the environment
+if "NB_UMASK" in os.environ:
+    os.umask(int(os.environ["NB_UMASK"], 8))

jupyter-python/start-notebook.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+import os
+import shlex
+import sys
+
+# If we are in a JupyterHub, we pass on to `start-singleuser.py` instead so it does the right thing
+if "JUPYTERHUB_API_TOKEN" in os.environ:
+    print(
+        "WARNING: using start-singleuser.py instead of start-notebook.py to start a server associated with JupyterHub."
+    )
+    command = ["/usr/local/bin/start-singleuser.py"] + sys.argv[1:]
+    os.execvp(command[0], command)
+
+
+# Entrypoint is start.sh
+command = []
+
+# If we want to survive restarts, launch the command using `run-one-constantly`
+if os.environ.get("RESTARTABLE") == "yes":
+    command.append("run-one-constantly")
+
+# We always launch a jupyter subcommand from this script
+command.append("jupyter")
+
+# Launch the configured subcommand.
+# Note that this should be a single string, so we don't split it.
+# We default to `lab`.
+jupyter_command = os.environ.get("DOCKER_STACKS_JUPYTER_CMD", "lab")
+command.append(jupyter_command)
+
+# Append any optional NOTEBOOK_ARGS we were passed in.
+# This is supposed to be multiple args passed on to the notebook command,
+# so we split it correctly with shlex
+if "NOTEBOOK_ARGS" in os.environ:
+    command += shlex.split(os.environ["NOTEBOOK_ARGS"])
+
+# Pass through any other args we were passed on the command line
+command += sys.argv[1:]
+
+# Execute the command!
+print("Executing: " + " ".join(command))
+os.execvp(command[0], command)

jupyter-python/start-singleuser.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+import os
+import shlex
+import sys
+
+# Entrypoint is start.sh
+command = ["jupyterhub-singleuser"]
+
+# set default ip to 0.0.0.0
+if "--ip=" not in os.environ.get("NOTEBOOK_ARGS", ""):
+    command.append("--ip=0.0.0.0")
+
+# Append any optional NOTEBOOK_ARGS we were passed in.
+# This is supposed to be multiple args passed on to the notebook command,
+# so we split it correctly with shlex
+if "NOTEBOOK_ARGS" in os.environ:
+    command += shlex.split(os.environ["NOTEBOOK_ARGS"])
+
+# Pass any other args we have been passed through
+command += sys.argv[1:]
+
+# Execute the command!
+print("Executing: " + " ".join(command))
+os.execvp(command[0], command)