Update the base image

.gitignore

@@ -0,0 +1,130 @@
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.yamllint.yaml

@@ -0,0 +1,46 @@
+# This config represents running the command `yamllint -d relaxed .` with the
+# following extra rules:
+#
+# new-line-at-end-of-file:
+#   level: warning
+# trailing-spaces:
+#   level: warning
+#
+# We also ignore the cookiecutter directories as these often contain
+# jinja-style templating functions that yamllint doesn't play nicely with
+#
+# cribbed from https://github.com/2i2c-org/infrastructure/blob/main/.yamllint.yaml
+---
+extends: default
+
+ignore: |
+  **/template/**
+  **/templates/**
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas:
+    level: warning
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length: disable
+  new-line-at-end-of-file:
+    level: warning
+  trailing-spaces:
+    level: warning
+  truthy: disable

Dockerfile

@@ -1,7 +1,7 @@
 # ===================================================================
 # Base image
 # ===================================================================
-FROM buildpack-deps:jammy-scm AS base
+FROM buildpack-deps:24.04 AS base
 
 # -------------------------------------------------------------------
 # Environment

README.md

@@ -1 +1,35 @@
-# base-python-image
+# base-python-image
+
+This is the repo for DataHub Python base image and intended for DataHub admin use only.
+
+## Steps
+
+### Step 1: 
+- Admins make changes in apt.txt to manage system packages and environment.yaml to manage Conda and Pip packages.
+- Once the PR is merged, the Github action for building the base image is triggered. 
+
+### Step 2:
+- In the Github logs, look for the new base image tag. Alternatively, you can navigate to the artifact registry on Google cloud console and find the tag for the latest image. 
+- Nagivate to a hub with the fancy profile configured (e.g. nature.datahub.berkeley.edu), and lauch a server with the newly built base image.
+- Test the basic functionalities, including:
+  1. Write a file in the terminal
+  2. Open a notebook, write a notebook, run a notebook, and save a notebook.
+- Test the recent changes, including:
+  1. Versions (by running pip show \<package\>)
+  2. New functionalities tied to a specific version
+
+### Step 3:
+Once the base image is tested and everything looks good, manaully dispatch the "Trigger Downstream Builds" workflow in Github actions. 
+
+1. Which downstream group to build?
+
+   Choose "base" if you want to build the downstream R base image.
+   Choose "user" if you want to build the downstream hub specific user images. 
+2. Base image name (e.g. ucb-datahub-2018/testing/base-python-image)
+
+   Use the base image name you have obtained in step 2.
+3. Base image SHA/tag to propagate
+
+   Use the base image tag you have obtained in step 2.
+
+

apt.txt

@@ -7,12 +7,14 @@ rsync
 vim
 wget
 zip
+tar
 screen
 man
 man-db
 manpages-posix
 manpages-dev
 manpages-posix-dev
+tini
 
 # Regular build tools for compiling common stuff
 build-essential
@@ -44,6 +46,6 @@ libxdamage1
 libxfixes3
 libxrandr2
 libgbm1
-libasound2
+libasound2t64
 
 

environment.yml

@@ -8,23 +8,33 @@ dependencies:
   # DH-418, bunch of stuff fails to install if git is set
   # higher to this e.g. git==2.47.1
   - git
+  # vscode related 
+  - jupyter-vscode-proxy==0.7
+  - code-server==4.118.0
+  # jupyter related
   - jupyter-archive==3.4.0
   - jupyter-resource-usage==1.2.0
   - jupyter-server-proxy==4.4.0
   - jupyter_server==2.17.0
   - jupyterhub==5.4.2
-  - jupyterlab==4.5.3
+  - jupyterlab==4.5.7
   - jupyterlab-git==0.51.3
   - jupyter-offlinenotebook==0.3.2
   - jupyterlab_rise==0.43.1
   - jupytext==1.18.1
-  - nbgitpuller==1.2.2
-  - notebook==7.5.3
-  - pip==26.0.1
+  - jupyterlab-favorites==3.5.0
+  - jupyterlab_server==2.28.0
+  - jupyterlab_widgets==3.0.16
+  - syncthing==2.0.16
+  - jupyter-syncthing-proxy==1.0.3
+  - ipywidgets==8.1.8
+  - nbgitpuller==1.3.0
+  - notebook==7.5.6
   - otter-grader==6.1.6
   - wrapt==1.17.3
   # Using python 3.11 for maximum compatibility with conda packages.
   - python==3.11
+  - pip==26.0.1
   # datascience packages
   - datascience==0.18.1
   - numpy==2.4.2
@@ -35,11 +45,18 @@ dependencies:
   - seaborn==0.13.2
   - statsmodels==0.14.6
   - matplotlib==3.10.3
+  - matplotlib-inline==0.2.1
+  - ipympl==0.10.0
+  - sympy==1.14.0
   # DH-654 conflicts with git-crendential-helpers
   - pyjwt==2.10.1
+  - nbclassic==1.3.3
+  - sqlite==3.53.1
 
   # For https://github.com/berkeley-dsep-infra/datahub/issues/1846
   # Conda does not have these
   - pip:
       - git-credential-helpers==0.2
       - nbconvert[webpdf]==7.17.0
+      - nb2pdf==0.6.2
+      - nbpdfexport==0.2.1

install-miniforge.bash

@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-MINIFORGE_VERSION='26.1.0-0'
+MINIFORGE_VERSION='26.3.2-0'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/miniforge-installer.sh