berkeley-dsep-infra · shaneknapp · Dec 18, 2023 · Dec 18, 2023 · Dec 18, 2023 · Dec 18, 2023
diff --git a/deployments/a11y/image/environment.yml b/deployments/a11y/image/environment.yml
@@ -11,6 +11,7 @@ dependencies:
 - jupyter-book==0.15.1
 - jupyter-resource-usage==0.7.1
 - jupyterhub==4.0.2
+- jupyterlab==4.0.9
 - matplotlib==3.7.1
 - nbgitpuller==1.1.1
 - nbclassic==1.0.0

diff --git a/deployments/a11y/image/infra-requirements.txt b/deployments/a11y/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/astro/image/environment.yml b/deployments/astro/image/environment.yml
@@ -10,7 +10,7 @@ dependencies:
 - websockify
 
 - syncthing==1.18.6
-
+- jupyterlab==4.0.9
 - numpy==1.22.*
 - matplotlib==3.5.*
 - graphviz>=2.50.0

diff --git a/deployments/astro/image/infra-requirements.txt b/deployments/astro/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -8,6 +8,8 @@ dependencies:
 # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2)
 - nb_conda_kernels=2.3.1
 
+- jupyterlab==4.0.9
+
 # Packages from bioconda for IB134L
 # - bwa=0.7.12
 - samtools=1.3.1

diff --git a/deployments/biology/image/infra-requirements.txt b/deployments/biology/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/cee/image/environment.yml b/deployments/cee/image/environment.yml
@@ -5,6 +5,9 @@ channels:
 # Only libraries *not* available in PyPI should be here
 dependencies:
 - python=3.9.*
+
+- jupyterlab==4.0.9
+
 #adding math functionality 
 - matplotlib=3.7.*
 - scipy=1.10.*

diff --git a/deployments/cee/image/infra-requirements.txt b/deployments/cee/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/data100/image/environment.yml b/deployments/data100/image/environment.yml
@@ -7,7 +7,7 @@ dependencies:
 - python==3.11.0
 - git==2.39.1
 - jupyter-resource-usage==1.0.0
-- jupyterlab==4.0.4
+- jupyterlab==4.0.9
 - jupyterlab-favorites==3.0.0
 - jupyterlab_server==2.23.0
 - jupyterlab_widgets==3.0.8
@@ -18,7 +18,7 @@ dependencies:
 - h5netcdf==1.0.2
 - ipywidgets==8.0.7
 - jupysql==0.8.0
-- jupyterlab==4.0.4
+- jupyter-archive==3.4.0
 - matplotlib==3.7.1
 - mdit-py-plugins==0.4.0
 - numpy==1.24.2

diff --git a/deployments/data100/image/infra-requirements.txt b/deployments/data100/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/data101/image/environment.yml b/deployments/data101/image/environment.yml
@@ -34,7 +34,7 @@ dependencies:
 - jupyter-book==0.15.1
 - jupyter-resource-usage==1.0.0
 - jupyter_bokeh
-- jupyterlab==4.0.4
+- jupyterlab==4.0.9
 - jupyterlab-favorites==3.0.0
 - jupyterlab-geojson==3.2.0
 - jupyterlab-variableinspector==3.0.9

diff --git a/deployments/data101/image/infra-requirements.txt b/deployments/data101/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/data102/image/environment.yml b/deployments/data102/image/environment.yml
@@ -10,7 +10,7 @@ dependencies:
 - bambi==0.12.0
 - graphviz==8.0.3
 - jupyter-resource-usage==1.0.0
-- jupyterlab==4.0.4
+- jupyterlab==4.0.9
 - jupyterlab-favorites==3.0.0
 - jupyterlab_server==2.23.0
 - jupyterlab_widgets==3.0.8

diff --git a/deployments/data102/image/infra-requirements.txt b/deployments/data102/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/data8/image/environment.yml b/deployments/data8/image/environment.yml
@@ -5,6 +5,8 @@ dependencies:
 
 - syncthing==1.18.6
 
+- jupyterlab==3.4.5
+
 # data8
 - matplotlib==3.4.3
 - ipympl==0.7.0
@@ -28,3 +30,4 @@ dependencies:
   - okpy==1.18.1
   - datascience==0.17.6
   - otter-grader==4.3.4 # Based on request from ericvd and sean.morris
+  - retrolab==0.3.21
diff --git a/deployments/data8/image/infra-requirements.txt b/deployments/data8/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml
@@ -7,6 +7,7 @@ dependencies:
 - pip=22.2.*
 - python=3.9.*
 - syncthing==1.18.6
+- jupyterlab==4.0.9
 
 # pymc3 needs this
 - mkl-service=2.4.*
@@ -88,7 +89,7 @@ dependencies:
 - linearmodels==4.27
 
 # JupyterLab pypi extensions
-- jupyterlab-geojson==3.1.2
+- jupyterlab-geojson==3.4.0
 
 # INDENG 142 Spring 2021 (future semesters as well) - https://github.com/berkeley-dsep-infra/datahub/issues/2314
 - fancyimpute==0.7.0

diff --git a/deployments/datahub/images/default/infra-requirements.txt b/deployments/datahub/images/default/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/dev-r/images/default/environment.yml b/deployments/dev-r/images/default/environment.yml
@@ -5,6 +5,7 @@ dependencies:
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 
+- jupyterlab==4.0.9
 - jupyter-server-proxy==4.0.0
 - jupyter-rsession-proxy==2.2.0
 

diff --git a/deployments/dev-r/images/default/infra-requirements.txt b/deployments/dev-r/images/default/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/dev-r/images/secondary/environment.yml b/deployments/dev-r/images/secondary/environment.yml
@@ -6,6 +6,7 @@ dependencies:
 - jupyterlab-myst==2.0.2
 - syncthing==1.25.0
 - pyppeteer==1.0.2
+- jupyterlab==4.0.9
 
 # for nbconvert
 - pandoc==3.1.3

diff --git a/deployments/dev-r/images/secondary/infra-requirements.txt b/deployments/dev-r/images/secondary/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/edx/image/infra-requirements.txt b/deployments/edx/image/infra-requirements.txt
@@ -0,0 +1,29 @@
+# WARNING: Original source at scripts/infra-packages/requirements.txt
+# PLEASE DO NOT EDIT ELSEWHERE
+# After editing scripts/infra-packages/requirements.txt, please run
+# scripts/infra-packages/sync.bash.
+
+# This file pins versions of notebook related python packages we want
+# across all hubs. This makes sure we don't need to upgrade them
+# everwhere one by one.
+
+# FIXME: Freeze this to get exact versions of all dependencies
+notebook==6.4.12
+nbgitpuller==1.1.0
+jupyter-resource-usage==0.6.1
+# Matches version in images/hub/Dockerfile
+jupyterhub==4.0.2
+appmode==0.8.0
+ipywidgets==7.7.2
+jupyter-tree-download==1.0.1
+git-credential-helpers==0.2
+# Enough people like this, let's load it in.
+jupyter-contrib-nbextensions==0.5.1
+jupyter_nbextensions_configurator==0.4.1
+# Measure popularity of different packages in our hubs
+# https://discourse.jupyter.org/t/request-for-implementation-instrument-libraries-actively-used-by-users-on-a-jupyterhub/7994?u=yuvipanda
+git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
+# RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
+RISE==5.7.1
+# syncthing for dropbox-like functionality
+jupyter-syncthing-proxy==1.0.3
diff --git a/deployments/eecs/image/environment.yml b/deployments/eecs/image/environment.yml
@@ -10,6 +10,8 @@ dependencies:
 - jupyter-vscode-proxy=0.1
 - code-server=4.5.2
 
+- jupyterlab==4.0.9
+
 - syncthing=1.18.6
 
 # A linux desktop environment

diff --git a/deployments/eecs/image/infra-requirements.txt b/deployments/eecs/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/ischool/image/environment.yml b/deployments/ischool/image/environment.yml
@@ -10,6 +10,9 @@ dependencies:
 - nodejs=16 # code-server requires node < 17
 - jupyter-vscode-proxy==0.5
 - code-server==4.10.1
+
+- jupyterlab==4.0.9
+
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 - pip:

diff --git a/deployments/ischool/image/infra-requirements.txt b/deployments/ischool/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/julia/image/environment.yml b/deployments/julia/image/environment.yml
@@ -6,6 +6,8 @@ dependencies:
 
 - syncthing==1.18.6
 
+- jupyterlab==4.0.9
+
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 

diff --git a/deployments/julia/image/infra-requirements.txt b/deployments/julia/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/publichealth/image/environment.yml b/deployments/publichealth/image/environment.yml
@@ -2,6 +2,7 @@ dependencies:
 - pip
 - syncthing==1.18.6
 - jupyter-rsession-proxy==2.2.0
+- jupyterlab==4.0.9
 - pip:
   # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
   - traitlets==5.9.0

diff --git a/deployments/publichealth/image/infra-requirements.txt b/deployments/publichealth/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/shiny/image/infra-requirements.txt b/deployments/shiny/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/stat159/image/environment.yml b/deployments/stat159/image/environment.yml
@@ -35,27 +35,38 @@ dependencies:
   - ipydatagrid==1.1.14
   - ipympl==0.9.2
   - ipyparallel==8.4.1
-  - ipywidgets==8.0.4
+  - ipywidgets==8.0.7
   - jupyter-resource-usage==0.7.1
-  - jupyter_bokeh==3.0.5
-  - jupyter_server==2.5.0
-  - jupyterlab==3.6.3
-  - jupyterlab-drawio==0.9.0
+  # commented out by sknapp 2023.12.18 due to JL4 incompatibility
+  # https://jira-secure.berkeley.edu/browse/DH-194
+  # 
+  # we can revisit when this class is taught again
+  # - jupyter_bokeh==3.0.7
+  - jupyter_server==2.7.0
+  - jupyterlab==4.0.9
+  # commented out by sknapp 2023.12.18 due to JL4 incompatibility
+  # https://jira-secure.berkeley.edu/browse/DH-194
+  #
+  # we can revisit when this class is taught again
+  # - jupyterlab-drawio==0.9.0
   - jupyterlab-favorites==3.1.1
   - jupyterlab-geojson==3.3.1
   - jupyterlab-git==0.41.0
 
   # LSP for JupyterLab/Python - enhanced completions/language support
-  - jupyterlab-lsp==4.0.0
+  - jupyterlab-lsp==5.0.0
   - python-lsp-server==1.7.0
 
-  - jupyterlab-link-share==0.2.5
+  # commented out by sknapp 2023.12.18 due to JL4 incompatibility
+  # https://jira-secure.berkeley.edu/browse/DH-194
+  #
+  # we can revisit when this class is taught again
+  # - jupyterlab-link-share==0.2.5
   - jupyterlab-variableinspector==3.0.9
-  - jupyterlab-myst==1.1.3
+  - jupyterlab-myst==2.1.0
   - jupyterlab_pygments==0.2.2
   - jupyterlab_server==2.19.0
-  - jupyterlab-spellchecker==0.7.3
-  - jupyterlab_widgets==3.0.5
+  - jupyterlab-spellchecker==0.8.3
   - jupyter_server_ydoc==0.8.0
   - jupytext==1.14.4
   - mamba==1.2.0

diff --git a/deployments/stat159/image/infra-requirements.txt b/deployments/stat159/image/infra-requirements.txt
@@ -9,8 +9,6 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==6.4.12
-jupyterlab==3.4.5
-retrolab==0.3.21
 nbgitpuller==1.1.0
 jupyter-resource-usage==0.6.1
 # Matches version in images/hub/Dockerfile

diff --git a/deployments/stat20/image/environment.yml b/deployments/stat20/image/environment.yml
@@ -6,6 +6,7 @@ channels:
 dependencies:
 - syncthing==1.22.2
 - jupyter-rsession-proxy==2.2.0
+- jupyterlab==4.0.9
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 - pip: