this should work now

berkeley-dsep-infra · Jan 13, 2024 · dc7b12e · dc7b12e
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commit dc7b12e
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diff --git a/deployments/datahub/images/default/Dockerfile b/deployments/datahub/images/default/Dockerfile
@@ -137,8 +137,9 @@ COPY environment.yml /tmp/environment.yml
 RUN echo "/srv/conda/bin/mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml" | /usr/bin/time -f "User\t%U\nSys\t%S\nReal\t%E\nCPU\t%P" /usr/bin/bash
 RUN echo "/srv/conda/bin/mamba clean -afy" | /usr/bin/time -f "User\t%U\nSys\t%S\nReal\t%E\nCPU\t%P" /usr/bin/bash
 
-RUN jupyter contrib nbextensions install --sys-prefix --symlink && \
-    jupyter nbextensions_configurator enable --sys-prefix
+# 2024-01-13 sknapp: incompatible due to notebook 7
+# RUN jupyter contrib nbextensions install --sys-prefix --symlink
+# RUN jupyter nbextensions_configurator enable --sys-prefix
 
 # Used by MCB32, but incompatible with ipywidgets 8.x
 # RUN jupyter nbextension enable --py --sys-prefix qgrid
@@ -154,8 +155,9 @@ RUN playwright install chromium
 # Install IR kernelspec
 RUN echo "/usr/bin/r -e \"IRkernel::installspec(user = FALSE, prefix='${CONDA_DIR}')\"" | /usr/bin/time -f "User\t%U\nSys\t%S\nReal\t%E\nCPU\t%P" /usr/bin/bash
 
-COPY d8extension.bash /usr/local/sbin/d8extension.bash
-RUN /usr/local/sbin/d8extension.bash
+# 2024-01-13 sknapp: incompatible due to notebook 7
+# COPY d8extension.bash /usr/local/sbin/d8extension.bash
+# RUN /usr/local/sbin/d8extension.bash
 
 ENV NLTK_DATA ${CONDA_DIR}/nltk_data
 COPY connectors/text.bash /usr/local/sbin/connector-text.bash

diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml
@@ -82,7 +82,7 @@ dependencies:
 - beautifulsoup4==4.9.3
 
 # PS88 https://github.com/berkeley-dsep-infra/datahub/issues/2925
-- linearmodels==4.27
+- linearmodels==5.4
 
 # JupyterLab pypi extensions
 - jupyterlab-geojson==3.4.0
@@ -107,25 +107,26 @@ dependencies:
   # Some things were moved up to conda above.
   #
   # Until https://github.com/okpy/ok-client/pull/473 is merged
-  - git+https://github.com/yuvipanda/ok-client@6961d778741fe61911be4d00beff9bd8afc1edf7
+  # - git+https://github.com/yuvipanda/ok-client@6961d778741fe61911be4d00beff9bd8afc1edf7
   #
   - jupyter-shiny-proxy==1.1
   #
   # nb2pdf==0.6.2 commented out by sknapp 06.10.2023 to unblock https://github.com/berkeley-dsep-infra/datahub/issues/5062
   #
 
   # astr 128/256; spring 2021
-  - astroquery==0.4.6
-  - astropy==5.1
-  - dustmaps==1.0.9
-  - george==0.4.0
-  - exoplanet==0.5.2
-  - torch==1.13.1
-  - torchvision==0.14.1
-  - pyvo==1.1
-  - joblib==1.3.1
-  - theano-pymc==1.1.2
-  - pymc3==3.11.2
+  # sknapp:  move these to astro hub if required
+  #- astroquery==0.4.6
+  #- astropy==5.1
+  #- dustmaps==1.0.9
+  #- george==0.4.0
+  #- exoplanet==0.5.2
+  #- torch==1.13.1
+  #- torchvision==0.14.1
+  #- pyvo==1.1
+  #- joblib==1.3.1
+  #- theano-pymc==1.1.2
+  #- pymc3==3.11.2
 
   # eep 153; spring 2019
   - requests==2.31.0
@@ -177,19 +178,19 @@ dependencies:
   - habanero==0.7.4
 
   # https://github.com/berkeley-dsep-infra/datahub/issues/1981
-  #  - ipycanvas==0.9.0
+  - ipycanvas==0.13.1
 
   # sknapp 2023-12-15:  we will eventually move prob140 back to datahub in FA24
   # https://jira-secure.berkeley.edu/browse/DH-203
   # - prob140==0.4.1.5
   # - sympy==1.8
 
   # IB 105 / ESPM 125, Fall 2021 - https://github.com/berkeley-dsep-infra/datahub/issues/2696
-  - geonomics==1.3.0
+  - geonomics==1.3.12
 
   # https://github.com/berkeley-dsep-infra/datahub/issues/2950
   # Needed to work with a new enough version of httplib2
-  - httplib2>=0.20.2
+  - httplib2>=0.22.0
 
   # Used by MCB32, but incompatible with ipywidgets 8.x
   # - qgrid==1.3.1

diff --git a/deployments/datahub/images/default/infra-requirements.txt b/deployments/datahub/images/default/infra-requirements.txt
@@ -9,9 +9,9 @@
 
 # FIXME: Freeze this to get exact versions of all dependencies
 notebook==7.0.6
-jupyterlab==4.0.4
+jupyterlab==4.0.10
 #retrolab==0.3.21
-nbgitpuller==1.1.0
+nbgitpuller==1.2.0
 jupyter-resource-usage==1.0.1
 # Matches version in images/hub/Dockerfile
 jupyterhub==4.0.2
@@ -21,8 +21,8 @@ ipywidgets==8.0.7
 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
+jupyter-contrib-nbextensions==0.7.0
+jupyter_nbextensions_configurator==0.6.3
 # 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