berkeley-dsep-infra · ryanlovett · Jun 17, 2024 · Jun 17, 2024 · Jun 17, 2024 · Jun 17, 2024
diff --git a/deployments/astro/image/environment.yml b/deployments/astro/image/environment.yml
@@ -6,7 +6,7 @@ channels:
 
 dependencies:
 - python=3.11.*
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 # A linux desktop environment
 - websockify
 

diff --git a/deployments/biology/image/bio1b-packages.bash b/deployments/biology/image/bio1b-packages.bash
@@ -1,5 +1,11 @@
 # Install PAUP* for BIO 1B
 # https://github.com/berkeley-dsep-infra/datahub/issues/1699
-wget http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz -O ${CONDA_DIR}/bin/paup.gz
+
+# This package was requested in 2020 for the instructor to try out.
+# The 168 version doesn't exist so I've bumped it to 169, but also disabled
+# it in case the package is no longer needed.
+return
+
+wget https://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz -O ${CONDA_DIR}/bin/paup.gz
 gunzip ${CONDA_DIR}/bin/paup.gz
 chmod +x ${CONDA_DIR}/bin/paup
diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -9,7 +9,7 @@ dependencies:
 - nb_conda_kernels=2.3.1
 
 # proxy web applications
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.0.1
 
 # Packages from bioconda for IB134L

diff --git a/deployments/cee/image/environment.yml b/deployments/cee/image/environment.yml
@@ -5,7 +5,7 @@ channels:
 # Only libraries *not* available in PyPI should be here
 dependencies:
 - python=3.11.*
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 #adding math functionality 
 - matplotlib=3.7.*
 - scipy=1.10.*

diff --git a/deployments/data101/image/environment.yml b/deployments/data101/image/environment.yml
@@ -34,7 +34,7 @@ dependencies:
 - jupyter-archive==3.4.0
 - jupyter-book==0.15.1
 - jupyter-resource-usage==1.0.0
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter_bokeh
 - jupyterlab==4.0.11
 - jupyterlab-favorites==3.0.0

diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml
@@ -73,7 +73,7 @@ dependencies:
 
 # data8; foundation
 - datascience==0.17.6
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.2.0
 - folium==0.12.1.post1
 

diff --git a/deployments/dev/images/default/environment.yml b/deployments/dev/images/default/environment.yml
@@ -5,7 +5,7 @@ dependencies:
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.2.0
 
 - syncthing==1.23.5

diff --git a/deployments/eecs/image/environment.yml b/deployments/eecs/image/environment.yml
@@ -7,7 +7,7 @@ dependencies:
 - python=3.11.*
 - nbclassic==1.0.0
 
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 # Visual Studio Code!
 - jupyter-vscode-proxy=0.1
 - code-server=4.5.2

diff --git a/deployments/ischool/image/environment.yml b/deployments/ischool/image/environment.yml
@@ -8,7 +8,7 @@ dependencies:
 - jupyter-rsession-proxy==2.2.0
 # https://github.com/berkeley-dsep-infra/datahub/issues/5251
 - nodejs=16 # code-server requires node < 17
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-vscode-proxy==0.5
 - code-server==4.10.1
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048

diff --git a/deployments/julia/image/environment.yml b/deployments/julia/image/environment.yml
@@ -1,5 +1,5 @@
 dependencies:
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - nodejs==20.8.1
 - pip==22.3.1
 - python==3.11.*

diff --git a/deployments/julia/image/install-julia-packages.jl b/deployments/julia/image/install-julia-packages.jl
@@ -15,7 +15,7 @@ Pkg.add.([
     Pkg.PackageSpec(;name="VegaLite", version="2.6.0"),
     Pkg.PackageSpec(;name="CSVFiles", version="1.0.1"),
     Pkg.PackageSpec(;name="Distributions", version="0.23.11"),
-    Pkg.PackageSpec(;name="DataFrames", version="0.21.8"),
+    Pkg.PackageSpec(;name="DataFrames"),
     Pkg.PackageSpec(;name="Plots", version="1.24.3"),
     Pkg.PackageSpec(;name="Images", version="0.24.1"),
     Pkg.PackageSpec(;name="PyPlot", version="2.10.0"),

diff --git a/deployments/publichealth/image/environment.yml b/deployments/publichealth/image/environment.yml
@@ -1,7 +1,7 @@
 dependencies:
 - pip
 - syncthing==1.18.6
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.2.0
 - pip:
   # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048

diff --git a/deployments/shiny/image/environment.yml b/deployments/shiny/image/environment.yml
@@ -3,7 +3,7 @@ dependencies:
 - ipywidgets==8.1.2
 - jupyter-archive==3.4.0
 - jupyter-resource-usage==1.0.1
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.2.0
 - jupyter-syncthing-proxy==1.0.3
 - jupyterhub==4.1.5

diff --git a/deployments/stat159/image/environment.yml b/deployments/stat159/image/environment.yml
@@ -137,7 +137,7 @@ dependencies:
   - syncthing==1.23.0
   - websockify==0.11.0
 
-  - jupyter-server-proxy==4.1.2
+  - jupyter-server-proxy==4.2.0
   # VS Code support
   - jupyter-vscode-proxy==0.2
   - code-server==4.10.1

diff --git a/deployments/stat20/image/environment.yml b/deployments/stat20/image/environment.yml
@@ -5,7 +5,7 @@ channels:
 
 dependencies:
 - syncthing==1.22.2
-- jupyter-server-proxy==4.1.2
+- jupyter-server-proxy==4.2.0
 - jupyter-rsession-proxy==2.2.0
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*