diff --git a/deployments/astro/image/environment.yml b/deployments/astro/image/environment.yml index 5edf61d8a..16d4ab815 100644 --- 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 index d46adb68a..d926eaddb 100644 --- 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 index a8997208f..e4c9924eb 100644 --- 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 index c084aa216..1c7f9b056 100644 --- 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 index 92a0e4a13..99cf7e93f 100644 --- 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 index e84ff3859..7e21be4d2 100644 --- 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 index 6e357b7b6..b8fabc4d7 100644 --- 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 index 8f5d709d8..c481bdd5a 100644 --- 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 index 28ce5e586..877fbc307 100644 --- 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 index 859659c6e..d2faefc2e 100644 --- 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 index d1cf6324e..c30f854eb 100755 --- 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 index d87507720..6a1ca02fd 100644 --- 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 index fc84d5b45..abc7bc0b1 100644 --- 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 index 9f941f17b..eb154eb65 100644 --- 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 index ff7148386..8d91f0335 100644 --- 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.*