Merge pull request #2316 from yuvipanda/new-hub

yuvipanda · web-flow · commit b4088ea5a054 · 2021-04-19T15:50:06.000+05:30
Fix Rprofile.site to point to correct mirror
diff --git a/deployments/biology/image/Rprofile.site b/deployments/biology/image/Rprofile.site
@@ -1,6 +1,10 @@
-local({
-    r <- getOption("repos")
-    r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
-    options(repos = r)
-    options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
-})
+# Use RStudio's CRAN mirror to get binary packages
+# 'latest' just means it has all available versions.
+# We can specify version numbers in devtools::install_version
+options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
+
+# RStudio's CRAN mirror needs this to figure out which binary package to serve.
+# If not set properly, it will just serve up source packages
+# Quite hilarious, IMO.
+# See https://docs.rstudio.com/rspm/admin/binaries.html
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
diff --git a/deployments/biology/image/infra-requirements.txt b/deployments/biology/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/data8x/image/infra-requirements.txt b/deployments/data8x/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/datahub/images/default/Dockerfile b/deployments/datahub/images/default/Dockerfile
@@ -228,7 +228,6 @@ RUN jlpm cache dir && mkdir -p /tmp/yarncache && \
     jupyter labextension install --debug \
         @jupyterlab/server-proxy \
         jupyterlab-plotly@4.14.3 plotlywidget@4.14.3 \
-        @jupyterlab/geojson-extension && \
     rm -rf /tmp/yarncache
 
 RUN pip install --no-cache numpy==1.19.5 cython==0.29.21
diff --git a/deployments/datahub/images/default/Rprofile.site b/deployments/datahub/images/default/Rprofile.site
@@ -1,6 +1,10 @@
-local({
-    r <- getOption("repos")
-    r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
-    options(repos = r)
-    options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
-})
+# Use RStudio's CRAN mirror to get binary packages
+# 'latest' just means it has all available versions.
+# We can specify version numbers in devtools::install_version
+options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
+
+# RStudio's CRAN mirror needs this to figure out which binary package to serve.
+# If not set properly, it will just serve up source packages
+# Quite hilarious, IMO.
+# See https://docs.rstudio.com/rspm/admin/binaries.html
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
diff --git a/deployments/datahub/images/default/infra-requirements.txt b/deployments/datahub/images/default/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/datahub/images/default/requirements.txt b/deployments/datahub/images/default/requirements.txt
@@ -206,3 +206,6 @@ dbt==0.19.1
 
 # ESPM 167 - https://github.com/berkeley-dsep-infra/datahub/issues/2278
 contextily==1.1.0
+
+# JupyterLab pypi extensions
+jupyterlab-geojson==3.1.2
diff --git a/deployments/dlab/image/infra-requirements.txt b/deployments/dlab/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/eecs/image/infra-requirements.txt b/deployments/eecs/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/julia/image/infra-requirements.txt b/deployments/julia/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/r/image/infra-requirements.txt b/deployments/r/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/stat159/image/infra-requirements.txt b/deployments/stat159/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/deployments/template/{{cookiecutter.hub_name}}/image/infra-requirements.txt b/deployments/template/{{cookiecutter.hub_name}}/image/infra-requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
diff --git a/scripts/infra-packages/requirements.txt b/scripts/infra-packages/requirements.txt
@@ -15,7 +15,9 @@ notebook==6.2.0
 # someone opens a notebook created w/ nbformat>=5.1.0. is it possible to pin
 # below 5.1.0 while notebook patches this?
 nbformat<5.1.0
-jupyterlab==3.0.11
+# Pin for https://github.com/jupyter/jupyter-packaging/issues/81
+setuptools>=56.0
+jupyterlab==3.0.14
 nbgitpuller==0.9.0
 jupyter-resource-usage==0.5.1
 jupyterhub==1.3.0
@@ -26,4 +28,4 @@ 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_nbextensions_configurator==0.4.1
