From 0529b60466c62357e85ab8dbcc417b9e54220ddb Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 14:40:24 +0530
Subject: [PATCH 01/16] Install python into a venv

- Continues to use python and venv from Ubuntu LTS repositories,
  so they are supported as with everything else that is gotten
  from apt (see https://github.com/rocker-org/rocker-versioned2/issues/670#issuecomment-1619748511)
- Doesn't currently change any permissions, so present behavior
  is preserved. However, in the future, we should probably change
  ownership so end users can install packages in there at runtime
  (see https://github.com/rocker-org/rocker-versioned2/issues/670#issuecomment-1624691981)
- Sets the VIRTUAL_ENV environment variable to path of the venv
  we create. This is what the `source activate` script does,
  and Reticulate also looks for this to discover which
  python to use (see point 4 of https://rstudio.github.io/reticulate/articles/versions.html#order-of-discovery)
- Sets up PATH appropriately, so python and python3 refer to
  what is in our venv. This, along with the previous step, ensures
  same behavior as users typing `source ${VIRTUAL_ENV}/bin/activate`
  without actually having to do that, preserving end user behavioral
  semantics.
- Remove the explicit symlink of python3 -> python, as venv handles
  this automatically.

Decisions to be made:

- Where do we set the appropriate env variables (VIRTUAL_ENV and
  PATH)? They need to be set for `install_python.sh` to work
  correctly. I've set them in the binder image for now, but it
  should probably be set on a more base image. This is a no-op if
  `install-python.sh` is not called anywhere.

Ref https://github.com/rocker-org/rocker-versioned2/issues/670
---
 dockerfiles/binder_devel.Dockerfile |  2 ++
 scripts/install_python.sh           | 10 +++++-----
 stacks/devel.json                   |  4 +++-
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/dockerfiles/binder_devel.Dockerfile b/dockerfiles/binder_devel.Dockerfile
index fe4710f9..524b5199 100644
--- a/dockerfiles/binder_devel.Dockerfile
+++ b/dockerfiles/binder_devel.Dockerfile
@@ -6,6 +6,8 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
       org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"
 
 ENV NB_USER=rstudio
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${PATH}:${VIRTUAL_ENV}/bin
 
 RUN /rocker_scripts/install_jupyter.sh
 
diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 1a07c23a..4903e996 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -22,14 +22,14 @@ apt_install \
     python3-venv \
     swig
 
+# Setup a virtualenv to install things into
+python3 -m venv ${VIRTUAL_ENV}
+export PATH=${VIRTUAL_ENV}:${PATH}
+
+# Upgrade version of pip inside the virtualenv
 python3 -m pip --no-cache-dir install --upgrade \
     pip
 
-# Some TF tools expect a "python" binary
-if [ ! -e /usr/local/bin/python ]; then
-    ln -s "$(which python3)" /usr/local/bin/python
-fi
-
 install2.r --error --skipmissing --skipinstalled -n "$NCPUS" reticulate
 
 # Clean up
diff --git a/stacks/devel.json b/stacks/devel.json
index 2aca598c..6b0b5f36 100644
--- a/stacks/devel.json
+++ b/stacks/devel.json
@@ -127,7 +127,9 @@
       },
       "FROM": "rocker/geospatial:devel",
       "ENV": {
-        "NB_USER": "rstudio"
+        "NB_USER": "rstudio",
+        "VIRTUAL_ENV": "/opt/venv",
+        "PATH": "${PATH}:${VIRTUAL_ENV}/bin"
       },
       "RUN": [
         "/rocker_scripts/install_jupyter.sh"

From 83a48b1820a1f4c31b2e725024d8d1eb8e99cb90 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:10:46 +0530
Subject: [PATCH 02/16] Use default value for VIRTUAL_ENV if not provided

---
 scripts/install_python.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 4903e996..cb2f246e 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -23,9 +23,13 @@ apt_install \
     swig
 
 # Setup a virtualenv to install things into
-python3 -m venv ${VIRTUAL_ENV}
+
+# Put things under /opt/venv, if nothing else is specified
+export VIRTUAL_ENV="${VIRTUAL_ENV:=/opt/venv}"
 export PATH=${VIRTUAL_ENV}:${PATH}
 
+python3 -m venv ${VIRTUAL_ENV}
+
 # Upgrade version of pip inside the virtualenv
 python3 -m pip --no-cache-dir install --upgrade \
     pip

From dcd8b03bbe6581bf705ec0b2facced2ee3ca1586 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:20:06 +0530
Subject: [PATCH 03/16] source install_python in install_jupyter.sh

So it sets PATH appropriately
---
 scripts/install_jupyter.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/install_jupyter.sh b/scripts/install_jupyter.sh
index 12260fff..1e9a01cf 100755
--- a/scripts/install_jupyter.sh
+++ b/scripts/install_jupyter.sh
@@ -27,7 +27,7 @@ if ! id -u "${NB_USER}" >/dev/null 2>&1; then
 fi
 
 # install python
-/rocker_scripts/install_python.sh
+source /rocker_scripts/install_python.sh
 
 python3 -m pip install --no-cache-dir jupyter-rsession-proxy notebook jupyterlab jupyterhub
 

From 7497edc50a96a139372d7733dfe43698d39e7f3a Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:26:35 +0530
Subject: [PATCH 04/16] Satisfy shellcheck

---
 scripts/install_python.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index cb2f246e..6f27f578 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -26,9 +26,9 @@ apt_install \
 
 # Put things under /opt/venv, if nothing else is specified
 export VIRTUAL_ENV="${VIRTUAL_ENV:=/opt/venv}"
-export PATH=${VIRTUAL_ENV}:${PATH}
+export PATH="${VIRTUAL_ENV}:${PATH}"
 
-python3 -m venv ${VIRTUAL_ENV}
+python3 -m venv "${VIRTUAL_ENV}"
 
 # Upgrade version of pip inside the virtualenv
 python3 -m pip --no-cache-dir install --upgrade \

From 63c823e19372062a4d6d532475146f2dc552b343 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:31:12 +0530
Subject: [PATCH 05/16] Don't try to lint install_python.sh

---
 scripts/install_jupyter.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/install_jupyter.sh b/scripts/install_jupyter.sh
index 1e9a01cf..00db0ab2 100755
--- a/scripts/install_jupyter.sh
+++ b/scripts/install_jupyter.sh
@@ -26,7 +26,8 @@ if ! id -u "${NB_USER}" >/dev/null 2>&1; then
     /rocker_scripts/default_user.sh "${NB_USER}"
 fi
 
-# install python
+# install python & setup venv
+# shellcheck source=/dev/null
 source /rocker_scripts/install_python.sh
 
 python3 -m pip install --no-cache-dir jupyter-rsession-proxy notebook jupyterlab jupyterhub

From dbb8453b786ed7b0a35236fc9bc3a7bfa56bb47b Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:47:40 +0530
Subject: [PATCH 06/16] Check that python & python3 point to the correct place

---
 scripts/install_python.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 6f27f578..c56c5c9e 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -56,6 +56,11 @@ if [ "${UBUNTU_CODENAME}" == "focal" ]; then
     fi
 fi
 
+# Check that python and python3 point to correct places
+echo -e "Check python and python3 executables point to the correct place...\n"
+which python
+which python3
+
 # Check Python version
 echo -e "Check the Python to use with reticulate...\n"
 

From ee5b9a8216782ee108b318722882e964dd931fcd Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 15:48:16 +0530
Subject: [PATCH 07/16] Prett-print python and python3 paths

---
 scripts/install_python.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index c56c5c9e..ac43565c 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -58,8 +58,8 @@ fi
 
 # Check that python and python3 point to correct places
 echo -e "Check python and python3 executables point to the correct place...\n"
-which python
-which python3
+echo -e "python -> $(which python)\n"
+echo -e "python3 -> $(which python3)\n"
 
 # Check Python version
 echo -e "Check the Python to use with reticulate...\n"

From 0bb27984ab9c7c9d361f783ecade6f184260c18d Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 16:09:27 +0530
Subject: [PATCH 08/16] Fix PATH export in install_python.sh

---
 scripts/install_python.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index ac43565c..f9a8c6ef 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -26,7 +26,7 @@ apt_install \
 
 # Put things under /opt/venv, if nothing else is specified
 export VIRTUAL_ENV="${VIRTUAL_ENV:=/opt/venv}"
-export PATH="${VIRTUAL_ENV}:${PATH}"
+export PATH="${VIRTUAL_ENV}/bin:${PATH}"
 
 python3 -m venv "${VIRTUAL_ENV}"
 

From 541b676e78c3a75020accf8b40f52abda582bedc Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 16:14:43 +0530
Subject: [PATCH 09/16] Rely on echo putting a newline at the end automatically

---
 scripts/install_python.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index f9a8c6ef..6816b089 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -57,9 +57,9 @@ if [ "${UBUNTU_CODENAME}" == "focal" ]; then
 fi
 
 # Check that python and python3 point to correct places
-echo -e "Check python and python3 executables point to the correct place...\n"
-echo -e "python -> $(which python)\n"
-echo -e "python3 -> $(which python3)\n"
+echo "Check python and python3 executables point to the correct place..."
+echo "python -> $(which python)"
+echo "python3 -> $(which python3)"
 
 # Check Python version
 echo -e "Check the Python to use with reticulate...\n"

From c1a472465532c8349cf0ad4f3f95c86e85787dc3 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 23:40:42 +0530
Subject: [PATCH 10/16] Make sure RStudio sees new env vars we set

---
 scripts/install_python.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 6816b089..e7953fa4 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -28,6 +28,10 @@ apt_install \
 export VIRTUAL_ENV="${VIRTUAL_ENV:=/opt/venv}"
 export PATH="${VIRTUAL_ENV}/bin:${PATH}"
 
+# Make sure that Rstudio sees these env vars too
+echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
+echo "VIRTUAL_ENV=${VIRTUAL_ENV}" >>"${R_HOME}/etc/Renviron.site"
+
 python3 -m venv "${VIRTUAL_ENV}"
 
 # Upgrade version of pip inside the virtualenv

From ca9d697eb58ed5194433a290b3e70b3921ceea10 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 6 Nov 2023 19:25:47 +0900
Subject: [PATCH 11/16] Automatic update of container definition files (#723)

- Auto-generated by [create-pull-request][1]

[1]: https://github.com/peter-evans/create-pull-request

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 bakefiles/devel.docker-bake.json                  | 2 +-
 dockerfiles/cuda11_4.1.0.Dockerfile               | 2 +-
 dockerfiles/cuda11_4.1.1.Dockerfile               | 2 +-
 dockerfiles/cuda11_4.1.2.Dockerfile               | 2 +-
 dockerfiles/cuda11_4.1.3.Dockerfile               | 2 +-
 dockerfiles/cuda11_4.2.0.Dockerfile               | 2 +-
 dockerfiles/cuda11_4.2.1.Dockerfile               | 2 +-
 dockerfiles/cuda_4.2.2.Dockerfile                 | 2 +-
 dockerfiles/cuda_4.2.3.Dockerfile                 | 2 +-
 dockerfiles/cuda_4.3.0.Dockerfile                 | 2 +-
 dockerfiles/cuda_4.3.1.Dockerfile                 | 2 +-
 dockerfiles/cuda_4.3.2.Dockerfile                 | 2 +-
 dockerfiles/cuda_devel.Dockerfile                 | 2 +-
 dockerfiles/geospatial-dev-osgeo_4.3.2.Dockerfile | 2 +-
 dockerfiles/r-ver_4.0.0.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.0.1.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.0.2.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.0.3.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.0.4.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.0.5.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.1.0.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.1.1.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.1.2.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.1.3.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.2.0.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.2.1.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.2.2.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.2.3.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.3.0.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.3.1.Dockerfile                | 2 +-
 dockerfiles/r-ver_4.3.2.Dockerfile                | 2 +-
 stacks/devel.json                                 | 2 +-
 stacks/extra.json                                 | 2 +-
 33 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/bakefiles/devel.docker-bake.json b/bakefiles/devel.docker-bake.json
index 354477ed..826fd11d 100644
--- a/bakefiles/devel.docker-bake.json
+++ b/bakefiles/devel.docker-bake.json
@@ -188,7 +188,7 @@
       "labels": {
         "org.opencontainers.image.title": "rocker/cuda",
         "org.opencontainers.image.description": "NVIDIA CUDA libraries added to Rocker image.",
-        "org.opencontainers.image.base.name": "docker.io/nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04"
+        "org.opencontainers.image.base.name": "docker.io/nvidia/cuda:11.8.0-cudnn8-devel-ubuntu24.04"
       },
       "tags": [
         "docker.io/rocker/cuda:devel"
diff --git a/dockerfiles/cuda11_4.1.0.Dockerfile b/dockerfiles/cuda11_4.1.0.Dockerfile
index 3473eda9..c95eeb7f 100644
--- a/dockerfiles/cuda11_4.1.0.Dockerfile
+++ b/dockerfiles/cuda11_4.1.0.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-08-09
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-08-09
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda11_4.1.1.Dockerfile b/dockerfiles/cuda11_4.1.1.Dockerfile
index 21c59197..a4cc2c15 100644
--- a/dockerfiles/cuda11_4.1.1.Dockerfile
+++ b/dockerfiles/cuda11_4.1.1.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-10-29
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-10-29
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda11_4.1.2.Dockerfile b/dockerfiles/cuda11_4.1.2.Dockerfile
index b905ce85..5bef610e 100644
--- a/dockerfiles/cuda11_4.1.2.Dockerfile
+++ b/dockerfiles/cuda11_4.1.2.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-03-09
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-03-09
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda11_4.1.3.Dockerfile b/dockerfiles/cuda11_4.1.3.Dockerfile
index 34b7376b..a09a83d8 100644
--- a/dockerfiles/cuda11_4.1.3.Dockerfile
+++ b/dockerfiles/cuda11_4.1.3.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-04-21
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-04-21
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda11_4.2.0.Dockerfile b/dockerfiles/cuda11_4.2.0.Dockerfile
index 39c03d54..13209c94 100644
--- a/dockerfiles/cuda11_4.2.0.Dockerfile
+++ b/dockerfiles/cuda11_4.2.0.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-06-22
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-06-22
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda11_4.2.1.Dockerfile b/dockerfiles/cuda11_4.2.1.Dockerfile
index 3f9853e5..7b38e74f 100644
--- a/dockerfiles/cuda11_4.2.1.Dockerfile
+++ b/dockerfiles/cuda11_4.2.1.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-10-28
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-10-28
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_4.2.2.Dockerfile b/dockerfiles/cuda_4.2.2.Dockerfile
index 5ac9770c..3d909e4a 100644
--- a/dockerfiles/cuda_4.2.2.Dockerfile
+++ b/dockerfiles/cuda_4.2.2.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-03-14
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-03-14
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_4.2.3.Dockerfile b/dockerfiles/cuda_4.2.3.Dockerfile
index 2ffc870b..c85fbdeb 100644
--- a/dockerfiles/cuda_4.2.3.Dockerfile
+++ b/dockerfiles/cuda_4.2.3.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-04-20
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-04-20
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_4.3.0.Dockerfile b/dockerfiles/cuda_4.3.0.Dockerfile
index efeddf46..47c15baf 100644
--- a/dockerfiles/cuda_4.3.0.Dockerfile
+++ b/dockerfiles/cuda_4.3.0.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-06-15
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-06-15
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_4.3.1.Dockerfile b/dockerfiles/cuda_4.3.1.Dockerfile
index d9329b8f..52516dc9 100644
--- a/dockerfiles/cuda_4.3.1.Dockerfile
+++ b/dockerfiles/cuda_4.3.1.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-10-30
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_4.3.2.Dockerfile b/dockerfiles/cuda_4.3.2.Dockerfile
index 44bd2001..92861572 100644
--- a/dockerfiles/cuda_4.3.2.Dockerfile
+++ b/dockerfiles/cuda_4.3.2.Dockerfile
@@ -17,7 +17,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/latest
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/latest
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/cuda_devel.Dockerfile b/dockerfiles/cuda_devel.Dockerfile
index efc49de8..dfafe70e 100644
--- a/dockerfiles/cuda_devel.Dockerfile
+++ b/dockerfiles/cuda_devel.Dockerfile
@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04
+FROM nvidia/cuda:11.8.0-cudnn8-devel-ubuntu24.04
 
 LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
       org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \
diff --git a/dockerfiles/geospatial-dev-osgeo_4.3.2.Dockerfile b/dockerfiles/geospatial-dev-osgeo_4.3.2.Dockerfile
index 9cf6f818..13907c90 100644
--- a/dockerfiles/geospatial-dev-osgeo_4.3.2.Dockerfile
+++ b/dockerfiles/geospatial-dev-osgeo_4.3.2.Dockerfile
@@ -6,7 +6,7 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
       org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"
 
 ENV PROJ_VERSION=9.3.0
-ENV GDAL_VERSION=3.7.2
+ENV GDAL_VERSION=3.7.3
 ENV GEOS_VERSION=3.12.0
 
 COPY scripts/experimental/install_dev_osgeo.sh /rocker_scripts/experimental/install_dev_osgeo.sh
diff --git a/dockerfiles/r-ver_4.0.0.Dockerfile b/dockerfiles/r-ver_4.0.0.Dockerfile
index b765ebc1..72a441e3 100644
--- a/dockerfiles/r-ver_4.0.0.Dockerfile
+++ b/dockerfiles/r-ver_4.0.0.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2020-06-04
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2020-06-04
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.0.1.Dockerfile b/dockerfiles/r-ver_4.0.1.Dockerfile
index a39d2d54..d13b4b58 100644
--- a/dockerfiles/r-ver_4.0.1.Dockerfile
+++ b/dockerfiles/r-ver_4.0.1.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2020-06-18
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2020-06-18
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.0.2.Dockerfile b/dockerfiles/r-ver_4.0.2.Dockerfile
index 33c9dd9e..5132a6a7 100644
--- a/dockerfiles/r-ver_4.0.2.Dockerfile
+++ b/dockerfiles/r-ver_4.0.2.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2020-10-09
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2020-10-09
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.0.3.Dockerfile b/dockerfiles/r-ver_4.0.3.Dockerfile
index f042249a..8922962a 100644
--- a/dockerfiles/r-ver_4.0.3.Dockerfile
+++ b/dockerfiles/r-ver_4.0.3.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-02-11
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-02-11
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.0.4.Dockerfile b/dockerfiles/r-ver_4.0.4.Dockerfile
index 88d2fe23..f044e6e7 100644
--- a/dockerfiles/r-ver_4.0.4.Dockerfile
+++ b/dockerfiles/r-ver_4.0.4.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-03-30
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-03-30
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.0.5.Dockerfile b/dockerfiles/r-ver_4.0.5.Dockerfile
index 2dfdbe50..85f6cdad 100644
--- a/dockerfiles/r-ver_4.0.5.Dockerfile
+++ b/dockerfiles/r-ver_4.0.5.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-05-17
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-05-17
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.1.0.Dockerfile b/dockerfiles/r-ver_4.1.0.Dockerfile
index 23e70440..c0d7c9e4 100644
--- a/dockerfiles/r-ver_4.1.0.Dockerfile
+++ b/dockerfiles/r-ver_4.1.0.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-08-09
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-08-09
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.1.1.Dockerfile b/dockerfiles/r-ver_4.1.1.Dockerfile
index f492b2da..7d5b3b31 100644
--- a/dockerfiles/r-ver_4.1.1.Dockerfile
+++ b/dockerfiles/r-ver_4.1.1.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2021-10-29
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2021-10-29
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.1.2.Dockerfile b/dockerfiles/r-ver_4.1.2.Dockerfile
index 2b3b87ce..4b6d2e73 100644
--- a/dockerfiles/r-ver_4.1.2.Dockerfile
+++ b/dockerfiles/r-ver_4.1.2.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-03-09
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-03-09
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.1.3.Dockerfile b/dockerfiles/r-ver_4.1.3.Dockerfile
index 655da427..7f8f780e 100644
--- a/dockerfiles/r-ver_4.1.3.Dockerfile
+++ b/dockerfiles/r-ver_4.1.3.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-04-21
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-04-21
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.2.0.Dockerfile b/dockerfiles/r-ver_4.2.0.Dockerfile
index bf9f8b04..a6faee6e 100644
--- a/dockerfiles/r-ver_4.2.0.Dockerfile
+++ b/dockerfiles/r-ver_4.2.0.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-06-22
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-06-22
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.2.1.Dockerfile b/dockerfiles/r-ver_4.2.1.Dockerfile
index 91fec69a..2caf094f 100644
--- a/dockerfiles/r-ver_4.2.1.Dockerfile
+++ b/dockerfiles/r-ver_4.2.1.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2022-10-28
+ENV CRAN=https://p3m.dev/cran/__linux__/focal/2022-10-28
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.2.2.Dockerfile b/dockerfiles/r-ver_4.2.2.Dockerfile
index 7d6485d7..c8bd137a 100644
--- a/dockerfiles/r-ver_4.2.2.Dockerfile
+++ b/dockerfiles/r-ver_4.2.2.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-03-14
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-03-14
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.2.3.Dockerfile b/dockerfiles/r-ver_4.2.3.Dockerfile
index d90fee01..ea309050 100644
--- a/dockerfiles/r-ver_4.2.3.Dockerfile
+++ b/dockerfiles/r-ver_4.2.3.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-04-20
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-04-20
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.3.0.Dockerfile b/dockerfiles/r-ver_4.3.0.Dockerfile
index ce39423a..1e54094e 100644
--- a/dockerfiles/r-ver_4.3.0.Dockerfile
+++ b/dockerfiles/r-ver_4.3.0.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-06-15
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-06-15
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.3.1.Dockerfile b/dockerfiles/r-ver_4.3.1.Dockerfile
index 88258fe6..b6092745 100644
--- a/dockerfiles/r-ver_4.3.1.Dockerfile
+++ b/dockerfiles/r-ver_4.3.1.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/2023-10-30
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/dockerfiles/r-ver_4.3.2.Dockerfile b/dockerfiles/r-ver_4.3.2.Dockerfile
index fe5f9726..5cf45095 100644
--- a/dockerfiles/r-ver_4.3.2.Dockerfile
+++ b/dockerfiles/r-ver_4.3.2.Dockerfile
@@ -13,7 +13,7 @@ COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 
 RUN /rocker_scripts/install_R_source.sh
 
-ENV CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/latest
+ENV CRAN=https://p3m.dev/cran/__linux__/jammy/latest
 ENV LANG=en_US.UTF-8
 
 COPY scripts /rocker_scripts
diff --git a/stacks/devel.json b/stacks/devel.json
index 6b0b5f36..8f2bd268 100644
--- a/stacks/devel.json
+++ b/stacks/devel.json
@@ -148,7 +148,7 @@
         "org.opencontainers.image.title": "rocker/cuda",
         "org.opencontainers.image.description": "NVIDIA CUDA libraries added to Rocker image."
       },
-      "FROM": "nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04",
+      "FROM": "nvidia/cuda:11.8.0-cudnn8-devel-ubuntu24.04",
       "ENV": {
         "R_VERSION": "devel",
         "R_HOME": "/usr/local/lib/R",
diff --git a/stacks/extra.json b/stacks/extra.json
index eeb6897f..6e62b86f 100644
--- a/stacks/extra.json
+++ b/stacks/extra.json
@@ -58,7 +58,7 @@
       "FROM": "rocker/verse:4.3.2",
       "ENV": {
         "PROJ_VERSION": "9.3.0",
-        "GDAL_VERSION": "3.7.2",
+        "GDAL_VERSION": "3.7.3",
         "GEOS_VERSION": "3.12.0"
       },
       "COPY": "scripts/experimental/install_dev_osgeo.sh /rocker_scripts/experimental/install_dev_osgeo.sh",

From aa601a22cda114e6888c06c410d1cd9de8af0427 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 20 Dec 2023 11:00:58 -0800
Subject: [PATCH 12/16] Swap the order of ${VIRTUAL_ENV}/bin

---
 dockerfiles/binder_devel.Dockerfile | 2 +-
 stacks/devel.json                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dockerfiles/binder_devel.Dockerfile b/dockerfiles/binder_devel.Dockerfile
index 524b5199..591d79bc 100644
--- a/dockerfiles/binder_devel.Dockerfile
+++ b/dockerfiles/binder_devel.Dockerfile
@@ -7,7 +7,7 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 ENV VIRTUAL_ENV=/opt/venv
-ENV PATH=${PATH}:${VIRTUAL_ENV}/bin
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
 
 RUN /rocker_scripts/install_jupyter.sh
 
diff --git a/stacks/devel.json b/stacks/devel.json
index 8f2bd268..0dc31365 100644
--- a/stacks/devel.json
+++ b/stacks/devel.json
@@ -129,7 +129,7 @@
       "ENV": {
         "NB_USER": "rstudio",
         "VIRTUAL_ENV": "/opt/venv",
-        "PATH": "${PATH}:${VIRTUAL_ENV}/bin"
+        "PATH": "${VIRTUAL_ENV}/bin:${PATH}"
       },
       "RUN": [
         "/rocker_scripts/install_jupyter.sh"

From c33f53cf9e939836a33a9160912a8d6d84a8e57f Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 20 Dec 2023 11:06:48 -0800
Subject: [PATCH 13/16] Check that pip points to the correct place too

---
 scripts/install_python.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index e7953fa4..171b96f1 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -61,9 +61,10 @@ if [ "${UBUNTU_CODENAME}" == "focal" ]; then
 fi
 
 # Check that python and python3 point to correct places
-echo "Check python and python3 executables point to the correct place..."
+echo "Check python, python3 and pip executables point to the correct place..."
 echo "python -> $(which python)"
 echo "python3 -> $(which python3)"
+echo "pip -> $(which pip)"
 
 # Check Python version
 echo -e "Check the Python to use with reticulate...\n"

From 96cdc36e3c6dcd17e7eb4b830ebd7d8147aedf51 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 20 Dec 2023 11:08:57 -0800
Subject: [PATCH 14/16] Make the venv be owned by non-root user

---
 scripts/install_python.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 171b96f1..974a474b 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -38,6 +38,10 @@ python3 -m venv "${VIRTUAL_ENV}"
 python3 -m pip --no-cache-dir install --upgrade \
     pip
 
+# Make the venv owned by the staff group, so users can install packages
+# without having to be root
+chown -R rstudio:staff /opt/venv
+
 install2.r --error --skipmissing --skipinstalled -n "$NCPUS" reticulate
 
 # Clean up

From 91622811207cd4296a0cd11919eb77b92c0e4f8b Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 20 Dec 2023 15:04:56 -0800
Subject: [PATCH 15/16] Set permissions + ownership correctly for venv dir

---
 scripts/install_python.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/install_python.sh b/scripts/install_python.sh
index 974a474b..a2add4da 100755
--- a/scripts/install_python.sh
+++ b/scripts/install_python.sh
@@ -40,7 +40,8 @@ python3 -m pip --no-cache-dir install --upgrade \
 
 # Make the venv owned by the staff group, so users can install packages
 # without having to be root
-chown -R rstudio:staff /opt/venv
+chown -R root:staff "${VIRTUAL_ENV}"
+chmod g+ws "${VIRTUAL_ENV}"
 
 install2.r --error --skipmissing --skipinstalled -n "$NCPUS" reticulate
 

From bda44e6c416c0250ed86483fd731cb817c29a2d6 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 20 Dec 2023 20:57:16 -0800
Subject: [PATCH 16/16] Add NEWS entry

---
 NEWS.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 491b9a11..8704bde5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,20 @@
 # News
 
+## 2023-12
+
+### Changes in pre-built images
+
+- For images that ship with a python environment installed, the default python
+  environment will now be a [virtual environment](https://docs.python.org/3/library/venv.html)
+  created at `/opt/venv`. ([#718](https://github.com/rocker-org/rocker-versioned2/pull/718))
+
+### Changes in rocker_scripts
+
+- `install_python.sh` will now setup a [virtual environment](https://docs.python.org/3/library/venv.html)
+  under `/opt/venv`, and this will be the default python environment (accomplished via setting
+  the `$PATH` and `$VIRTUAL_ENV` variables). `/opt/venv` will be owned by the `staff` group so non-root
+  users can safely install python packages. ([#718](https://github.com/rocker-org/rocker-versioned2/pull/718))
+
 ## 2023-11
 
 ### Changes in pre-built images