From 61e498b3b77a0d78a481d90621a6f647ac416c4a Mon Sep 17 00:00:00 2001
From: Jonathan Felder <felder@berkeley.edu>
Date: Wed, 9 Oct 2024 18:13:19 -0700
Subject: [PATCH 1/3] [DH-394] fix publichealth

---
 Dockerfile                        | 12 +++-------
 environment.yml                   | 39 ++++++++++++++++++++++++-------
 infra-requirements.txt            | 29 -----------------------
 install-mambaforge.bash           |  2 +-
 r-packages/2021-spring-phw-272a.r |  0
 r-packages/ph-142.r               |  4 ++--
 r-packages/ph-252.r               |  2 +-
 7 files changed, 38 insertions(+), 50 deletions(-)
 delete mode 100644 infra-requirements.txt
 mode change 100644 => 100755 r-packages/2021-spring-phw-272a.r

diff --git a/Dockerfile b/Dockerfile
index 802e5ba..c18dc70 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -54,15 +54,15 @@ RUN apt-get update > /dev/null && \
 COPY install-mambaforge.bash /tmp/install-mambaforge.bash
 RUN /tmp/install-mambaforge.bash
 
+RUN chown -Rh rstudio:rstudio /home/rstudio
+RUN chown -Rh rstudio:rstudio /srv/conda
+
 USER ${NB_USER}
 
 COPY environment.yml /tmp/environment.yml
 RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
     mamba clean -afy
 
-COPY infra-requirements.txt /tmp/infra-requirements.txt
-RUN pip install --no-cache-dir -r /tmp/infra-requirements.txt
-
 # DH-331, very similar to what was done for datahub in DH-164
 ENV PLAYWRIGHT_BROWSERS_PATH ${CONDA_DIR}
 RUN playwright install chromium
@@ -74,12 +74,6 @@ RUN R --quiet -e "install.packages('IRkernel', quiet = TRUE)" && \
 COPY class-libs.R /tmp/class-libs.R
 RUN mkdir -p /tmp/r-packages
 
-# Workaround to install ottr, issue 3342
-#RUN wget https://github.com/ucbds-infra/ottr/archive/refs/tags/0.1.0.tar.gz -O /tmp/ottr.tar.gz && R CMD INSTALL /tmp/ottr.tar.gz && rm /tmp/ottr.tar.gz
-
-#COPY install.R /tmp/install.R
-#RUN /tmp/install.R && rm -rf /tmp/downloaded_packages
-
 COPY r-packages/ottr.r /tmp/r-packages/
 RUN r /tmp/r-packages/ottr.r
 
diff --git a/environment.yml b/environment.yml
index e55c3d4..198c0f4 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,16 +1,39 @@
+channels:
+- conda-forge
+
 dependencies:
-- pip
-- syncthing==1.18.6
-- jupyter-server-proxy==4.2.0
-- jupyter-rsession-proxy==2.2.0
+# Items required for basic level functionality
+- gh-scoped-creds==4.1
+- git==2.47.0
+- jupyter-resource-usage==1.1.0
+- jupyter_server==2.14.2
+- jupyterhub==4.1.6
+- jupyterlab==4.2.5
+- jupyterlab-git==0.50.1
+- jupytext==1.16.4
+- nbgitpuller==1.2.1
+- notebook==7.2.2
+- python==3.11.*
+
+# Other items
+- jupyter-server-proxy==4.4.0
+- syncthing==1.27.12
+- jupyter-rsession-proxy==2.2.1
+- jupyter-syncthing-proxy==1.0.3
+- traitlets==5.14.3
+- appmode==1.0.0
+
+# pip installed packages, conda is preferred
+- pip==24.2
 - pip:
-  # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
-  - traitlets==5.9.0
   # RStudio support
   - otter-grader==2.2.7
   # for notebook exporting
   - nbconvert[webpdf]==7.16.4
   - nb2pdf==0.6.2
   - nbpdfexport==0.2.1
-  # pulled in by ottr, if not pinned to 1.16.2, 1.16.3 causes DH-323
-  - jupytext==1.16.2
+  - jupyter-archive==3.4.0
+  - rise==5.7.1
+  - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
+  - git-credential-helpers==0.2
+  - jupyter-tree-download==1.0.1
diff --git a/infra-requirements.txt b/infra-requirements.txt
deleted file mode 100644
index 0fb0bd9..0000000
--- a/infra-requirements.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-# WARNING: Original source at scripts/infra-packages/requirements.txt
-# PLEASE DO NOT EDIT ELSEWHERE
-# After editing scripts/infra-packages/requirements.txt, please run
-# scripts/infra-packages/sync.bash.
-
-# This file pins versions of notebook related python packages we want
-# across all hubs. This makes sure we don't need to upgrade them
-# everwhere one by one.
-
-# FIXME: Freeze this to get exact versions of all dependencies
-notebook==7.0.7
-jupyterlab==4.0.11
-nbgitpuller==1.2.1
-jupyter-resource-usage==1.0.1
-# Matches version in images/hub/Dockerfile
-jupyterhub==4.1.6
-appmode==0.8.0
-ipywidgets==8.0.7
-jupyter-tree-download==1.0.1
-git-credential-helpers==0.2
-# 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
-# RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
-RISE==5.7.1
-# syncthing for dropbox-like functionality
-jupyter-syncthing-proxy==1.0.3
-# jupyter archival tool for easy user downloads
-jupyter-archive==3.4.0
diff --git a/install-mambaforge.bash b/install-mambaforge.bash
index 812319e..c27ba02 100755
--- a/install-mambaforge.bash
+++ b/install-mambaforge.bash
@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=22.9.0-2
+MAMBAFORGE_VERSION=24.7.1-0
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
diff --git a/r-packages/2021-spring-phw-272a.r b/r-packages/2021-spring-phw-272a.r
old mode 100644
new mode 100755
diff --git a/r-packages/ph-142.r b/r-packages/ph-142.r
index b83c95c..75e3c7b 100755
--- a/r-packages/ph-142.r
+++ b/r-packages/ph-142.r
@@ -18,8 +18,8 @@ class_libs = c(
   "measurements", "1.4.0",
   "dagitty", "0.3-0",
   "cowplot", "1.1.1",
-  "patchwork", "1.1.1",
-  "tigris", "1.0",
+  "patchwork", "1.3.0",
+  "tigris", "2.1",
   "googlesheets4", "1.0.0",
   "coxed", "0.3.3"
 )
diff --git a/r-packages/ph-252.r b/r-packages/ph-252.r
index 41e2665..76afe16 100755
--- a/r-packages/ph-252.r
+++ b/r-packages/ph-252.r
@@ -18,7 +18,7 @@ class_libs = c(
   "epitools", "0.5-10.1",
   "rms", "6.2-0",
   "lmtest","0.9-38",
-  "car","3.0-10",
+  "car","3.1-3",
   "SurvRegCensCov","1.4",
   "ProfileLikelihood","1.1",
   "biostat3","0.1.5"

From bd48eb9df75887a47af59f5cdabd0073221587b5 Mon Sep 17 00:00:00 2001
From: Jonathan Felder <felder@berkeley.edu>
Date: Wed, 9 Oct 2024 18:46:03 -0700
Subject: [PATCH 2/3] [DH-394] fixing publichealth

---
 install.R | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100755 install.R

diff --git a/install.R b/install.R
deleted file mode 100755
index 2f337bd..0000000
--- a/install.R
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env r
-
-source("/tmp/class-libs.R")
-
-# install ottr, needs to go first issue #3216, #3263
-devtools::install_github('ucbds-infra/ottr', ref='0.1.0', upgrade_dependencies=FALSE, quiet=FALSE)

From ae0d3c79404df54757952c748bbccf6e5098cef2 Mon Sep 17 00:00:00 2001
From: Jonathan Felder <felder@berkeley.edu>
Date: Thu, 10 Oct 2024 11:10:30 -0700
Subject: [PATCH 3/3] [DH-394] just a couple of minor tweaks

---
 Dockerfile              | 8 ++++++--
 install-mambaforge.bash | 2 +-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c18dc70..44db757 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -54,8 +54,8 @@ RUN apt-get update > /dev/null && \
 COPY install-mambaforge.bash /tmp/install-mambaforge.bash
 RUN /tmp/install-mambaforge.bash
 
-RUN chown -Rh rstudio:rstudio /home/rstudio
-RUN chown -Rh rstudio:rstudio /srv/conda
+# needed for building on mac see DH-394
+RUN chown -Rh ${NB_USER}:${NB_USER} ${HOME}
 
 USER ${NB_USER}
 
@@ -92,4 +92,8 @@ RUN r /tmp/r-packages/2021-spring-phw-272a.r
 # Use simpler locking strategy
 COPY file-locks /etc/rstudio/file-locks
 
+# Doing a little cleanup
+RUN rm -rf /tmp/downloaded_packages
+RUN rm -rf ${HOME}/.cache
+
 ENTRYPOINT ["tini", "--"]
diff --git a/install-mambaforge.bash b/install-mambaforge.bash
index c27ba02..42e86ae 100755
--- a/install-mambaforge.bash
+++ b/install-mambaforge.bash
@@ -37,6 +37,6 @@ rm ${INSTALLER_PATH}
 # Remove the pip cache created as part of installing mambaforge
 rm -rf /root/.cache
 
-chown -R $NB_USER:$NB_USER ${CONDA_DIR}
+chown -Rh $NB_USER:$NB_USER ${CONDA_DIR}
 
 conda list -n root