From bf624abeaf1a7749a196d9eec147083a62e0d5a6 Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Wed, 1 Nov 2023 23:21:34 +0530
Subject: [PATCH 1/2] Switch base to rocker/binder image

- Matches what we do in other images
- Simplifies this image *a lot*
- Knitting still takes time the *first time* even if we just switch to
  new base image. But https://github.com/rocker-org/rocker-versioned2/pull/714
  installs some of the texlive packages that are being installed the
  first time, and should speed things up.

Ref https://github.com/2i2c-org/infrastructure/issues/3178
---
 Dockerfile       | 48 +++---------------------------------------------
 environment.yml  | 23 -----------------------
 requirements.txt |  9 +++++++++
 3 files changed, 12 insertions(+), 68 deletions(-)
 delete mode 100644 environment.yml
 create mode 100644 requirements.txt

diff --git a/Dockerfile b/Dockerfile
index c5ea039..466bad3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,47 +1,7 @@
-FROM rocker/geospatial:4.3.1
+FROM rocker/binder:4.3.1
 
-# Install conda here, to match what repo2docker does
-ENV CONDA_DIR=/srv/conda
-
-# Add our conda environment to PATH, so python, mamba and other tools are found in $PATH
-ENV PATH ${CONDA_DIR}/bin:${PATH}
-
-# RStudio doesn't actually inherit the ENV set in Dockerfiles, so we
-# have to explicitly set it in Renviron.site
-RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site
-
-# The terminal inside RStudio doesn't read from Renviron.site, but does read
-# from /etc/profile - so we rexport here.
-RUN echo "export PATH=${PATH}" >> /etc/profile
-
-# Install shiny-server
-RUN /rocker_scripts/install_shiny_server.sh
-
-# Install a specific version of mambaforge in ${CONDA_DIR}
-# Pick latest version from https://github.com/conda-forge/miniforge/releases
-ENV MAMBAFORGE_VERSION=22.9.0-2
-RUN echo "Installing Mambaforge..." \
-    && curl -sSL "https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-$(uname -m).sh" > installer.sh \
-    && /bin/bash installer.sh -u -b -p ${CONDA_DIR} \
-    && rm installer.sh \
-    && mamba clean -afy \
-    # After installing the packages, we cleanup some unnecessary files
-    # to try reduce image size - see https://jcristharif.com/conda-docker-tips.html
-    && find ${CONDA_DIR} -follow -type f -name '*.a' -delete \
-    && find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete
-
-COPY environment.yml /tmp/environment.yml
-
-RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml \
-    && mamba clean -afy \
-    && find ${CONDA_DIR} -follow -type f -name '*.a' -delete \
-    && find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete
-
-# Install IRKernel
-RUN install2.r --skipinstalled \
-       IRkernel \
-       rstan \
-    && rm -rf /tmp/downloaded_packages
+COPY requirements.txt /tmp/requirements.txt
+RUN pip install --no-cache -r /tmp/requirements.txt
 
 # Install learnr and other requested packages in https://2i2c.freshdesk.com/a/tickets/741
 # mosaic installed per https://2i2c.freshdesk.com/a/tickets/973
@@ -64,8 +24,6 @@ RUN install2.r --skipinstalled \
     mosaic \
     && rm -rf /tmp/downloaded_packages
 
-RUN r -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
-
 # Set working directory so Jupyter knows where to start
 WORKDIR /home/rstudio
 
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 61c5469..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-channels:
-  - conda-forge
-  - nodefaults
-
-dependencies:
-  # Required to work with JupyterHub
-  - jupyterhub-singleuser>=3.0
-  # Required to work with RStudio
-  - jupyter-rsession-proxy>=2
-  # Let's provide Jupyter Interfaces too
-  - jupyterlab>=3.0
-  - retrolab
-  # Provide info on memory usage in JupyterLab & RetroLab
-  - jupyter-resource-usage
-  # People still wanna pull stuff, even if into RStudio
-  - nbgitpuller==1.1.1
-
-  - pip
-
-  - pip:
-    - jupyter-shiny-proxy==1.1
-    # Based on request from Nathan Taback
-    - otter-grader==4.3.4
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..2d54ab9
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,9 @@
+retrolab
+# Provide info on memory usage in JupyterLab & RetroLab
+jupyter-resource-usage
+# People still wanna pull stuff, even if into RStudio
+nbgitpuller==1.2.0
+
+jupyter-shiny-proxy==1.1
+# Based on request from Nathan Taback
+otter-grader==4.3.4

From dd5c5d66360a724a44b34bc4b80305104ef67f3f Mon Sep 17 00:00:00 2001
From: YuviPanda <yuvipanda@gmail.com>
Date: Thu, 2 Nov 2023 14:31:26 +0530
Subject: [PATCH 2/2] Install python packages as root

---
 Dockerfile | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 466bad3..0a63236 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,14 @@
 FROM rocker/binder:4.3.1
 
+USER root
+
+# Install python packages as root, since that's what is done upstream
+# This may change soon https://github.com/rocker-org/rocker-versioned2/issues/670
 COPY requirements.txt /tmp/requirements.txt
 RUN pip install --no-cache -r /tmp/requirements.txt
 
+USER ${NB_USER}
+
 # Install learnr and other requested packages in https://2i2c.freshdesk.com/a/tickets/741
 # mosaic installed per https://2i2c.freshdesk.com/a/tickets/973
 RUN install2.r --skipinstalled \