From ed4d19af83fc52eaa7ffff20d79166081f8159f2 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Mon, 12 Feb 2024 15:55:56 -0800
Subject: [PATCH] update libs

---
 images/Dockerfile          | 28 ++++++++++++++++++----------
 images/Dockerfile.gpu      | 31 ++++++++++++++++---------------
 images/apt.txt             |  5 +++++
 images/install.R           | 17 +++++++++++------
 images/rl-requirements.txt |  1 +
 images/spatial_install.R   | 20 ++++++++++++++++++++
 6 files changed, 71 insertions(+), 31 deletions(-)
 create mode 100644 images/apt.txt
 create mode 100755 images/spatial_install.R

diff --git a/images/Dockerfile b/images/Dockerfile
index d64792a..b169c01 100644
--- a/images/Dockerfile
+++ b/images/Dockerfile
@@ -9,25 +9,33 @@ RUN /rocker_scripts/install_jupyter.sh
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
 RUN chown -R rstudio:staff ${VIRTUAL_ENV} && chmod -R g+rw ${VIRTUAL_ENV}
 
-COPY install.R /tmp/install.R
-COPY jupyter-requirements.txt /tmp/jupyter-requirements.txt
-COPY spatial-requirements.txt /tmp/spatial-requirements.txt
-COPY rl-requirements.txt /tmp/rl-requirements.txt
+# install codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
+COPY apt.txt apt.txt
+RUN apt-get update -qq && xargs sudo apt-get -y install < apt.txt
+
+COPY install.R /tmp/install.R
 RUN Rscript /tmp/install.R 
 
+
+# some git preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=30000'
+
+
 USER ${NB_USER}
 WORKDIR /home/${NB_USER}
 
 RUN usermod -s /bin/bash ${NB_USER}
-RUN python3 -m pip install -r /tmp/jupyter-requirements.txt
-RUN python3 -m pip install -r /tmp/spatial-requirements.txt
-RUN python3 -m pip install -r /tmp/rl-requirements.txt
+COPY jupyter-requirements.txt /tmp/jupyter-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/jupyter-requirements.txt
+COPY spatial-requirements.txt /tmp/spatial-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/spatial-requirements.txt
+COPY rl-requirements.txt /tmp/rl-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/rl-requirements.txt
 
 ## no need to register the environment
 #RUN python3 -m ipykernel install --user --name=spatial
 
-# some git preferences
-RUN git config --global pull.rebase false && \
-    git config --global credential.helper 'cache --timeout=30000'
 
diff --git a/images/Dockerfile.gpu b/images/Dockerfile.gpu
index d8adb8c..2914c96 100644
--- a/images/Dockerfile.gpu
+++ b/images/Dockerfile.gpu
@@ -4,34 +4,35 @@ ENV NB_USER rstudio
 ENV VIRTUAL_ENV /opt/venv
 ENV PATH ${VIRTUAL_ENV}/bin:$PATH
 
-
 RUN /rocker_scripts/install_jupyter.sh
 RUN chown -R ${NB_USER}:staff ${VIRTUAL_ENV} && chmod -R g+rw ${VIRTUAL_ENV}
 
 # install codeserver
-RUN curl -fsSL https://code-server.dev/install.sh | sh
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
-COPY install.R /tmp/install.R
-COPY jupyter-requirements.txt /tmp/jupyter-requirements.txt
-COPY spatial-requirements.txt /tmp/spatial-requirements.txt
-COPY rl-requirements.txt /tmp/rl-requirements.txt
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh
 
-RUN Rscript /tmp/install.R 
+COPY apt.txt apt.txt
+RUN apt-get update -qq && xargs sudo apt-get -y install < apt.txt
 
-RUN apt-get update -qq && apt-get -y install vim
+COPY install.R /tmp/install.R
+RUN Rscript /tmp/install.R && rm /tmp/install.R 
+
+# some git preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=30000'
 
 USER ${NB_USER}
 WORKDIR /home/${NB_USER}
 
 RUN usermod -s /bin/bash ${NB_USER}
-RUN python3 -m pip install -r /tmp/jupyter-requirements.txt
-RUN python3 -m pip install -r /tmp/spatial-requirements.txt
-RUN python3 -m pip install -r /tmp/rl-requirements.txt
+COPY jupyter-requirements.txt /tmp/jupyter-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/jupyter-requirements.txt
+COPY spatial-requirements.txt /tmp/spatial-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/spatial-requirements.txt
+COPY rl-requirements.txt /tmp/rl-requirements.txt
+RUN python3 -m pip install --no-cache-dir -r /tmp/rl-requirements.txt
 
 ## no need to register the environment
 #RUN python3 -m ipykernel install --user --name=spatial
 
-# some git preferences
-RUN git config --global pull.rebase false && \
-    git config --global credential.helper 'cache --timeout=30000'
-
diff --git a/images/apt.txt b/images/apt.txt
new file mode 100644
index 0000000..c09ae14
--- /dev/null
+++ b/images/apt.txt
@@ -0,0 +1,5 @@
+vim
+cmake
+nano
+exuberant-ctags
+
diff --git a/images/install.R b/images/install.R
index d8e6c39..77f63e7 100755
--- a/images/install.R
+++ b/images/install.R
@@ -1,16 +1,21 @@
 #! /usr/local/bin/Rscript
 # install R dependencies
 
+## Ensure spatial packages are installed from source
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
 # Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
-# install.packages("pak")
-install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap", "pak"))
-remotes::install_github('r-tmap/tmap')
+install.packages("pak")
+pak::pkg_install(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "pak", "duckdbfs", "minioclient"))
+pak::pkg_install("r-tmap/tmap")
+
+#remotes::install_github('r-tmap/tmap', upgrade="never", repos="https://cloud.r-project.org", dep=TRUE)
+
 
 pak::pkg_install("igraph")
+pak::pkg_install("ropensci-review-tools/pkgcheck")
 
-#pak::pkg_install("httpgd")
-#pak::pkg_install(c("IRkernel", "languageserver"))
-#IRkernel::installspec()
+# pak::pkg_install("httpgd")
+pak::pkg_install(c("IRkernel", "languageserver"))
+IRkernel::installspec()
 
diff --git a/images/rl-requirements.txt b/images/rl-requirements.txt
index 08e16be..d934f0e 100644
--- a/images/rl-requirements.txt
+++ b/images/rl-requirements.txt
@@ -9,4 +9,5 @@ ray[rllib,tune]
 stable-baselines3
 sb3-contrib
 huggingface_sb3
+darts[all]
 
diff --git a/images/spatial_install.R b/images/spatial_install.R
new file mode 100755
index 0000000..77da830
--- /dev/null
+++ b/images/spatial_install.R
@@ -0,0 +1,20 @@
+#! /usr/local/bin/Rscript
+# install R dependencies
+
+## Ensure spatial packages are installed from source
+Sys.setenv(GITHUB_PAT="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")
+remotes::install_github('r-tmap/tmap', upgrade="never", repos="https://cloud.r-project.org", dep=TRUE)
+
+# We could use renv.lock approach here instead, but will force re-creation of environment from scratch
+# Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
+# Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
+install.packages("pak")
+pak::pkg_install(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "pak", "duckdbfs", "minioclient"))
+
+pak::pkg_install("igraph")
+pak::pkg_install("ropensci-review-tools/pkgcheck")
+
+pak::pkg_install("httpgd")
+pak::pkg_install(c("IRkernel", "languageserver"))
+IRkernel::installspec()
+