Merge branch 'main' of github.com:bsurc/container

.github/workflows/build.yml

@@ -0,0 +1,30 @@
+name: build
+
+on:
+  push:
+    branches: [ main ]
+    # Run when container or environment is changed
+    paths:
+        - 'jukes-micromamba/Dockerfile'
+  # Allows workflow to be manually triggered
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@main
+
+      - name: 'Login to GitHub Container Registry'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+
+      - name: 'Build Inventory Image'
+        run: |
+          docker build ./jukes-micromamba/ --tag ghcr.io/bsurc/jukes-micromamba:latest
+          docker push ghcr.io/bsurc/jukes-micromamba:latest

.gitignore

@@ -13,3 +13,10 @@
 
 # alpine minirootfs
 *alpine-minirootfs-*.tar.gz*
+
+# tar and zip files
+*.tar*
+*.zip
+
+# guix to squashfs output
+*guix.out

README.md

@@ -30,6 +30,15 @@ To add the testing repository to `apk` after switching to `edge`:
 
 ### R
 
+R packages can be difficult to build, especially with dependencies on various
+systems.  Posit (creators of RStudio) have ppa repositories to help with some of
+these dependencies, and handles them especially well in conjuction with RStudio
+server.  See the `r-spatial` build for an example.
+
+Another option that appears to work well is using `guix` to create a squashfs
+image directly.  There is an HPC/cran channel for guix that mirrors R packages.
+See the `peregrine` build for an example.
+
 #### Issues on Alpine
 
 If you are getting `iconv` translation errors, set `LC_ALL=en_US.UTF-8`.
@@ -47,3 +56,33 @@ text libraries:
 Also, the `linux-headers` package is frequently needed for packages:
 
     apk add linux-headers
+
+### GUIX
+
+In order to use a `guix` based build, the user should test the environment using
+`guix shell`, then dump the channel configuration to a `channels.scm` file
+using:
+
+  guix describe --format=channels > channels.scm
+
+Then `guix time-machine` to build the environment/squashfs.  The full process
+may look like:
+
+    $ # optional
+    $ guix pull
+    $ guix shell bash go
+    $ # test environment...
+    $ guix shell --export-manifest shell bash go > manifest.scm
+    $ # export the current channel definition
+    $ guix describe --format=channels > channels.scm
+    $ # test
+    $ guix time-machine -C channels.scm -- shell -m manifest
+    $ # build squashfs
+    $ guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm
+
+To build a container from the squashfs, simply use the squashfs as the source:
+
+    appatiner build --fakeroot x.sif /gnu/store/${guixhash}.squashfs
+
+For simple examples of adding metadata to the container, see
+`peregrine/Makefile`

codeserver/codeserver.def

@@ -0,0 +1,14 @@
+bootstrap: docker
+from: debian:bookworm
+
+%environment
+    export LC_ALL=C
+    export PATH=/opt/code-server-4.22.1-linux-amd64/bin:$PATH
+
+%post
+    apt update
+    apt install -y curl tar
+    cd /opt
+    export VERSION=4.22.1
+    curl -fL https://github.com/coder/code-server/releases/download/v$VERSION/code-server-$VERSION-linux-amd64.tar.gz | \
+        tar -xz -C /opt

jukes-micromamba/Dockerfile

@@ -0,0 +1,18 @@
+FROM mambaorg/micromamba:1.5.8-bookworm-slim
+
+USER root
+RUN apt update && \
+    apt install -y libgl1 && \
+    apt clean
+USER $MAMBA_USER
+RUN micromamba create -n cautorift -c conda-forge python autorift=1.1.0 \
+        notebook matplotlib pandas opencv rasterio && \
+    micromamba clean --all --yes
+RUN export SITEPACKAGES=`micromamba run -n cautorift python -m site | \
+    grep -m 1 site-packages | sed "s/[,']//g"` && \
+    export AUTORIFT=${SITEPACKAGES}/autoRIFT/autoRIFT.py && \
+    sed -i 's/np.bool/bool/g' $AUTORIFT && \
+    sed -i 's/np.int/int/g' $AUTORIFT
+
+ENV MAMBA_DOCKERFILE_ACTIVATE=1
+ENV ENV_NAME=cautorift

jukes-micromamba/micromamba.def

@@ -0,0 +1,18 @@
+bootstrap: docker
+from: mambaorg/micromamba:1.5.8-bookworm-slim
+
+%environment
+    export MAMBA_DOCKERFILE_ACTIVATE=1
+    export ENV_NAME=cautorift
+
+%post
+    apt update && apt install -y libgl1 libegl1 libopengl0
+    apt clean
+    micromamba create -n cautorift -c conda-forge python autorift=1.1.0 \
+        notebook matplotlib pandas opencv rasterio
+    micromamba clean --all --yes
+    export SITEPACKAGES=`micromamba run -n cautorift python -m site \
+        | grep -m 1 site-packages | sed "s/[,']//g"` #'
+    export AUTORIFT=${SITEPACKAGES}/autoRIFT/autoRIFT.py
+    sed -i 's/np.bool/bool/g' $AUTORIFT
+    sed -i 's/np.int/int/g' $AUTORIFT

peregrine/Makefile

@@ -1,11 +1,11 @@
 GIT_REV = $(shell git rev-parse --short=16 HEAD)
-peregrine.sif: peregrine.def peregrine-guix.out
-	apptainer build -F --fakeroot --build-arg GIT_REV=$(GIT_REV) --build-arg GUIX_SQUASHFS=$$(tail -1 peregrine-guix.out) peregrine.sif peregrine.def
+peregrine.sif: peregrine.def guix.out
+	apptainer build -F --fakeroot --build-arg GIT_REV=$(GIT_REV) --build-arg GUIX_SQUASHFS=$$(tail -1 guix.out) peregrine.sif peregrine.def
 
-peregrine-guix.out: channels.scm manifest.scm
-	guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm | tee peregrine-guix.out
+guix.out: channels.scm manifest.scm
+	guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm | tee guix.out
 
 .PHONY: clean
 clean:
-	rm -f *.sif
-	rm -f peregrine-guix.out
+	rm -f peregrine.sif
+	rm -f guix.out

r-mollyastell/Makefile

@@ -0,0 +1,11 @@
+GIT_REV = $(shell git rev-parse --short=16 HEAD)
+r-mollyastell.sif: r-mollyastell.def r-mollyastell-guix.out
+	apptainer build -F --fakeroot --build-arg GIT_REV=$(GIT_REV) --build-arg GUIX_SQUASHFS=$$(tail -1 r-mollyastell-guix.out) r-mollyastell.sif r-mollyastell.def
+
+r-mollyastell-guix.out: channels.scm manifest.scm
+	guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm | tee r-mollyastell-guix.out
+
+.PHONY: clean
+clean:
+	rm -f *.sif
+	rm -f r-mollyastell-guix.out

r-mollyastell/channels.scm

@@ -0,0 +1,28 @@
+(list (channel
+        (name 'guix-cran)
+        (url "https://github.com/guix-science/guix-cran.git")
+        (branch "master")
+        (commit
+          "466d876bcc15a1a6c2053eb150548f7f471f75b7"))
+      (channel
+        (name 'guix-science)
+        (url "https://github.com/guix-science/guix-science.git")
+        (branch "master")
+        (commit
+          "7c6ca7e1c19c92bfe5e6add688662e08b07db2bf")
+        (introduction
+          (make-channel-introduction
+            "b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"
+            (openpgp-fingerprint
+              "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"))))
+      (channel
+        (name 'guix)
+        (url "https://git.savannah.gnu.org/git/guix.git")
+        (branch "master")
+        (commit
+          "d616e85ac8a380d5126da3184f7037c20866c884")
+        (introduction
+          (make-channel-introduction
+            "9edb3f66fd807b096b48283debdcddccfea34bad"
+            (openpgp-fingerprint
+              "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA")))))

r-mollyastell/manifest.scm

@@ -0,0 +1,41 @@
+(specifications->manifest (list
+                            ;; base packages
+                            "bash-minimal"
+                            "glibc-locales"
+                            "nss-certs"
+                            ;; Common command line tools lest the container is too empty.
+                            "coreutils"
+                            "grep"
+                            "which"
+                            "wget"
+                            "sed"
+                            ;; Toolchain and common libraries for "install.packages"
+                            "gcc-toolchain@10"
+                            "gfortran-toolchain"
+                            "gawk"
+                            "tar"
+                            "gzip"
+                            "unzip"
+                            "make"
+                            "cmake"
+                            "pkg-config"
+                            "cairo"
+                            "libxt"
+                            "openssl"
+                            "curl"
+                            "zlib"
+                            ;; gdal
+                            "gdal"
+                            ;; r stuff
+                            "r"
+                            "r-tidyverse"
+                            "r-mgcv"
+                            "r-plotly"
+                            "r-patchwork"
+                            "r-lubridate"
+                            "r-iranges"
+                            "r-data-table"
+                            "r-brms"
+                            "r-tidybayes"
+                            "r-broom"
+                          ))

r-mollyastell/r-mollyastell-guix.out

@@ -0,0 +1 @@
+/gnu/store/ql301y556rlgyg40p6adwsxm60m68ya2-bash-minimal-glibc-locales-nss-certs-squashfs-pack.gz.squashfs

r-mollyastell/r-mollyastell.def

@@ -0,0 +1,6 @@
+Bootstrap: localimage
+From: {{GUIX_SQUASHFS}}
+
+%labels
+author Kyle Shannon <[email protected]>
+github.com/bsurc/container git rev={{GIT_REV}}

rstudio-server/rstudio.def

@@ -0,0 +1,22 @@
+bootstrap: docker
+From: ubuntu:jammy
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/lib/rstudio-server/bin:$PATH
+
+%post
+    export LC_ALL=C
+
+    apt update
+    DEBIAN_FRONTEND=NONINTERACTIVE apt install -y \
+        gdebi-core \
+        libreadline-dev \
+        wget
+    apt clean all
+    cd /lib/x86_64-linux-gnu/
+    ln -s libreadline.so.8 libreadline.so.6
+
+    wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.1-402-amd64.deb
+    gdebi --n rstudio-server-2023.12.1-402-amd64.deb
+    rm rstudio-server-2023.12.1-402-amd64.deb

rstudio/Makefile

@@ -0,0 +1,11 @@
+GIT_REV = $(shell git rev-parse --short=16 HEAD)
+rstudio.sif: rstudio.def guix.out
+	apptainer build -F --fakeroot --build-arg GIT_REV=$(GIT_REV) --build-arg GUIX_SQUASHFS=$$(tail -1 guix.out) rstudio.sif rstudio.def
+
+guix.out: channels.scm manifest.scm
+	guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm | tee guix.out
+
+.PHONY: clean
+clean:
+	rm -f rstudio.sif
+	rm -f guix.out

rstudio/channels.scm

@@ -0,0 +1,28 @@
+(list (channel
+        (name 'guix-cran)
+        (url "https://github.com/guix-science/guix-cran.git")
+        (branch "master")
+        (commit
+          "466d876bcc15a1a6c2053eb150548f7f471f75b7"))
+      (channel
+        (name 'guix-science)
+        (url "https://github.com/guix-science/guix-science.git")
+        (branch "master")
+        (commit
+          "7c6ca7e1c19c92bfe5e6add688662e08b07db2bf")
+        (introduction
+          (make-channel-introduction
+            "b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"
+            (openpgp-fingerprint
+              "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"))))
+      (channel
+        (name 'guix)
+        (url "https://git.savannah.gnu.org/git/guix.git")
+        (branch "master")
+        (commit
+          "d616e85ac8a380d5126da3184f7037c20866c884")
+        (introduction
+          (make-channel-introduction
+            "9edb3f66fd807b096b48283debdcddccfea34bad"
+            (openpgp-fingerprint
+              "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA")))))

rstudio/manifest.scm

@@ -0,0 +1,42 @@
+(specifications->manifest (list
+                            ;; base packages
+                            ;;"bash-minimal"
+                            "bash"
+                            "bash-completion"
+                            "glibc-locales"
+                            "nss-certs"
+                            ;; Common command line tools lest the container is too empty.
+                            "coreutils"
+                            "curl"
+                            "grep"
+                            "sed"
+                            "wget"
+                            "which"
+                            ;; Toolchain and common libraries for "install.packages"
+                            "cairo"
+                            "cmake"
+                            "gcc-toolchain@10"
+                            "gfortran-toolchain"
+                            "gawk"
+                            "gzip"
+                            "libxt"
+                            "make"
+                            "openssl"
+                            "pkg-config"
+                            "r"
+                            "rstudio"
+                            "rstudio-server"
+                            "tar"
+                            "tcl"
+                            "unzip"
+                            "zlib"
+                            ;; GIS/Geospatial crap
+                            "gdal"
+                            "libspatialite"
+                            "proj"
+                            ;; common dependencies for r
+                            "fontconfig"
+                            "fribidi"
+                            "harfbuzz"
+                            "libxml2"
+                          ))

rstudio/rstudio.def

@@ -0,0 +1,6 @@
+Bootstrap: localimage
+From: {{GUIX_SQUASHFS}}
+
+%labels
+author Kyle Shannon <[email protected]>
+github.com/bsurc/container git rev={{GIT_REV}}