From 6763d3254e9259ebc2a80117196ec6e4171f7924 Mon Sep 17 00:00:00 2001
From: MillironX <25492070+MillironX@users.noreply.github.com>
Date: Mon, 9 Aug 2021 11:30:40 -0500
Subject: [PATCH] Update Julia to 1.6.2 and switched to Alpine base image

---
 julia/julia.def | 129 +++++++++++++++++++++++++-----------------------
 1 file changed, 66 insertions(+), 63 deletions(-)

diff --git a/julia/julia.def b/julia/julia.def
index dbf0bed..03cc464 100644
--- a/julia/julia.def
+++ b/julia/julia.def
@@ -1,82 +1,85 @@
 Bootstrap: library
-From: default/debian:10
+From: default/alpine:3.14.0
 
 %post
-    # Copied from https://github.com/docker-library/julia/blob/master/1.6/buster/Dockerfile
-    apt-get -y update
-    apt-get install -y --no-install-recommends \
-        ca-certificates \
-        curl \
-        procps
-    rm -rf /var/lib/apt/lists/*
+  # Install dependencies
+  apk add --no-cache bash
+  apd add --no-cache --virtual .build-deps gpg curl
 
-    export JULIA_GPG="3673DF529D9049477F76B37566E3C7DC03D6E495"
-    export JULIA_VERSION="1.6.1"
-    export JULIA_PATH=/usr/local/julia
-    export PATH=$JULIA_PATH/bin:$PATH
+  # Make our lives easier by declaring some constants
+  export JULIA_GPG="3673DF529D9049477F76B37566E3C7DC03D6E495"
+  export JULIA_VERSION="1.6.2"
+  export JULIA_PATH=/usr/local/julia
+  export PATH=$JULIA_PATH/bin:$PATH
+  export tarArch='x86_64'
+  export dirArch='x64'
+  export sha256='5ff279bc733a99a9582fd9b39eb3d18a3fa77b9d3d2733039279a250c8c5d49c'
 
-    savedAptMark="$(apt-mark showmanual)"
+  # Download Julia
+  export folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"
+  curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/musl/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz.asc"
+  curl -fL -o julia.tar.gz     "https://julialang-s3.julialang.org/bin/musl/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz"
 
-    if ! command -v gpg > /dev/null; then
-        apt-get update
-        apt-get install -y --no-install-recommends \
-            gnupg \
-            dirmngr
-        rm -rf /var/lib/apt/lists/*
-    fi
+  # Security check step 1: verify via sha256
+  echo "${sha256} *julia.tar.gz" | sha256sum -c -
 
-    export tarArch='x86_64'
-    export dirArch='x64'
-    export sha256='7c888adec3ea42afbfed2ce756ce1164a570d50fa7506c3f2e1e2cbc49d52506'
+  # Security check step 2: verify via GPG
+  export GNUPGHOME="$(mktemp -d)"
+  gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$JULIA_GPG"
+  gpg --batch --verify julia.tar.gz.asc julia.tar.gz
+  command -v gpgconf > /dev/null && gpgconf --kill all
+  rm -rf "$GNUPGHOME" julia.tar.gz.asc
 
-    export folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"
-    curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz.asc"
-    curl -fL -o julia.tar.gz     "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz"
+  # Extract Julia
+  mkdir "$JULIA_PATH"
+  tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1
+  rm julia.tar.gz
 
-    echo "${sha256} *julia.tar.gz" | sha256sum -c -
-
-    export GNUPGHOME="$(mktemp -d)"
-    gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$JULIA_GPG"
-    gpg --batch --verify julia.tar.gz.asc julia.tar.gz
-    command -v gpgconf > /dev/null && gpgconf --kill all
-    rm -rf "$GNUPGHOME" julia.tar.gz.asc
-
-    mkdir "$JULIA_PATH"
-    tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1
-    rm julia.tar.gz
-
-    apt-mark auto '.*' > /dev/null
-    [ -z "$savedAptMark" ] || apt-mark manual $savedAptMark
-    apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false
+  # Cleanup build dependencies
+  apk del --no-cache .build-deps
 
 %environment
-    export JULIA_PATH=/usr/local/julia
-    export PATH=$JULIA_PATH/bin:$PATH
+  export JULIA_PATH=/usr/local/julia
+  export PATH=$JULIA_PATH/bin:$PATH
 
 %test
-    if [ ! "$(command -v julia)" ]; then
-        echo "command julia not found!"
-        FAILED_TESTS="TRUE"
-    fi
-
-    if [ ! "$(command -v bash)" ]; then
-        echo "command bash not found!"
-        FAILED_TESTS="TRUE"
-    fi
-
-    if [ ! "$(command -v ps)" ]; then
-        echo "command ps not found!"
-        FAILED_TESTS="TRUE"
-    fi
-
-    if [ -n "$FAILED_TESTS" ]; then
-        exit 1
+  cat << "EOF" > /tmp/singularity-test.sh
+  #!/bin/bash
+  CMDS=('bash' 'ps' 'julia')
+  for CMD in "${CMDS[@]}"; do
+    if ! command -v "$CMD"; then
+      echo "command $CMD not found!"
+      FAILED_TESTS=1
     fi
+  done
+  # Abort if a test failed
+  if [ -n "$FAILED_TESTS" ]; then
+    exit 1
+  fi
+  EOF
+  chmod +x /tmp/singularity-test.sh
+  bash /tmp/singularity-test.sh
 
 
 %runscript
-    julia "$@"
+  julia "$@"
 
 %labels
-    Author 25492070+MillironX@users.noreply.github.com
-    Version v2.3.1
+  Author 25492070+MillironX@users.noreply.github.com
+  SoftwareVersion v1.6.2
+  SingularityDefinitionVersion 1
+
+%help
+  Julia
+  =====
+
+  Julia is a high-level dynamic programming language designed to address the
+  needs of high-performance numerical analysis and computational science. It
+  provides a sophisticated compiler, distributed parallel execution, numerical
+  accuracy, and an extensive mathematical function library.
+  Source: GitHub (<https://github.com/topics/julia>)
+
+  For more help, see
+  - <https://julialang.org>
+  - <https://github.com/JuliaLang/julia>
+  - <https://github.com/MillironX/singularity-builds>