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#!/bin/bash
#
# An ultimate helper to use to setup a CI with some git-annex installation
# Arguments:
# First argument would be which "schema" would it be.
# Some schemas might like additional arguments.
#
# This script
# - needs to be "source"d since some schemas would need to modify env vars
# - might use "sudo" for some operations
# - might exit with 0 if e.g. specific installation "is not needed" (e.g. devel annex == default annex)
function _show_schemes() {
_schemes_doc=(
"autobuild # Linux, macOS"
"brew # macOS"
"conda-forge [version] # Linux"
"conda-forge-last [version] # Linux"
"datalad-extensions-build # Linux, macOS"
"deb-url URL # Linux"
"neurodebian # Linux"
"neurodebian-devel # Linux"
"snapshot # Linux, macOS"
)
for s in "${_schemes_doc[@]}"; do
echo " $s"
done
}
function _usage() {
cat >&2 <<EOF
usage: source $0 [--help] [--adjust-bashrc] [SCHEME [ARGS...]]
*Options*
--adjust-bashrc
If the scheme tweaks PATH, prepend a snippet to ~/.bashrc that exports that
path. Note: This should be positiioned before SCHEME.
--help
Display this help and exit.
SCHEME
Type of git-annex installation (default "conda-forge").
$(_show_schemes)
EOF
}
function setup_neurodebian_devel() {
# configure
sed -e 's,/debian ,/debian-devel ,g' /etc/apt/sources.list.d/neurodebian.sources.list | sudo tee /etc/apt/sources.list.d/neurodebian-devel.sources.list
sudo apt-get update
}
function install_from_dmg() {
hdiutil attach "$1"
rsync -a /Volumes/git-annex/git-annex.app /Applications/
hdiutil detach /Volumes/git-annex/
_annex_bin=/Applications/git-annex.app/Contents/MacOS
export PATH="$_annex_bin:$PATH"
}
_conda_annex_version=
scenario="conda-forge"
adjust_bashrc=
url=
while [ $# != 0 ]; do
case "$1" in
--adjust-bashrc)
adjust_bashrc=1
shift
;;
--help)
_usage
exit 0
;;
-*)
_usage
exit 1
;;
*)
scenario="$1"
shift
case "$scenario" in
neurodebian|neurodebian-devel|autobuild|snapshot|datalad-extensions-build|brew)
;;
conda-forge|conda-forge-last)
if [ -n "$1" ]; then
_conda_annex_version="=$1"
shift
fi
;;
deb-url)
url="${1?deb-url scheme requires URL}"
shift
;;
*)
echo "Unknown git-annex installation scheme '$scenario'" >&2
echo "Known schemes:" >&2
_show_schemes >&2
exit 1
;;
esac
if [ -n "$1" ]; then
# There are unexpected arguments left over.
_usage
exit 1
fi
;;
esac
done
_this_dir=$(dirname "$0")
# Most common location of installation - /usr/bin
_annex_bin=/usr/bin
_PATH_OLD="$PATH"
# we do not want to `cd` anywhere but all temp stuff should get unique temp prefix
_TMPDIR=$(mktemp -d "${TMPDIR:-/tmp}/ga-XXXXXXX")
echo "I: top directory $_TMPDIR"
case "$scenario" in
neurodebian) # TODO: use nd_freeze_install for an arbitrary version specified
# we assume neurodebian is generally configured
sudo apt-get install git-annex-standalone
;;
neurodebian-devel)
# if debian-devel is not setup -- set it up
apt-cache policy git-annex-standalone | grep -q '/debian-devel ' \
|| setup_neurodebian_devel
# check versions
# devel:
devel_annex_version=$(apt-cache policy git-annex-standalone | grep -B1 '/debian-devel ' | awk '/ndall/{print $1;}')
current_annex_version=$(apt-cache policy git-annex-standalone | awk '/\*\*\*/{print $2}')
if dpkg --compare-versions "$devel_annex_version" gt "$current_annex_version"; then
sudo apt-get install "git-annex-standalone=$devel_annex_version"
else
echo "I: devel version $devel_annex_version is not newer than installed $current_annex_version"
exit 0
fi
;;
deb-url)
(
wget -O "$_TMPDIR/git-annex.deb" "$url"
sudo dpkg -i "$_TMPDIR/git-annex.deb"
)
;;
autobuild|snapshot)
case "$(uname)" in
Linux)
_annex_bin="$_TMPDIR/git-annex.linux"
echo "I: downloading and extracting under $_annex_bin"
case "$scenario" in
autobuild)
_subpath=autobuild/amd64
;;
snapshot)
_subpath=linux/current
;;
*)
echo "E: internal error: scenario '$scenario' should not reach here" >&2
exit 1
;;
esac
tar -C "$_TMPDIR" -xzf <(
wget -q -O- https://downloads.kitenet.net/git-annex/$_subpath/git-annex-standalone-amd64.tar.gz
)
export PATH="${_annex_bin}:$PATH"
;;
Darwin)
case "$scenario" in
autobuild)
_subpath=autobuild/x86_64-apple-yosemite
;;
snapshot)
_subpath=OSX/current/10.10_Yosemite
;;
*)
echo "E: internal error: scenario '$scenario' should not reach here" >&2
exit 1
;;
esac
wget -q -O "$_TMPDIR/git-annex.dmg" https://downloads.kitenet.net/git-annex/$_subpath/git-annex.dmg
install_from_dmg "$_TMPDIR"/*.dmg
;;
*)
echo "E: Unsupported OS: $(uname)"
exit 1
;;
esac
;;
conda-forge|conda-forge-last)
_miniconda_script=Miniconda3-latest-Linux-x86_64.sh
_conda_bin="$_TMPDIR/miniconda/bin"
# we will symlink git-annex only under a didicated directory, so it could be
# used with default Python etc. If names changed here, possibly adjust hardcoded
# duplicates below where we establish relative symlinks
_annex_bin="$_TMPDIR/annex-bin"
case "$scenario" in
conda-forge-last)
if hash git-annex; then
echo "W: git annex already installed. In this case this setup has no sense" >&2
exit 1
fi
# We are interested only to get git-annex into our environment
# So to not interfere with "system wide" Python etc, we will add miniconda at the
# end of the path
export PATH="$PATH:${_annex_bin}";;
conda-forge)
export PATH="${_annex_bin}:$PATH";;
*)
echo "E: internal error - $scenario is unknown"
exit 1;;
esac
echo "I: downloading and running miniconda installer"
wget -q -O "$_TMPDIR/${_miniconda_script}" \
"${ANACONDA_URL:-https://repo.anaconda.com/miniconda/}${_miniconda_script}"
HOME="$_TMPDIR" bash "$_TMPDIR/${_miniconda_script}" -b -p "$_TMPDIR/miniconda"
"${_conda_bin}/conda" install -q -c conda-forge -y "git-annex${_conda_annex_version}"
if [[ "$_annex_bin" != "$_conda_bin" ]]; then
mkdir -p "$_annex_bin"
(
cd "$_annex_bin" || exit 1
ln -s ../miniconda/bin/git-annex* .
)
fi
unset _miniconda_script
unset _conda_bin
unset _conda_annex_version
;;
datalad-extensions-build)
case "$(uname)" in
Linux)
TARGET_PATH="$_TMPDIR" "$_this_dir/download-latest-artifact"
sudo dpkg -i "$_TMPDIR"/*.deb
;;
Darwin)
TARGET_PATH="$_TMPDIR" TARGET_ARTIFACT=git-annex-macos-dmg "$_this_dir/download-latest-artifact"
install_from_dmg "$_TMPDIR"/*.dmg
;;
*)
echo "E: Unsupported OS: $(uname)"
exit 1
;;
esac
;;
brew)
brew install git-annex
_annex_bin=/usr/local/bin
;;
*)
echo "E: internal error: '$scenario' should be handled above" >&2
exit 1
esac
if [ -n "$adjust_bashrc" ]; then
# If PATH was changed, we need to make it available to SSH commands.
# Note: Prepending is necessary. SSH commands load .bashrc, but many
# distributions (including Debian and Ubuntu) come with a snippet to exit
# early in that case.
if [ "$PATH" != "$_PATH_OLD" ]; then
perl -pli -e 'print "PATH=\"$ENV{PATH}\"" if $. == 1' ~/.bashrc
echo "I: Adjusted first line of ~/.bashrc:"
head -n1 ~/.bashrc
fi
fi
# Rudimentary test of installation and inform user about location
test -x "${_annex_bin}/git-annex"
test -x "${_annex_bin}/git-annex-shell"
echo "I: git-annex is available under '${_annex_bin}'"
unset _annex_bin
unset _show_schemes
unset _this_dir
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