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Fix absolute paths in scripts #41

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Fix absolute paths in scripts #41

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41 changes: 41 additions & 0 deletions linuxdeploy-plugin-conda.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ fi

script=$(readlink -f "$0")

CONDA_SKIP_ADJUST_PATHS=${CONDA_SKIP_ADJUST_PATHS:-"1"}
ARCH="${ARCH:-"$(uname -m)"}"

show_usage() {
Expand All @@ -23,6 +24,7 @@ show_usage() {
echo " PIP_REQUIREMENTS=\"packageA packageB -r requirements.txt -e git+https://...\""
echo " PIP_PREFIX=\"AppDir/usr/share/conda\""
echo " ARCH=\"$ARCH\" (supported values: x86_64, i368, i686)"
echo " CONDA_SKIP_ADJUST_PATHS=\"1\" (default: skip)"
echo " CONDA_SKIP_CLEANUP=\"[all;][conda-pkgs;][__pycache__;][strip;][.a;][cmake;][doc;][man;][site-packages;]\""
}

Expand Down Expand Up @@ -187,6 +189,45 @@ for i in usr/conda/bin/*; do
done
popd

# adjust absolute paths, by default skipped via $CONDA_SKIP_ADJUST_PATHS
if [ "$CONDA_SKIP_ADJUST_PATHS" != "1" ]; then
# disable history substitution, b/c we use ! in quoted strings
set +H
APPDIR_FULL="$(pwd)/$APPDIR"
pushd "$APPDIR_FULL"
# NOTE: --follow-symlinks is only working for GNU sed
# replace absolute paths in some specific files (regex could result in false replacements in other files)
[ -f usr/conda/etc/profile.d/conda.sh ] && sed -i --follow-symlinks "s|'$APPDIR_FULL|\"\${APPDIR}\"'|g" usr/conda/etc/profile.d/conda.sh
[ -f usr/conda/etc/profile.d/conda.sh ] && sed -i --follow-symlinks "s|$APPDIR_FULL|\${APPDIR}|g" usr/conda/etc/profile.d/conda.sh
[ -f usr/conda/etc/profile.d/conda.csh ] && sed -i --follow-symlinks "s|$APPDIR_FULL|\${APPDIR}|g" usr/conda/etc/profile.d/conda.csh
[ -f usr/conda/etc/fish/conf.d/conda.fish ] && sed -i --follow-symlinks "s|$APPDIR_FULL|\$APPDIR|g" usr/conda/etc/fish/conf.d/conda.fish
# generic files in usr/conda/bin/ and usr/conda/condabin/
for i in usr/conda/bin/* usr/conda/condabin/*; do
[ -f "$i" ] || continue
# shebangs
sed -i --follow-symlinks "s|^#!$APPDIR_FULL/usr/conda/bin/|#!/usr/bin/env |" "$i"
# perl assignments (must be before bash assignments)
sed -ri --follow-symlinks "s|^(my.*=[[:space:]]*\")$APPDIR_FULL|\1\$ENV{APPDIR} . \"|g" "$i"
# bash assignments
sed -ri --follow-symlinks "s|(=[[:space:]]*\")$APPDIR_FULL|\1\${APPDIR}|g" "$i"
done
# specific files in usr/conda/bin/ (regex could result in false replacements in other files)
[ -f usr/conda/bin/python3-config ] && sed -i --follow-symlinks "s|$APPDIR_FULL|\${APPDIR}|g" usr/conda/bin/python3-config
[ -f usr/conda/bin/ncursesw6-config ] && sed -i --follow-symlinks "s|$APPDIR_FULL|\${APPDIR}|g" usr/conda/bin/ncursesw6-config
popd

# generate linuxdeploy-plugin-conda-hook
mkdir -p "$APPDIR"/apprun-hooks
cat > "$APPDIR"/apprun-hooks/linuxdeploy-plugin-conda-hook.sh <<\EOF
# generated by linuxdeploy-plugin-conda

# export APPDIR variable to allow for running from extracted AppDir as well
export APPDIR="${APPDIR:-$(readlink -f "$(dirname "$0")")}"
# export PATH to allow /usr/bin/env shebangs to use the supplied applications
export PATH="$APPDIR"/usr/bin:"$PATH"
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This will break calling any sorts of external tools, because they'll then also have to use all tools contained in the AppDir. Can you think of a different solution perhaps? The use of environment variables like PATH and LD_LIBRARY_PATH is actually an antipattern and has to be done with great care.

To limit the effects, one possible solution would be to create a separate bin dir somewhere in the AppDir that only points to the bundled Python binary/binaries, but none of the other stuff in AppDir/usr/bin. But that's also a hack. I think you could even further limit the effects by generating some sort of unique name for the symlink to the main binary. Then, you can safely use /usr/bin/env linuxdeploy-plugin-conda-python or something like that with bundled tools.

Of course, bundled scripts that just point to /usr/bin/env python would still fail to run. But I'm not sure that issue can be fixed.

EOF

fi

# remove bloat, optionally skipped via $CONDA_SKIP_CLEANUP
IFS=';' read -ra cleanup <<< "$CONDA_SKIP_CLEANUP"
Expand Down