Fix absolute paths in scripts

This removes some of the wrong, absolute paths pointing to the build location
of the AppImage by using a different shebang and some environment variables,
set by the linuxdeploy-plugin-conda-hook at the AppImage start.

Fixes #12, fixes #25 and fixes #32

linuxdeploy-plugin-conda.sh

@@ -9,6 +9,7 @@ fi
 
 script=$(readlink -f "$0")
 
+CONDA_SKIP_ADJUST_PATHS=${CONDA_SKIP_ADJUST_PATHS:-"1"}
 ARCH="${ARCH:-"$(uname -m)"}"
 
 show_usage() {
@@ -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;]\""
 }
 
@@ -187,6 +189,44 @@ 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.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"
+EOF
+
+fi
 
 # remove bloat, optionally skipped via $CONDA_SKIP_CLEANUP
 IFS=';' read -ra cleanup <<< "$CONDA_SKIP_CLEANUP"