Merge pull request #107 from ReproNim/enh-pidlock

ENH: make pass_git_config to allow to have no default + pass annex.pidlock if defined

scripts/singularity_cmd

@@ -8,7 +8,7 @@
 #  - cleansed environment variables
 # while bind mounting (and starting from) current directory.
 #
-# COPYRIGHT: Yaroslav Halchenko 2019
+# COPYRIGHT: Yaroslav Halchenko 2019-2023
 #
 # LICENSE: MIT
 #
@@ -31,8 +31,6 @@
 #  THE SOFTWARE.
 #
 
-set -eu
-
 function info() {
 	: #	echo -e "I: " "$@" >&2
 }
@@ -43,11 +41,21 @@ function info() {
 #
 function pass_git_config() {
 	var="$1"
-	default="$2"
 
 	# git config reads without locking, but could lock for writing
 	# so we might need to try multiple times setting the value
-	value=$(git config "$var" || echo "$default")
+	set +e
+	value=$(git config "$var")
+	ret=$?
+	set -e
+
+	# if variable is not defined at all
+	if [ "$ret" = 1 ] ; then
+		# and default was not provided - nothing for us to do
+		[ "$#" -ge 2 ] || return 0
+		# otherwise, use that default
+		value="$2"
+	fi
 	# shellcheck disable=SC2034
 	for attempt in {1..5}; do
 		git config -f "$BHOME/.gitconfig" "$var" >/dev/null \
@@ -62,6 +70,13 @@ function readlink_f() {
 	readlink -f "$1" 2> /dev/null || python -c 'import sys, os ; print(os.path.realpath(sys.argv[1]))' "$1"
 }
 
+if [ "$#" = 0 ]; then
+	echo "Using as a library. Run with 'exec' or 'run' command and options."
+	exit 0
+fi
+
+set -eu
+
 info "PWD=$PWD"
 
 thisfile=$(readlink_f "$0")
@@ -78,7 +93,7 @@ if [ -n "${DATALAD_CONTAINER_NAME:-}" ]; then
 	export APPTAINERENV_DATALAD_CONTAINER_NAME="$DATALAD_CONTAINER_NAME"
 fi
 
-# fix non-writable matplotlib cache dir in apptainer https://github.com/ReproNim/containers/issues/97                                  
+# fix non-writable matplotlib cache dir in apptainer https://github.com/ReproNim/containers/issues/97
 export SINGULARITYENV_MPLCONFIGDIR=/tmp/mpl-config
 export APPTAINERENV_MPLCONFIGDIR=/tmp/mpl-config
 
@@ -89,9 +104,9 @@ export APPTAINERENV_MPLCONFIGDIR=/tmp/mpl-config
 # (double-bound) directory.  Shortening the name of the directory is one way 
 # to fix the problem.  See https://github.com/ReproNim/containers/issues/57
 if [ "$(uname -s)" = Darwin ]; then
-    tmpdir=$(mktemp -d -t s)
+	tmpdir=$(mktemp -d -t s)
 else
-    tmpdir=$(mktemp -d -t singtmp.XXXXXX)
+	tmpdir=$(mktemp -d -t singtmp.XXXXXX)
 fi
 
 # To know what base would need to be mounted within docker
@@ -103,6 +118,8 @@ trap 'rm -fr "$tmpdir" && info "removed temp dir $tmpdir"' exit
 
 pass_git_config "user.name" "ReproNim User"
 pass_git_config "user.email" "[email protected]"
+# only if set - pass pidlock so we could operate on NFS mounts, like on rolando
+pass_git_config "annex.pidlock"
 
 # Common arguments for the singularity run
 SARGS=( -e -B "$PWD" -H "$BHOME" --pwd "$PWD" "$@" )

scripts/tests/test_singularity_cmd.bats

@@ -1,4 +1,6 @@
 #!/usr/bin/env bats
+#emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: t -*-
+#ex: set sts=4 ts=4 sw=4 noet:
 #
 # This test uses the Bash Automated Testing System
 # See: https://github.com/bats-core/bats-core
@@ -22,6 +24,7 @@ cd "$BATS_TEST_DIRNAME"
 git annex get "$arg_test_img"
 
 
+# bats test_tags=docker
 @test "verifying arguments passed to singularity_cmd Docker shim" {
 	pull_singularity_shim
 
@@ -41,22 +44,26 @@ git annex get "$arg_test_img"
 }
 
 
+# bats test_tags=docker
 @test "verifying ability to singularity exec under /tmp subdir" {
 	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
 	check_subdir "$(_mktemp_dir_under /tmp)"
 }
 
+# bats test_tags=docker
 @test "verifying ability to singularity exec under /tmp subdir (explicit use of docker)" {
 	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
 	export REPRONIM_USE_DOCKER=1
 	check_subdir "$(_mktemp_dir_under /tmp)"
 }
 
+# bats test_tags=docker
 @test "verifying ability to singularity exec under $HOME subdir" {
 	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
 	check_subdir "$(_mktemp_dir_under $HOME)"
 }
 
+# bats test_tags=docker
 @test "verifying ability to singularity exec under $HOME subdir (explicit use of docker)" {
 	skip_if_travis_osx "skipping Singularity directory test on Travis OSX"
 	export REPRONIM_USE_DOCKER=1