From 3b00f6f736ea9d8fcd27f0512a5cf6930f5854c4 Mon Sep 17 00:00:00 2001
From: Dustin Machi <dmachi@virginia.edu>
Date: Fri, 26 Jan 2024 07:43:37 -0500
Subject: [PATCH] Reworked app.run exit code (#73)

* allow run to return exit_code in non-interactive mode
* add tests for exit code from run.  Add variable substituion test for exec
* remove unneeded apptainer def
* bump version
* validate the substitution in test_exec.sh
---
 CHANGELOG.md            | 1 +
 docs/hello-world.scif   | 3 +++
 scif/main/commands.py   | 6 +++++-
 scif/tests/test_exec.sh | 8 ++++++++
 scif/tests/test_run.sh  | 2 ++
 scif/version.py         | 2 +-
 6 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cab15bc..4113356 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ represented by the pull requests that fixed them.
 Versions in parentheses coincide with what is available on [pypi](https://pypi.org/project/scif/).
 
 ## [xxx](https://github.com/vsoch/scif/tree/master) (master)
+ - (re)add exit code to app.run (0.0.84)
  - revert exit code to app.run until further notice (0.0.83)
  - add exit code to app.run (0.0.82)
  - install return value non zero should stop build (0.0.81)
diff --git a/docs/hello-world.scif b/docs/hello-world.scif
index 4ff54a4..18952f7 100644
--- a/docs/hello-world.scif
+++ b/docs/hello-world.scif
@@ -39,3 +39,6 @@
         fi
     echo "Argument supplied, exiting with ${1}"
     exit ${1}
+%apprun hello-world-exit-code
+  echo "Exiting with code 155"
+	exit 155
diff --git a/scif/main/commands.py b/scif/main/commands.py
index 739f725..d634896 100644
--- a/scif/main/commands.py
+++ b/scif/main/commands.py
@@ -89,11 +89,15 @@ def _exec(self, app=None, interactive=False, exit=False):
             os.system("".join(cmd))
 
     else:
-        for line in os.popen(cmd):
+        f = os.popen(cmd)
+        for line in f.readlines():
             try:
                 print(line.rstrip())
             except:
                 print(line.rstrip().encode(loc))
+        status = f.close()
+        if status:
+            sys.exit(os.waitstatus_to_exitcode(status))
 
 
 def execute(self, app, cmd=None, args=None):
diff --git a/scif/tests/test_exec.sh b/scif/tests/test_exec.sh
index d29123c..f105f8a 100755
--- a/scif/tests/test_exec.sh
+++ b/scif/tests/test_exec.sh
@@ -6,3 +6,11 @@ echo "Testing exec of commands:"
 docker run -it "${CONTAINER_NAME}" exec hello-world-echo echo "Hello World!"
 docker run -it "${CONTAINER_NAME}" exec hello-world-script ls /
 docker run -it "${CONTAINER_NAME}" exec hello-world-env env
+
+OUT=$(docker run -it "${CONTAINER_NAME}" --quiet exec hello-world-env echo [e]OMG | tr -d '\n\t\r ')
+if [ "$OUT" == "TACOS" ]; then
+   echo "Variable Substitution Success: $OUT"
+else
+   echo "Variable subsitution for e[OMG] failed"
+	 exit 1
+fi
diff --git a/scif/tests/test_run.sh b/scif/tests/test_run.sh
index 93e51e4..db1e539 100755
--- a/scif/tests/test_run.sh
+++ b/scif/tests/test_run.sh
@@ -7,3 +7,5 @@ docker run -it "${CONTAINER_NAME}" run hello-world-echo
 docker run -it "${CONTAINER_NAME}" run hello-world-script
 docker run -it "${CONTAINER_NAME}" run hello-world-custom "Meatball"
 docker run -it "${CONTAINER_NAME}" run hello-world-env | echo "Success"
+docker run -it "${CONTAINER_NAME}" run hello-world-exit-code ; echo "Exit code: $?  [should be 155]"
+docker run -it "${CONTAINER_NAME}" run hello-world-echo; echo "Exit code: $? [should be 0]"
diff --git a/scif/version.py b/scif/version.py
index 7b5bce5..0da7eed 100644
--- a/scif/version.py
+++ b/scif/version.py
@@ -10,7 +10,7 @@
 
 """
 
-__version__ = "0.0.83"
+__version__ = "0.0.84"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "vsochat@stanford.edu"
 NAME = "scif"