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

@@ -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)

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

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):

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

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]"

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"