Merge pull request #68 from dmachi/master

exit with the exit code from a app when run()

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)
+ - return exit code of app in run command (0.0.82)
  - install return value non zero should stop build (0.0.81)
  - removing Python less than 3.6 support (0.0.80)
  - code formatting with black, shell entrypoint bug (0.0.79)

docs/examples/exit-from-run/README.md

@@ -0,0 +1,25 @@
+# Exit Code from run
+
+This should be built from the root of the repository as follows:
+
+```
+# apptainer build scif.sif docs/examples/exit-from-run/apptainer.def 
+```
+
+The force_fail app returns exit code 155
+```
+$ apptainer run scif.sif run force_fail ; echo "Exit Code: $?";
+[force_fail] executing /bin/bash /scif/apps/force_fail/scif/runscript
+Calling exit 155
+ERROR Return code 155
+Exit Code: 155
+```
+
+The 'success' app returns exit code 0
+
+```
+$ apptainer run scif.sif run success ; echo "Exit Code: $?";
+[success] executing /bin/bash /scif/apps/success/scif/runscript
+Running successfully
+Exit Code: 0
+```

docs/examples/exit-from-run/apptainer.def

@@ -0,0 +1,19 @@
+Bootstrap: docker
+From: continuumio/miniconda3
+
+# apptainer build scif.simg docs/examples/exit-from-run/apptainer.def
+
+%runscript
+    exec /opt/conda/bin/scif "$@"
+
+%files
+  docs/examples/exit-from-run/recipe.scif /recipe.scif
+  . /opt/scif
+%post
+    apt-get update && apt-get install -y git build-essential
+
+    # Install SCIF
+    cd /opt/scif
+    /opt/conda/bin/pip install setuptools
+    /opt/conda/bin/pip install .
+    scif install /recipe.scif

docs/examples/exit-from-run/recipe.scif

@@ -0,0 +1,7 @@
+%apprun force_fail
+echo "Calling exit 155"
+exit 155
+
+%apprun success
+echo "Running successfully"
+exit 0

scif/main/commands.py

@@ -87,13 +87,10 @@ def _exec(self, app=None, interactive=False, exit=False):
             sys.exit(result["return_code"])
         else:
             os.system("".join(cmd))
-
     else:
-        for line in os.popen(cmd):
-            try:
-                print(line.rstrip())
-            except:
-                print(line.rstrip().encode(loc))
+        cmd = cmd.split(" ")
+        result = self._run_command(cmd=cmd, spinner=False, quiet=False)
+        sys.exit(result["return_code"])
 
 
 def execute(self, app, cmd=None, args=None):
@@ -173,7 +170,6 @@ def run(self, app=None, args=None):
     # updates environment
     # sets entrypoint
     # sets entryfolder
-
     return self._exec(app, interactive=interactive)
 
 

scif/version.py

@@ -10,7 +10,7 @@
 
 """
 
-__version__ = "0.0.81"
+__version__ = "0.0.82"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "vsochat@stanford.edu"
 NAME = "scif"