adding optio to remove image

Author: vsoch

singularity/analysis/classify.py

@@ -177,23 +177,23 @@ def get_tags(container=None,image_package=None,sudopw=None,search_folders=None,d
 ###################################################################################
 
 
-def get_files(container,S=None):
+def get_files(container,S=None,tmpdir=None):
     '''get_files will return a list of files inside a container, sorted by name
     :param container: the container to use, either shub:// or docker:// or actual
     '''
     files = None
-    tmpdir = tempfile.mkdtemp()
+    if tmpdir == None:
+        tmpdir = tempfile.mkdtemp()
     tmpfile = "%s/files.txt" %tmpdir
     container_name = remove_uri(container)
-    command = 'ls -LR >> %s 2>/dev/null' %(tmpfile)
+    command = ' ls -LR >> %s 2>/dev/null' %(tmpfile)
     if S==None:
         S = Singularity(sudo=None)
     result = S.execute(container,command)
     if os.path.exists(tmpfile):
         os.system("sed -i '/^$/d' %s" %(tmpfile))
         os.system('sort %s -or %s' %(tmpfile,tmpfile))
         files = read_file(tmpfile)
-        rootfs=None
         if len(files) > 0:
             files = [x for x in files if x.startswith('.')]
             files = [x.split(container_name)[1:] for x in files]

singularity/scripts.py

@@ -40,6 +40,11 @@ def get_parser():
                         help="package a singularity container for singularity hub", 
                         default=False, action='store_true')
 
+    # Does the user want to package an image?
+    parser.add_argument('--remove-image', dest="remove_image", 
+                        help="remove image file from the package", 
+                        default=False, action='store_true')
+
     # Does the user want to estimate the os?
     parser.add_argument('--os', dest="os", 
                         help="estimate the operating system of your container.", 
@@ -165,7 +170,8 @@ def main():
                package(image_path=image,
                        output_folder=output_folder,
                        runscript=True,
-                       software=True)
+                       software=True,
+                       remove_image=args.remove_image)
            else:
                print("Not sure what to do?")
                parser.print_help()