updates

Author: vsoch

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 Vanessa Sochat
+Copyright (c) 2016-2017 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

singularity/__init__.py

@@ -1,3 +1,29 @@
+'''
+
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+'''
+
 from singularity.version import __version__
 
 __all__ = ['analysis', 'build', 'views', 'api',

singularity/analysis/classify.py

@@ -4,6 +4,28 @@
 classify.py: part of singularity package
 functions to tag and classify images
 
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 '''
 
 from glob import glob
@@ -66,6 +88,7 @@ def get_diff(container=None,image_package=None,sudopw=None):
     similar_package = "%s/docker-os/%s.img.zip" %(get_package_base(),most_similar)
 
     comparison = compare_containers(image_package1=image_package,
+                                    container1=container,
                                     image_package2=similar_package,
                                     by='files.txt')['files.txt']
 

singularity/app.py

@@ -1,3 +1,29 @@
+'''
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+'''
+
+
 from singularity.views.trees import (
     container_tree, 
     container_similarity,

singularity/cli.py

@@ -5,6 +5,28 @@
 
 Last updated: Singularity version 2.1
 
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 '''
 
 from singularity.utils import (

singularity/package.py

@@ -3,6 +3,28 @@
 '''
 package.py: part of singularity package
 
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 '''
 
 from singularity.logman import bot
@@ -18,8 +40,8 @@
 from singularity.reproduce import (
     get_image_hash,
     get_image_hashes,
-    get_memory_tar
-
+    get_memory_tar,
+    extract_content
 )
 import tempfile
 import tarfile
@@ -146,22 +168,20 @@ def package(image_path,spec_path=None,output_folder=None,runscript=True,
         to_package = {"files":[image_path]}
 
     # If the specfile is provided, it should also be packaged
-    if spec_path != None:
+    if spec_path is not None:
         singularity_spec = "".join(read_file(spec_path))
         to_package['Singularity'] = singularity_spec
 
-    # Package the image with an sha1, replication standard,  as VERSION
+    # Package the image with an sha1, identical standard, as VERSION
     hashes = get_image_hashes(image_path)
     to_package["VERSION"] = hashes['REPLICATE']
     to_package["HASHES"] = hashes
+
     # Look for runscript
 
-    if runscript == True:
+    if runscript is True:
         try:
-            runscript_member = tar.getmember("./singularity")
-            runscript_file = tar.extractfile("./singularity")
-            runscript = runscript_file.read()
-            to_package["runscript"] = runscript
+            to_package["runscript"] = extract_content(image_path,'./singularity',cli=S)
             bot.logger.debug("Found runscript.")
         except KeyError:
             bot.logger.warning("No runscript found")

singularity/scripts.py

@@ -4,13 +4,37 @@
 script.py: part of singularity command line tool
 Runtime executable, "shub"
 
+The MIT License (MIT)
+
+Copyright (c) 2016-2017 Vanessa Sochat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 '''
 
 from glob import glob
+import singularity
 import argparse
 import sys
 import os
 
+
 def get_parser():
     parser = argparse.ArgumentParser(
     description="Singularity Hub command line tool")
@@ -20,6 +44,10 @@ def get_parser():
                         help="full path to singularity image (for use with --package and --tree)", 
                         type=str, default=None)
 
+    parser.add_argument("--version", dest='version', 
+                        help="show software version", 
+                        default=False, action='store_true')
+
     # Two images, for similarity function
     parser.add_argument("--images", dest='images', 
                         help="images, separated by commas (for use with --simtree and --subtract", 
@@ -106,66 +134,70 @@ def main():
     os.environ['SINGULARITY_HUB'] = "False"
 
     # if environment logging variable not set, make silent
-    if args.debug == False:
+    if args.debug is False:
         os.environ['MESSAGELEVEL'] = "CRITICAL"
 
+    if args.version is True:
+        print(singularity.__version__)
+        sys.exit(0)
+
     # Initialize the message bot, with level above
     from singularity.logman import bot
     from singularity.utils import check_install
     from singularity.cli import get_image
 
     # Output folder will be pwd if not specified
-    if args.outfolder == None:
+    if args.outfolder is None:
         output_folder = os.getcwd()
     else:
         output_folder = args.outfolder
 
     # We can only continue if singularity is installed
-    if check_install() == True:
+    if check_install() is True:
 
        # If we are given an image, ensure full path
-       if args.image != None:
+       if args.image is not None:
 
            image,existed = get_image(args.image,
                                      return_existed=True,
                                      size=args.size)
 
-           if image == None:
+           if image is None:
                bot.logger.error("Cannot find image. Exiting.")
                sys.exit(1)
 
            # the user wants to make a tree
-           if args.tree == True:
+           if args.tree is True:
                from singularity.app import make_tree
                make_tree(image)
                clean_up(image,existed)
 
            # The user wants to estimate the os
-           elif args.os == True:
+           elif args.os is True:
                from singularity.analysis.classify import estimate_os
                estimated_os = estimate_os(container=image)
                print(estimated_os)
 
            # The user wants to get a list of all os
-           elif args.oscalc == True:
+           elif args.oscalc is True:
                from singularity.analysis.classify import estimate_os
                estimated_os = estimate_os(container=image,return_top=False)
                print(estimated_os["SCORE"].to_dict())
 
            # The user wants to get a list of tags
-           elif args.tags == True:
+           elif args.tags is True:
                from singularity.analysis.classify import get_tags
                tags = get_tags(container=image)
                print(tags)
 
            # The user wants to plot image vs. the docker os
-           elif args.osplot == True:
+           elif args.osplot is True:
                from singularity.app import plot_os_sims
                plot_os_sims(image)
                clean_up(image,existed)
 
            # The user wants to package the image
-           elif args.package == True:
+           elif args.package is True:
                from singularity.package import package
                remove_image = not args.include_image
                package(image_path=image,
@@ -178,7 +210,7 @@ def main():
                parser.print_help()
 
        # If we are given two image, we probably want a similar tree
-       elif args.images != None:
+       elif args.images is not None:
 
            image1,image2 = args.images.split(',')
            bot.logger.debug("Image1: %s",image1)
@@ -190,22 +222,21 @@ def main():
                                        return_existed=True,
                                        size=args.size)
 
-           if image1 == None or image2 == None:
+           if image1 is None or image2 is None:
                bot.logger.error("Cannot find image. Exiting.")
                sys.exit(1)
 
            # the user wants to make a similarity tree
-           if args.simtree == True:
+           if args.simtree is True:
                from singularity.app import make_sim_tree
                make_sim_tree(image1,image2)
 
            # the user wants to make a difference tree
-           if args.subtract == True:
+           if args.subtract is True:
                from singularity.app import make_diff_tree
                make_diff_tree(image1,image2)
 
-
-           if args.simcalc == True:
+           if args.simcalc is True:
                from singularity.analysis.compare import calculate_similarity
                score = calculate_similarity(image1,image2,by="files.txt")
                print(score["files.txt"])