Fix/testing

.circleci/config.yml

@@ -0,0 +1,144 @@
+# CircleCI build config to test different versions of Singuarity
+version: 2.1
+
+orbs:
+  singularity: singularity/singularity@1.0.3
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - test-singularity-3-python-3:
+          filters:
+            branches:
+              ignore: master
+      - test-singularity-3-python-2:
+          filters:
+            branches:
+              ignore: master
+      - test-singularity-2-python-2:
+          filters:
+            branches:
+              ignore: master
+      - test-singularity-2-python-3:
+          filters:
+            branches:
+              ignore: master
+
+install_spython: &install_spython
+  name: install spython
+  command: |
+     $HOME/conda/bin/python setup.py install
+
+install_python_3: &install_python_3
+  name: install Python 3.5 dependencies
+  command: | 
+      ls $HOME
+      if [ ! -d "/home/circleci/conda" ]; then
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+          /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/conda
+          export PATH=$HOME/conda/bin:$PATH
+          $HOME/conda/bin/python setup.py install
+       else
+           echo "Miniconda 3 is already installed, continuing to build."
+       fi
+
+install_python_2: &install_python_2
+  name: install Python 3.5 dependencies
+  command: | 
+      ls $HOME
+      if [ ! -d "/home/circleci/conda" ]; then
+          wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
+          /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p $HOME/conda
+          export PATH=$HOME/conda/bin:$PATH
+          $HOME/conda/bin/python setup.py install
+       else
+           echo "Miniconda 2 is already installed, continuing to build."
+       fi
+
+test_spython: &test_spython
+  name: Test Singularity Python
+  command: |
+        cd ~/repo/spython
+        ls
+        export PATH=$PATH:/opt/circleci/.pyenv/shims
+        $HOME/conda/bin/python -m unittest tests.test_client
+        $HOME/conda/bin/python -m unittest tests.test_utils
+
+
+jobs:
+  test-singularity-3-python-3:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_3
+      - singularity/install-go:
+          go-version: 1.11.5
+      - singularity/debian-install-3:
+          singularity-version: 3.1.0
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython
+
+  test-singularity-3-python-2:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_2
+      - singularity/install-go:
+          go-version: 1.11.5
+      - singularity/debian-install-3:
+          singularity-version: 3.1.0
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython
+
+  test-singularity-2-python-3:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_3
+      - singularity/debian-install-2:
+          singularity-version: 2.6.1
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython
+
+  test-singularity-2-python-2:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_2
+      - singularity/debian-install-2:
+          singularity-version: 2.6.1
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython

CHANGELOG.md

@@ -17,6 +17,8 @@ The client here will eventually be released as "spython" (and eventually to
 singularity on pypi), and the versions here will coincide with these releases.
 
 ## [master](https://github.com/singularityhub/singularity-cli/tree/master)
+ - adding testing for 3.1.0 with Singularity Orbs (0.0.53)
+ - inspect returns parsed json on success, or full message / return code otherwise
  - instance stop all missing check for Singularity V3.+ (0.0.52)
  - fixing bug with instances list, name not taken into account (0.0.51)
  - additional of args to instance start commands (0.0.50)

spython/main/inspect.py

@@ -5,21 +5,26 @@
 # Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
+import json as jsonp
 
 from spython.logger import bot
+from spython.utils import ( 
+    check_install, 
+    get_singularity_version, 
+    run_command
+)
 
-def inspect(self,image=None, json=True, app=None):
+def inspect(self, image=None, json=True, app=None, quiet=True):
     '''inspect will show labels, defile, runscript, and tests for an image
 
-
        Parameters
        ==========
-       image_path: path of image to inspect
+       image: path of image to inspect
        json: print json instead of raw text (default True)
+       quiet: Don't print result to the screen (default True)
        app: if defined, return help in context of an app
 
     '''
-    from spython.utils import check_install
     check_install()
 
     # No image provided, default to use the client's loaded image
@@ -31,12 +36,57 @@ def inspect(self,image=None, json=True, app=None):
         cmd = cmd + ['--app', app]
 
     options = ['e','d','l','r','hf','t']
+
+    # After Singularity 3.0, helpfile was changed to H from
+
+    if "version 3" in get_singularity_version():
+        options = ['e','d','l','r','H','t']
+
     [cmd.append('-%s' % x) for x in options]
 
     if json is True:
         cmd.append('--json')
 
     cmd.append(image)
-    output = self._run_command(cmd)
-    #self.println(output,quiet=self.quiet)    
-    return output
+    result = run_command(cmd, quiet=False)
+
+    if result['return_code'] == 0:
+        result = jsonp.loads(result['message'][0])
+
+        # Fix up labels
+        labels = parse_labels(result)
+
+        if not quiet:
+            print(jsonp.dumps(result, indent=4))
+
+    return result
+
+
+def parse_labels(result):
+    '''fix up the labels, meaning parse to json if needed, and return
+       original updated object
+
+       Parameters
+       ==========
+       result: the json object to parse from inspect
+    '''
+
+    if "data" in result:
+        labels = result['data']['attributes'].get('labels') or {}
+
+    elif 'attributes' in result:
+        labels = result['attributes'].get('labels') or {}
+
+    # If labels included, try parsing to json
+
+    try:
+        labels = jsonp.loads(labels)
+    except:
+        pass
+
+    if "data" in result:
+        result['data']['attributes']['labels'] = labels
+    else:
+        result['attributes']['labels'] = labels
+
+    return result

spython/main/pull.py

@@ -7,7 +7,7 @@
 
 
 from spython.logger import bot
-from spython.utils import stream_command
+from spython.utils import ( stream_command, get_singularity_version )
 import os
 import re
 import shutil
@@ -44,6 +44,10 @@ def pull(self,
 
     cmd = self._init_command('pull')
 
+    # If Singularity version > 3.0, we have sif format
+    if 'version 3' in get_singularity_version():
+        ext = 'sif'
+
     # No image provided, default to use the client's loaded image
     if image is None:
         image = self._get_uri()
@@ -74,7 +78,14 @@ def pull(self,
 
     # Only add name if we aren't naming by hash or commit
     if not name_by_commit and not name_by_hash:
-        cmd = cmd + ["--name", name]
+
+        # Regression Singularity 3.* onward, PULLFOLDER not honored
+        # https://github.com/sylabs/singularity/issues/2788
+        if pull_folder and 'version 3' in get_singularity_version():
+            pull_folder_name = os.path.join(pull_folder, os.path.basename(name))
+            cmd = cmd + ["--name", pull_folder_name]          
+        else:
+            cmd = cmd + ["--name", name]
 
     if force is True:
         cmd = cmd + ["--force"]

spython/tests/test_client.py

@@ -31,10 +31,10 @@ def tearDown(self):
     def test_commands(self):
 
         print('Testing client.build command')
-        container = "%s/container.img" %(self.tmpdir)
+        container = "%s/container.sif" %(self.tmpdir)
 
         print("...Case 1: Build from docker uri")
-        created_container = self.cli.build('docker://ubuntu', 
+        created_container = self.cli.build('docker://busybox:1.30.1', 
                                            image=container,
                                            sudo=False)
         self.assertEqual(created_container, container)
@@ -56,24 +56,22 @@ def test_commands(self):
         os.remove(image)
 
         print("...Case 2: Testing docker pull")
-        container = self.cli.pull("docker://ubuntu:14.04",
+        container = self.cli.pull("docker://busybox:1.30.1",
                                    pull_folder=self.tmpdir)
-        self.assertTrue("ubuntu:14.04" in container)
+        self.assertTrue("busybox:1.30.1" in container)
 
         print(container)
         self.assertTrue(os.path.exists(container))
 
         print('Testing client.execute command')
         result = self.cli.execute(container,'ls /')
         print(result)
-        self.assertTrue('bin\nboot\ndev' in result)
+        self.assertTrue('tmp\nusr\nvar' in result)
 
         print("Testing client.inspect command")
-        result = self.cli.inspect(container)
-        labels = json.loads(result)
-        self.assertTrue('data' in labels)     
-        os.remove(container)
+        labels = self.cli.inspect(container)
 
+        os.remove(container)
 
 
 if __name__ == '__main__':

spython/version.py

@@ -6,7 +6,7 @@
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 
-__version__ = "0.0.52"
+__version__ = "0.0.53"
 AUTHOR = 'Vanessa Sochat'
 AUTHOR_EMAIL = 'vsochat@stanford.edu'
 NAME = 'spython'