Adding command for shell, uses execvp

CHANGELOG.md

@@ -17,6 +17,7 @@ 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)
+ - client should support shell (0.0.67)
  - adding test for entrypoint + cmd and fixing testing requirements (0.0.66)
  - fixing bug that inspect does not honor quiet (0.0.65)
  - refactor recipe parsers, writers, and base (0.0.64)

spython/main/__init__.py

@@ -26,7 +26,7 @@ def get_client(quiet=False, debug=False):
     # Do imports here, can be customized
     from .apps import apps
     from .build import build
-    from .execute import execute 
+    from .execute import (execute, shell) 
     from .help import helpcmd
     from .inspect import inspect
     from .instances import (list_instances, stopall) # global instance commands
@@ -44,6 +44,7 @@ def get_client(quiet=False, debug=False):
     client.inspect = inspect
     client.instances = list_instances
     client.run = run
+    client.shell = shell
     client.pull = pull
 
     # Command Groups, Images

spython/main/build.py

@@ -18,7 +18,7 @@ def build(self, recipe=None,
                 writable=False,
                 build_folder=None,
                 robot_name=False,
-                ext='simg',
+                ext='sif',
                 sudo=True,
                 stream=False,
                 force=False):

spython/main/execute.py

@@ -7,8 +7,12 @@
 
 
 from spython.logger import bot
-from spython.utils import stream_command
+from spython.utils import (
+    stream_command, 
+    which
+)
 
+import os
 
 def execute(self, 
             image=None, 
@@ -19,7 +23,9 @@ def execute(self,
             bind=None,
             stream=False,
             nv=False,
-            return_result=False):
+            return_result=False,
+            sudo=False,
+            quiet=True):
     ''' execute: send a command to a container
 
         Parameters
@@ -75,7 +81,6 @@ def execute(self,
         if app is not None:
             cmd = cmd + ['--app', app]
 
-        sudo = False
         if writable:
             sudo = True
 
@@ -87,7 +92,60 @@ def execute(self,
         if not stream:
             return self._run_command(cmd,
                                      sudo=sudo,
-                                     return_result=return_result)
+                                     return_result=return_result,
+                                     quiet=quiet)
         return stream_command(cmd, sudo=sudo)
 
     bot.error('Please include a command (list) to execute.')
+
+
+def shell(self, 
+          image, 
+          app=None,
+          writable=False,
+          contain=False,
+          bind=None,
+          nv=False,
+          sudo=False):
+    ''' shell into a container. A user is advised to use singularity to do
+        this directly, however this function is useful for supporting tools.
+
+        Parameters
+        ==========
+
+        image: full path to singularity image
+        app: if not None, execute a shell in context of an app
+        writable: This option makes the file system accessible as read/write
+        contain: This option disables the automatic sharing of writable
+                 filesystems on your host
+        bind: list or single string of bind paths.
+             This option allows you to map directories on your host system to
+             directories within your container using bind mounts
+        nv: if True, load Nvidia Drivers in runtime (default False)
+    '''
+    from spython.utils import check_install
+    check_install()
+
+    cmd = self._init_command('shell')
+
+    # nv option leverages any GPU cards
+    if nv:
+        cmd += ['--nv']
+
+    # Does the user want to use bind paths option?
+    if bind is not None:
+        cmd += self._generate_bind_list(bind)
+
+    # Does the user want to run an app?
+    if app is not None:
+        cmd = cmd + ['--app', app]
+
+    # Finally, add the image or uri
+    cmd.append(image)
+    singularity = which('singularity')
+
+    if writable or sudo:
+        os.execvp("sudo", ["sudo"] + cmd)
+
+    else:
+        os.execvp(singularity, cmd)

spython/main/instances.py

@@ -9,7 +9,7 @@
 from spython.logger import bot
 from spython.utils import run_command
 
-def list_instances(self, name=None, return_json=False, quiet=False):
+def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
     '''list instances. For Singularity, this is provided as a command sub
        group.
 
@@ -44,7 +44,7 @@ def list_instances(self, name=None, return_json=False, quiet=False):
     if name is not None:
         cmd.append(name)
 
-    output = run_command(cmd, quiet=True)
+    output = run_command(cmd, quiet=True, sudo=sudo)
     instances = []
 
     # Success, we have instances

spython/utils/__init__.py

@@ -10,12 +10,13 @@
 
 from .terminal import (
     check_install, 
+    format_container_name,
     get_installdir,
     get_singularity_version,
     get_singularity_version_info,
-    stream_command,
+    remove_uri,
     run_command,
-    format_container_name,
+    stream_command,
     split_uri,
-    remove_uri
+    which
 )

spython/utils/terminal.py

@@ -46,6 +46,14 @@ def check_install(software='singularity', quiet=True):
     return found
 
 
+def which(software='singularity'):
+    '''which returns the full path to where software is installed.
+    '''
+    cmd = ['which', software]
+    result = run_command(cmd, quiet=True)['message'][0]
+    return result.strip('\n')
+
+
 def get_singularity_version():
     '''get the full singularity client version as reported by 
        singularity --version [...]. For Singularity 3.x, this means:
@@ -173,8 +181,6 @@ def run_command(cmd,
 ################################################################################
 
 
-
-
 def format_container_name(name, special_characters=None):
     '''format_container_name will take a name supplied by the user,
     remove all special characters (except for those defined by "special-characters"

spython/version.py

@@ -6,7 +6,7 @@
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 
-__version__ = "0.0.66"
+__version__ = "0.0.67"
 AUTHOR = 'Vanessa Sochat'
 AUTHOR_EMAIL = 'vsochat@stanford.edu'
 NAME = 'spython'
@@ -21,6 +21,4 @@
 
 TESTS_REQUIRES = (
     ('pytest', {'min_version': '4.6.2'}),
-    ('pytest-cov', {'min_version': '2.5.1'}),
-    ('pytest-fixtures', {'min_version': '0.1.0'}),
 )