adding flags (singularity_options) to init command

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)
+ - add singularity options parameters to send to singularity (0.0.79)
  - add support for library:// urls (0.0.78)
  - instance stop with timeout argument (0.0.77)
  - instance list includes ip address (0.0.76)

spython/image/cmd/create.py

@@ -9,21 +9,21 @@
 from spython.logger import bot
 
 
-def create(self, image_path, size=1024, sudo=False):
+def create(self, image_path, size=1024, sudo=False, singularity_options=None):
     """create will create a a new image
 
         Parameters
         ==========
         image_path: full path to image
         size: image sizein MiB, default is 1024MiB
         filesystem: supported file systems ext3/ext4 (ext[2/3]: default ext3
-
+        singularity_options: a list of options to provide to the singularity client
     """
     from spython.utils import check_install
 
     check_install()
 
-    cmd = self.init_command("image.create")
+    cmd = self.init_command("image.create", singularity_options)
     cmd = cmd + ["--size", str(size), image_path]
 
     output = self.run_command(cmd, sudo=sudo)

spython/instance/cmd/iutils.py

@@ -35,7 +35,7 @@ def parse_table(table_string, header, remove_rows=1):
     return parsed
 
 
-def get(self, name, return_json=False, quiet=False):
+def get(self, name, return_json=False, quiet=False, singularity_options=None):
     """get is a list for a single instance. It is assumed to be running,
        and we need to look up the PID, etc.
     """
@@ -49,7 +49,7 @@ def get(self, name, return_json=False, quiet=False):
     if "version 3" in self.version():
         subgroup = ["instance", "list"]
 
-    cmd = self._init_command(subgroup)
+    cmd = self._init_command(subgroup, singularity_options)
 
     cmd.append(name)
     output = self.run_command(cmd, quiet=True)

spython/instance/cmd/start.py

@@ -9,7 +9,14 @@
 
 
 def start(
-    self, image=None, name=None, args=None, sudo=False, options=None, capture=False
+    self,
+    image=None,
+    name=None,
+    args=None,
+    sudo=False,
+    options=None,
+    capture=False,
+    singularity_options=None,
 ):
     """start an instance. This is done by default when an instance is created.
 
@@ -20,6 +27,7 @@ def start(
        sudo: if the user wants to run the command with sudo
        capture: capture output, default is False. With True likely to hang.
        args: arguments to provide to the instance (supported Singularity 3.1+)
+       singularity_options: a list of options to provide to the singularity client
        options: a list of tuples, each an option to give to the start command
                 [("--bind", "/tmp"),...]
 
@@ -49,7 +57,7 @@ def start(
     if "version 3" in self.version():
         subgroup = ["instance", "start"]
 
-    cmd = self._init_command(subgroup)
+    cmd = self._init_command(subgroup, singularity_options)
 
     # Add options, if they are provided
     if not isinstance(options, list):

spython/instance/cmd/stop.py

@@ -8,13 +8,14 @@
 from spython.logger import bot
 
 
-def stop(self, name=None, sudo=False, timeout=None):
+def stop(self, name=None, sudo=False, timeout=None, singularity_options=None):
     """stop an instance. This is done by default when an instance is created.
 
        Parameters
        ==========
        name: a name for the instance
        sudo: if the user wants to run the command with sudo
+       singularity_options: a list of options to provide to the singularity client
        timeout: forcebly kill non-stopped instance after the
                 timeout specified in seconds
 
@@ -33,7 +34,7 @@ def stop(self, name=None, sudo=False, timeout=None):
         if timeout:
             subgroup += ["-t", str(timeout)]
 
-    cmd = self._init_command(subgroup)
+    cmd = self._init_command(subgroup, singularity_options)
 
     # If name is provided assume referencing an instance
     instance_name = self.name

spython/main/apps.py

@@ -10,7 +10,8 @@ def apps(self, image=None, full_path=False, root=""):
        return list of SCIF apps in image. The Singularity software serves
        a scientific filesystem integration that will install apps to
        /scif/apps and associated data to /scif/data. For more information 
-       about SCIF, see https://sci-f.github.io
+       about SCIF, see https://sci-f.github.io. Note that this seems
+       to be deprecated in Singularity 3.x.
 
        Parameters
        ==========

spython/main/base/command.py

@@ -20,13 +20,13 @@ def init_command(self, action, flags=None):
        Parameters
        ==========
        action: the main action to perform (e.g., build)
-       flags: one or more additional flags (e.g, volumes) 
-              not implemented yet.
+       flags: one or more additional singularity options
     """
+    flags = flags or []
 
     if not isinstance(action, list):
         action = [action]
-    cmd = ["singularity"] + action
+    cmd = ["singularity"] + flags + action
 
     if self.quiet:
         cmd.insert(1, "--quiet")

spython/main/build.py

@@ -28,6 +28,7 @@ def build(
     quiet=False,
     return_result=False,
     sudo_options=None,
+    singularity_options=None,
 ):
 
     """build a singularity image, optionally for an isolated build
@@ -53,18 +54,18 @@ def build(
        sudo: give sudo to the command (or not) default is True for build
        sudo_options: options to pass to sudo (e.g. --preserve-env=SINGULARITY_CACHEDIR,SINGULARITY_TMPDIR)
        options: for all other options, specify them in this list.   
+       singularity_options: a list of options to provide to the singularity client
        quiet: quiet verbose printing from the client.
        return_result: if True, return complete error code / message dictionary
     """
     from spython.utils import check_install
 
     check_install()
 
-    cmd = self._init_command("build")
+    cmd = self._init_command("build", singularity_options)
 
     # If no extra options
-    if not options:
-        options = []
+    options = options or []
 
     if "version 3" in self.version():
         ext = "sif"

spython/main/execute.py

@@ -23,6 +23,7 @@ def execute(
     nv=False,
     return_result=False,
     options=None,
+    singularity_options=None,
     sudo=False,
     quiet=True,
 ):
@@ -38,6 +39,7 @@ def execute(
         contain: This option disables the automatic sharing of writable
                  filesystems on your host
         options: an optional list of options to provide to execute.
+        singularity_options: a list of options to provide to the singularity client
         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
@@ -49,7 +51,7 @@ def execute(
 
     check_install()
 
-    cmd = self._init_command("exec")
+    cmd = self._init_command("exec", singularity_options)
 
     # nv option leverages any GPU cards
     if nv:
@@ -113,6 +115,7 @@ def shell(
     bind=None,
     nv=False,
     options=None,
+    singularity_options=None,
     sudo=False,
 ):
     """ shell into a container. A user is advised to use singularity to do
@@ -127,6 +130,7 @@ def shell(
         contain: This option disables the automatic sharing of writable
                  filesystems on your host
         options: an optional list of options to provide to shell.
+        singularity_options: a list of options to provide to the singularity client
         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
@@ -136,7 +140,7 @@ def shell(
 
     check_install()
 
-    cmd = self._init_command("shell")
+    cmd = self._init_command("shell", singularity_options)
 
     # nv option leverages any GPU cards
     if nv:

spython/main/export.py

@@ -11,7 +11,15 @@
 import os
 
 
-def export(self, image_path, pipe=False, output_file=None, command=None, sudo=False):
+def export(
+    self,
+    image_path,
+    pipe=False,
+    output_file=None,
+    command=None,
+    sudo=False,
+    singularity_options=None,
+):
 
     """export will export an image, sudo must be used. If we have Singularity
        versions after 3, export is replaced with building into a sandbox.
@@ -20,6 +28,7 @@ def export(self, image_path, pipe=False, output_file=None, command=None, sudo=Fa
        ==========
        image_path: full path to image
        pipe: export to pipe and not file (default, False)
+       singularity_options: a list of options to provide to the singularity client
        output_file: if pipe=False, export tar to this file. If not specified, 
        will generate temporary directory.
     """
@@ -39,19 +48,35 @@ def export(self, image_path, pipe=False, output_file=None, command=None, sudo=Fa
             output_file = self._get_filename(basename, "sandbox", pwd=False)
 
         return self.build(
-            recipe=image_path, image=output_file, sandbox=True, force=True, sudo=sudo
+            recipe=image_path,
+            image=output_file,
+            sandbox=True,
+            force=True,
+            sudo=sudo,
+            singularity_options=singularity_options,
         )
 
     # If not version 3, run deprecated command
     elif "2.5" in self.version():
         return self._export(
-            image_path=image_path, pipe=pipe, output_file=output_file, command=command
+            image_path=image_path,
+            pipe=pipe,
+            output_file=output_file,
+            command=command,
+            singularity_options=singularity_options,
         )
 
     bot.warning("Unsupported version of Singularity, %s" % self.version())
 
 
-def _export(self, image_path, pipe=False, output_file=None, command=None):
+def _export(
+    self,
+    image_path,
+    pipe=False,
+    output_file=None,
+    command=None,
+    singularity_options=None,
+):
     """ the older deprecated function, running export for previous
                versions of Singularity that support it
 
@@ -69,7 +94,7 @@ def _export(self, image_path, pipe=False, output_file=None, command=None):
 
     """
     sudo = True
-    cmd = self._init_command("export")
+    cmd = self._init_command("export", singularity_options)
 
     # If the user has specified export to pipe, we don't need a file
     if pipe:

spython/main/inspect.py

@@ -10,7 +10,9 @@
 from spython.utils import check_install, run_command
 
 
-def inspect(self, image=None, json=True, app=None, quiet=True):
+def inspect(
+    self, image=None, json=True, app=None, quiet=True, singularity_options=None
+):
     """inspect will show labels, defile, runscript, and tests for an image
 
        Parameters
@@ -19,6 +21,7 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
        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
+       singularity_options: a list of options to provide to the singularity client
 
     """
     check_install()
@@ -31,7 +34,7 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
     if not image:
         bot.exit("Please provide an image to inspect.")
 
-    cmd = self._init_command("inspect")
+    cmd = self._init_command("inspect", singularity_options)
     if app:
         cmd = cmd + ["--app", app]
 

spython/main/instances.py

@@ -9,7 +9,14 @@
 from spython.utils import run_command
 
 
-def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
+def list_instances(
+    self,
+    name=None,
+    return_json=False,
+    quiet=False,
+    sudo=False,
+    singularity_options=None,
+):
     """list instances. For Singularity, this is provided as a command sub
        group.
 
@@ -22,6 +29,7 @@ def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
        ==========
        return_json: return a json list of instances instead of objects (False)
        name: if defined, return the list for just one instance (used to ged pid)
+       singularity_options: a list of options to provide to the singularity client
 
        Return Code  --   Reason
        0 -- Instances Found
@@ -39,7 +47,7 @@ def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
     if "version 3" in self.version():
         subgroup = ["instance", "list"]
 
-    cmd = self._init_command(subgroup)
+    cmd = self._init_command(subgroup, singularity_options)
 
     # If the user has provided a name, we want to see a particular instance
     if name is not None:
@@ -103,7 +111,7 @@ def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
     return instances
 
 
-def stopall(self, sudo=False, quiet=True):
+def stopall(self, sudo=False, quiet=True, singularity_options=None):
     """stop ALL instances. This command is only added to the command group
        as it doesn't make sense to call from a single instance
 
@@ -122,7 +130,7 @@ def stopall(self, sudo=False, quiet=True):
     if "version 3" in self.version():
         subgroup = ["instance", "stop"]
 
-    cmd = self._init_command(subgroup)
+    cmd = self._init_command(subgroup, singularity_options)
     cmd = cmd + ["--all"]
     output = run_command(cmd, sudo=sudo, quiet=quiet)
 

spython/main/pull.py

@@ -21,13 +21,15 @@ def pull(
     capture=False,
     stream=False,
     quiet=False,
+    singularity_options=None,
 ):
 
     """pull will pull a singularity hub or Docker image
 
        Parameters
        ==========
        image: the complete image uri. If not provided, the client loaded is used
+       singularity_options: a list of options to provide to the singularity client
        pull_folder: if not defined, pulls to $PWD (''). If defined, pulls to
                     user specified location instead.
 
@@ -41,7 +43,7 @@ def pull(
 
     check_install()
 
-    cmd = self._init_command("pull")
+    cmd = self._init_command("pull", singularity_options)
 
     # Quiet is honored if set by the client, or user
     quiet = quiet or self.quiet