spython.main package
Subpackages
Submodules
spython.main.apps module
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spython.main.apps.apps(self, image=None, full_path=False, root='')[source] 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. Note that this seems to be deprecated in Singularity 3.x.
Parameters: - full_path (if True, return relative to scif base folder)
- image_path (full path to the image)
spython.main.build module
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spython.main.build.build(self, recipe=None, image=None, isolated=False, sandbox=False, writable=False, build_folder=None, robot_name=False, ext='sif', sudo=True, stream=False, force=False, options=None, quiet=False, return_result=False, sudo_options=None, singularity_options=None)[source] build a singularity image, optionally for an isolated build (requires sudo). If you specify to stream, expect the image name and an iterator to be returned.
image, builder = Client.build(…)
Parameters: - recipe (the path to the recipe file (or source to build from). If not) – defined, we look for “Singularity” file in $PWD
- image (the image to build (if None, will use arbitrary name)
- isolated (if True, run build with –isolated flag)
- sandbox (if True, create a writable sandbox)
- writable (if True, use writable ext3 (sandbox takes preference))
- build_folder (where the container should be built.)
- ext (the image extension to use.)
- robot_name (boolean, default False. if you don’t give your image a) – name (with “image”) then a fun robot name will be generated instead. Highly recommended :)
- 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)
spython.main.execute module
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spython.main.execute.execute(self, image=None, command=None, app=None, writable=False, contain=False, bind=None, stream=False, nv=False, return_result=False, options=None, singularity_options=None, sudo=False, sudo_options=None, quiet=True, environ=None)[source] execute: send a command to a container
Parameters: - image (full path to singularity image)
- command (command to send to container)
- app (if not None, execute a command 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
- 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
- nv (if True, load Nvidia Drivers in runtime (default False))
- return_result (if True, return entire json object with return code) – and message result not (default)
- quiet (Do not print verbose output.)
- environ (extra environment to add.)
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spython.main.execute.shell(self, image, app=None, writable=False, contain=False, bind=None, nv=False, options=None, singularity_options=None, sudo=False, quiet=True)[source] 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
- 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
- nv (if True, load Nvidia Drivers in runtime (default False))
spython.main.help module
spython.main.inspect module
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spython.main.inspect.inspect(self, image=None, json=True, app=None, quiet=True, singularity_options=None)[source] inspect will show labels, defile, runscript, and tests for an image
Parameters: - 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)
- singularity_options (a list of options to provide to the singularity client)
spython.main.instances module
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spython.main.instances.list_instances(self, name=None, return_json=False, quiet=False, sudo=False, sudo_options=None, singularity_options=None)[source] list instances. For Singularity, this is provided as a command sub group.
singularity instance list
Return codes provided are different from standard linux: see https://github.com/singularityware/singularity/issues/1706 Since we expect json output, we don’t support older versions of Singularity.
Parameters: - 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
- 1 – No Instances, libexecdir value not found, functions file not found
- 255 – Couldn’t get UID
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spython.main.instances.stopall(self, sudo=False, quiet=True, singularity_options=None)[source] stop ALL instances. This command is only added to the command group as it doesn’t make sense to call from a single instance
Parameters: sudo (if the command should be done with sudo (exposes different set of) – instances)
spython.main.pull module
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spython.main.pull.pull(self, image=None, name=None, pull_folder='', ext='sif', force=False, capture=False, stream=False, quiet=False, singularity_options=None)[source] 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.
- Docker and Singularity Hub Naming
- ———————————
- name (a custom name to use, to override default)
- ext (if no name specified, the default extension to use.)
spython.main.run module
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spython.main.run.run(self, image=None, args=None, app=None, sudo=False, writable=False, contain=False, bind=None, stream=False, nv=False, options=None, singularity_options=None, return_result=False, quiet=False)[source] run will run the container, with or withour arguments (which should be provided in a list)
Parameters: - image (full path to singularity image)
- args (args to include with the run)
- app (if not None, execute a command in context of an app)
- writable (This option makes the file system accessible as read/write)
- options (an optional list of options to provide to run.)
- singularity_options (a list of options to provide to the singularity client)
- 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
- stream (if True, return <generator> for the user to run)
- nv (if True, load Nvidia Drivers in runtime (default False))
- return_result (if True, return entire json object with return code) – and message result (default is False)
- quiet (print the command to the user)