From adcd481ce1430e788a34e9badbb7d5145a23e703 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 20 Aug 2021 12:46:14 +0100
Subject: [PATCH] RF: fsl.utils.run now uses fsl.wrappers.fsl_sub instead of
fsl.utils.fslsub
---
fsl/utils/run.py | 37 ++++++++++++++++++++++---------------
1 file changed, 22 insertions(+), 15 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index a7e4971ba..f67103570 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -31,10 +31,10 @@ import os.path as op
import os
from fsl.utils.platform import platform as fslplatform
-import fsl.utils.fslsub as fslsub
import fsl.utils.tempdir as tempdir
import fsl.utils.path as fslpath
+
log = logging.getLogger(__name__)
@@ -146,7 +146,7 @@ def run(*args, **kwargs):
:arg submit: Must be passed as a keyword argument. Defaults to ``None``.
If ``True``, the command is submitted as a cluster job via
- the :func:`.fslsub.submit` function. May also be a
+ the :mod:`fsl.wrappers.fsl_sub` function. May also be a
dictionary containing arguments to that function.
:arg cmdonly: Defaults to ``False``. If ``True``, the command is not
@@ -173,10 +173,10 @@ def run(*args, **kwargs):
object (via :func:`_realrun`), unless ``submit=True``, in which case they
are passed through to the :func:`.fslsub.submit` function.
- :returns: If ``submit`` is provided, the return value of
- :func:`.fslsub` is returned. Otherwise returns a single
- value or a tuple, based on the based on the ``stdout``,
- ``stderr``, and ``exitcode`` arguments.
+ :returns: If ``submit`` is provided, the ID of the submitted job is
+ returned as a string. Otherwise returns a single value or a
+ tuple, based on the based on the ``stdout``, ``stderr``, and
+ ``exitcode`` arguments.
"""
returnStdout = kwargs.pop('stdout', True)
@@ -217,9 +217,12 @@ def run(*args, **kwargs):
return _dryrun(
submit, returnStdout, returnStderr, returnExitcode, *args)
- # submit - delegate to fslsub
+ # submit - delegate to fsl_sub. This will induce a nested
+ # call back to this run function, which is a bit confusing,
+ # but harmless, as we've popped the "submit" arg above.
if submit is not None:
- return fslsub.submit(' '.join(args), **submit, **kwargs)
+ from fsl.wrappers import fsl_sub # pylint: disable=import-outside-toplevel # noqa: E501
+ return fsl_sub(*args, **submit, **kwargs)[0].strip()
# Run directly - delegate to _realrun
stdout, stderr, exitcode = _realrun(
@@ -438,13 +441,17 @@ def wslcmd(cmdpath, *args):
def hold(job_ids, hold_filename=None):
- """
- Waits until all jobs have finished
+ """Waits until all jobs have finished
+
+ :param job_ids: possibly nested sequence of job ids. The job ids
+ themselves should be strings.
- :param job_ids: possibly nested sequence of job ids. The job ids themselves should be strings.
- :param hold_filename: filename to use as a hold file.
- The containing directory should exist, but the file itself should not.
- Defaults to a ./.<random characters>.hold in the current directory.
- :return: only returns when all the jobs have finished
+ :param hold_filename: filename to use as a hold file. The
+ containing directory should exist, but the
+ file itself should not. Defaults to a
+ ./.<random characters>.hold in the current
+ directory. :return: only returns when all
+ the jobs have finished
"""
+ import fsl.utils.fslsub as fslsub # pylint: disable=import-outside-toplevel # noqa: E501
fslsub.hold(job_ids, hold_filename)
--
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