From 30184553c18b82a886ed9a4a1d88e2a6679dd98e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 16 Nov 2023 12:03:46 +0000
Subject: [PATCH] MNT: New 'silent' option to run function, which is equivalent
to passing log={'tee':false}. When calling run(..., submit=True), any log
argument is passed through to fsl_sub - this means that calling run(...,
submit=True, silent=True) will prevent the job ID from being printed
---
fsl/utils/run.py | 12 ++++++++----
fsl/wrappers/wrapperutils.py | 11 ++++++++++-
2 files changed, 18 insertions(+), 5 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 99187527d..04d382ff7 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -188,6 +188,9 @@ def run(*args, **kwargs):
- cmd: Optional file-like or callable to which
the command itself is logged.
+ :arg silent: Suppress standard output/error. Equivalent to passing
+ ``log={'tee' : False}``. Ignored if `log` is also passed.
+
All other keyword arguments are passed through to the ``subprocess.Popen``
object (via :func:`_realrun`), unless ``submit=True``, in which case they
are passed through to the :func:`.fsl_sub` function.
@@ -204,10 +207,11 @@ def run(*args, **kwargs):
submit = kwargs.pop('submit', {})
cmdonly = kwargs.pop('cmdonly', False)
logg = kwargs.pop('log', None)
+ silent = kwargs.pop('silent', False)
args = prepareArgs(args)
if logg is None:
- logg = {}
+ logg = {'tee' : not silent}
tee = logg.get('tee', True)
logStdout = logg.get('stdout', None)
@@ -237,7 +241,7 @@ def run(*args, **kwargs):
# but harmless, as we've popped the "submit" arg above.
if submit is not None:
from fsl.wrappers import fsl_sub # pylint: disable=import-outside-toplevel # noqa: E501
- return fsl_sub(*args, **submit, **kwargs)[0].strip()
+ return fsl_sub(*args, log=logg, **submit, **kwargs)[0].strip()
# Run directly - delegate to _realrun
stdout, stderr, exitcode = _realrun(
@@ -633,10 +637,10 @@ def hold(job_ids, hold_filename=None, timeout=10):
submit = {
'jobhold' : _flatten_job_ids(job_ids),
'jobtime' : 1,
- 'name' : '.hold'
+ 'name' : '.hold',
}
- run(f'touch {hold_filename}', submit=submit)
+ run(f'touch {hold_filename}', submit=submit, silent=True)
while not op.exists(hold_filename):
time.sleep(timeout)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 3fc318d2c..1a931de2a 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -193,7 +193,16 @@ def genxwrapper(func, runner, funccmd=False):
exitcode = kwargs.pop('exitcode', opts['exitcode'])
submit = kwargs.pop('submit', opts['submit'])
cmdonly = kwargs.pop('cmdonly', opts['cmdonly'])
- logg = kwargs.pop('log', opts['log'])
+ silent = kwargs.pop('silent', False)
+
+ # If silent=True, we need to explicitly set
+ # log, as the run function will otherwise
+ # ignore silent and preferentially use the
+ # value we pass for log.
+ if silent:
+ logg = kwargs.pop('log', {'tee' : False})
+ else:
+ logg = kwargs.pop('log', opts['log'])
if funccmd:
cmd = run.func_to_cmd(func, args=args, kwargs=kwargs,
--
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