From 3ebae6b190612becd990d7b0a0dbe0e5efa08bed Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 20 Oct 2020 15:05:16 +0100
Subject: [PATCH] RF: when cmdonly is used with a wrapper function, assertions
are disabled
---
fsl/utils/assertions.py | 7 +++++--
fsl/wrappers/wrapperutils.py | 18 +++++++++++++-----
2 files changed, 18 insertions(+), 7 deletions(-)
diff --git a/fsl/utils/assertions.py b/fsl/utils/assertions.py
index b8e5a43b5..63b004d1f 100644
--- a/fsl/utils/assertions.py
+++ b/fsl/utils/assertions.py
@@ -39,14 +39,17 @@ _DISABLE_ASSERTIONS = False
@contextlib.contextmanager
-def disabled():
+def disabled(disable=True):
"""Context manager which allows assertion checks to be temporarily
disabled.
+
+ :arg disable: Set to ``True`` (the default) to disable assertions,
+ or ``False`` to enable them.
"""
global _DISABLE_ASSERTIONS
oldval = _DISABLE_ASSERTIONS
- _DISABLE_ASSERTIONS = True
+ _DISABLE_ASSERTIONS = disable
try:
yield
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 51f269bcb..ff6fcc06d 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -108,10 +108,11 @@ import six
import nibabel as nib
import numpy as np
-import fsl.utils.run as run
-import fsl.utils.path as fslpath
-import fsl.utils.tempdir as tempdir
-import fsl.data.image as fslimage
+import fsl.utils.run as run
+import fsl.utils.assertions as asrt
+import fsl.utils.path as fslpath
+import fsl.utils.tempdir as tempdir
+import fsl.data.image as fslimage
log = logging.getLogger(__name__)
@@ -185,7 +186,14 @@ def genxwrapper(func, runner):
submit = kwargs.pop('submit', None)
cmdonly = kwargs.pop('cmdonly', False)
log = kwargs.pop('log', {'tee' : True})
- cmd = func(*args, **kwargs)
+
+ # many wrapper functions use fsl.utils.assertions
+ # statements to check that input arguments are
+ # valid. Disable these if the cmdonly argument is
+ # being used to generate a command without running
+ # it.
+ with asrt.disabled(cmdonly):
+ cmd = func(*args, **kwargs)
return runner(cmd,
stderr=stderr,
--
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