From 46b6ff719416836a9ba5699ff894631e9b3adfb4 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 28 Feb 2018 13:12:22 +0000
Subject: [PATCH] New module fsl.utils.run, to replace fsl.utils.callfsl
---
fsl/utils/callfsl.py | 5 ++++
fsl/utils/run.py | 71 ++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 76 insertions(+)
create mode 100644 fsl/utils/run.py
diff --git a/fsl/utils/callfsl.py b/fsl/utils/callfsl.py
index d86856ebe..1f01d34f9 100644
--- a/fsl/utils/callfsl.py
+++ b/fsl/utils/callfsl.py
@@ -13,12 +13,17 @@ import logging
import subprocess as sp
import os.path as op
+import deprecation
+
from fsl.utils.platform import platform as fslplatform
log = logging.getLogger(__name__)
+@deprecation.deprecated(deprecated_in='1.7.0',
+ removed_in='2.0.0',
+ details='Use fsl.utils.run.runfsl instead')
def callFSL(*args):
"""Call a FSL command and return the result.
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
new file mode 100644
index 000000000..8ee484885
--- /dev/null
+++ b/fsl/utils/run.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+#
+# run.py - Functions for running shell commands
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module provides some functions for running shell commands.
+
+.. autosummary::
+ :nosignatures:
+
+ run
+ runfsl
+ fslsub
+"""
+
+
+import logging
+import subprocess as sp
+import os.path as op
+
+from fsl.utils.platform import platform as fslplatform
+
+
+log = logging.getLogger(__name__)
+
+
+def run(*args):
+ """Call a command and return its output. You can pass the command and
+ arguments as a single string, or as an unpacked sequence.
+ """
+
+ # If we've been given a single argument,
+ # assume it is a string containing the
+ # command and its arguments. Otherwise,
+ # assume it is a sequence containing
+ # separate command and arguments.
+ if len(args) == 1:
+ args = args[0].split()
+
+ args = list(args)
+
+ log.debug('run: {}'.format(' '.join(args)))
+
+ result = sp.check_output(args).decode('utf-8').strip()
+
+ log.debug('result: {}'.format(result))
+
+ return result
+
+
+def runfsl(*args):
+ """Call a FSL command and return its output. This function simply prepends
+ $FSLDIR/bin/ to the command before passing it to :func:`run`.
+ """
+
+ if fslplatform.fsldir is None:
+ raise RuntimeError('$FSLDIR is not set - FSL cannot be found!')
+
+ if len(args) == 1:
+ args = args[0].split()
+
+ args = list(args)
+ args[0] = op.join(fslplatform.fsldir, 'bin', args[0])
+
+ return run(*args)
+
+
+def fslsub(*args):
+ """Not implemented yet. """
+ raise NotImplementedError('')
--
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