Merge branch 'mnt/v3.3/recover' into 'v3.3'

Mnt/v3.3/recover

See merge request fsl/fslpy!259

CHANGELOG.rst

 This document contains the ``fslpy`` release history in reverse chronological
 order.
 
+
+3.3.3 (Wednesday 13th October 2020)
+-----------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fileOrImage` (and related) decorators will not manipulate the
+  return value of a decorated function if an argument ``cmdonly=True`` is
+  passed. This is so that wrapper functions will directly return the command
+  that would be executed when ``cmdonly=True``.
+
+
+3.3.2 (Tuesday 12th October 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Most :func:`.wrapper` functions now accept an argument called ``cmdonly``
+  which, if ``True``, will cause the generated command-line call to be
+  returned, instead of executed.
+
+
 3.3.1 (Thursday 8th October 2020)
 ---------------------------------
 

fsl/utils/run.py

@@ -151,6 +151,10 @@ def run(*args, **kwargs):
                    the :func:`.fslsub.submit` function.  May also be a
                    dictionary containing arguments to that function.
 
+    :arg cmdonly:  Defaults to ``False``. If ``True``, the command is not
+                   executed, but rather is returned directly, as a list of
+                   arguments.
+
     :arg log:      Must be passed as a keyword argument.  An optional ``dict``
                    which may be used to redirect the command's standard output
                    and error. The following keys are recognised:
@@ -181,6 +185,7 @@ def run(*args, **kwargs):
     returnStderr   = kwargs.pop('stderr',   False)
     returnExitcode = kwargs.pop('exitcode', False)
     submit         = kwargs.pop('submit',   {})
+    cmdonly        = kwargs.pop('cmdonly',  False)
     log            = kwargs.pop('log',      None)
     args           = prepareArgs(args)
 
@@ -207,6 +212,9 @@ def run(*args, **kwargs):
         raise ValueError('submit must be a mapping containing '
                          'options for fsl.utils.fslsub.submit')
 
+    if cmdonly:
+        return args
+
     if DRY_RUN:
         return _dryrun(
             submit, returnStdout, returnStderr, returnExitcode, *args)

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.3.1'
+__version__ = '3.3.3'
 """Current version number, as a string. """
 
 

fsl/wrappers/wrapperutils.py

@@ -149,46 +149,73 @@ def _unwrap(func):
     return func
 
 
-def cmdwrapper(func):
-    """This decorator can be used on functions which generate a command line.
-    It will pass the return value of the function to the
-    :func:`fsl.utils.run.run` function in a standardised manner.
+def genxwrapper(func, runner):
+    """This function is used by :func:`cmdwrapper` and :func:`fslwrapper`.
+    It is not intended to be used in any other circumstances.
+
+    This function generates a wrapper function which calls ``func`` to
+    generate a command-line call, and then uses ``runner`` to invoke that
+    command.
+
+    ``func`` is assumed to be a wrapper function which generates a command-
+    line. ``runner`` is assumed to be Either :func:`.run.run` or
+    :func:`.run.runfsl`.
+
+    The generated wrapper function will pass all of its arguments to ``func``,
+    and will then pass the generated command-line to ``runner``, returning
+    whatever is returned.
+
+    The following keyword arguments will be intercepted by the wrapper
+    function, and will *not* be passed to ``func``:
+      - ``stdout``:   Passed to ``runner``. Defaults to ``True``.
+      - ``stderr``:   Passed to ``runner``. Defaults to ``True``.
+      - ``exitcode``: Passed to ``runner``. Defaults to ``False``.
+      - ``submit``:   Passed to ``runner``. Defaults to ``None``.
+      - ``log``:      Passed to ``runner``. Defaults to ``{'tee':True}``.
+      - ``cmdonly``:  Passed to ``runner``. Defaults to ``False``.
+
+    :arg func:   A function which generates a command line.
+    :arg runner: Either :func:`.run.run` or :func:`.run.runfsl`.
     """
+
     def wrapper(*args, **kwargs):
         stdout   = kwargs.pop('stdout',   True)
         stderr   = kwargs.pop('stderr',   True)
         exitcode = kwargs.pop('exitcode', False)
         submit   = kwargs.pop('submit',   None)
+        cmdonly  = kwargs.pop('cmdonly',  False)
         log      = kwargs.pop('log',      {'tee' : True})
         cmd      = func(*args, **kwargs)
-        return run.run(cmd,
-                       stderr=stderr,
-                       log=log,
-                       submit=submit,
-                       stdout=stdout,
-                       exitcode=exitcode)
+
+        return runner(cmd,
+                      stderr=stderr,
+                      log=log,
+                      submit=submit,
+                      cmdonly=cmdonly,
+                      stdout=stdout,
+                      exitcode=exitcode)
+
     return _update_wrapper(wrapper, func)
 
 
+def cmdwrapper(func):
+    """This decorator can be used on functions which generate a command line.
+    It will pass the return value of the function to the
+    :func:`fsl.utils.run.run` function in a standardised manner.
+
+    See the :func:`genxwrapper` function for details.
+    """
+    return genxwrapper(func, run.run)
+
+
 def fslwrapper(func):
     """This decorator can be used on functions which generate a FSL command
     line. It will pass the return value of the function to the
     :func:`fsl.utils.run.runfsl` function in a standardised manner.
+
+    See the :func:`genxwrapper` function for details.
     """
-    def wrapper(*args, **kwargs):
-        stdout   = kwargs.pop('stdout',   True)
-        stderr   = kwargs.pop('stderr',   True)
-        exitcode = kwargs.pop('exitcode', False)
-        submit   = kwargs.pop('submit',   None)
-        log      = kwargs.pop('log',      {'tee' : True})
-        cmd      = func(*args, **kwargs)
-        return run.runfsl(cmd,
-                          stderr=stderr,
-                          log=log,
-                          submit=submit,
-                          stdout=stdout,
-                          exitcode=exitcode)
-    return _update_wrapper(wrapper, func)
+    return genxwrapper(func, run.runfsl)
 
 
 SHOW_IF_TRUE = object()
@@ -455,25 +482,27 @@ class FileOrThing(object):
     the dictionary.
 
 
-    **Cluster submission**
-
+    **Exceptions**
 
-    The above description holds in all situations, except when an argument
-    called ``submit`` is passed, and is set to a value which evaluates to
-    ``True``. In this case, the ``FileOrThing`` decorator will pass all
-    arguments straight through to the decorated function, and will return its
-    return value unchanged.
 
+    The above description holds in all situations, except when arguments called
+    ``submit`` and/or ``cmdonly`` are passed, and are set to values which
+    evaluate to ``True``. In this case, the ``FileOrThing`` decorator will pass
+    all arguments straight through to the decorated function, and will return
+    its return value unchanged.
 
     This is because most functions that are decorated with the
     :func:`fileOrImage` or :func:`fileOrArray` decorators will invoke a call
-    to :func:`.run.run` or :func:`.runfsl`, where a value of ``submit=True``
-    will cause the command to be executed asynchronously on a cluster
-    platform.
+    to :func:`.run.run` or :func:`.runfsl`, where:
 
+      - a value of ``submit=True`` will cause the command to be executed
+        asynchronously on a cluster platform.
+      - a value of ``cmdonly=True`` will cause the command to *not* be executed,
+        but instead the command that would have been executed is returned.
 
     A :exc:`ValueError` will be raised if the decorated function is called
-    with ``submit=True``, and with any in-memory objects or ``LOAD`` symbols.
+    with ``submit=True`` and/or ``cmdonly=True``, and with any in-memory
+    objects or ``LOAD`` symbols.
 
 
     **Example**
@@ -657,9 +686,11 @@ class FileOrThing(object):
 
         # Special case - if fsl.utils.run[fsl] is
         # being decorated (e.g. via cmdwrapper/
-        # fslwrapper), and submit=True, this call
-        # will ultimately submit the job to the
-        # cluster, and will return immediately.
+        # fslwrapper), and submit=True or
+        # cmdonly=True, this call will ultimately
+        # submit the job to the cluster, or will
+        # return the command that would have been
+        # executed, and will return immediately.
         #
         # We error if we are given any in-memory
         # things, or LOAD symbols.
@@ -667,7 +698,8 @@ class FileOrThing(object):
         # n.b. testing values to be strings could
         # interfere with the fileOrText decorator.
         # Possible solution is to use pathlib?
-        if kwargs.get('submit', False):
+        if kwargs.get('submit',  False) or \
+           kwargs.get('cmdonly', False):
             allargs = {**dict(zip(argnames, args)), **kwargs}
             for name, val in allargs.items():
                 if (name in self.__things) and \

tests/test_run.py

@@ -179,6 +179,13 @@ def test_run_passthrough():
         assert run.run('./script.sh', env=env) == expstdout
 
 
+def test_cmdonly():
+    assert run.run('script.sh',        cmdonly=True) == ['script.sh']
+    assert run.run('script.sh 1 2 3',  cmdonly=True) == ['script.sh', '1', '2', '3']
+    assert run.run(['script.sh'],      cmdonly=True) == ['script.sh']
+    assert run.run(['script.sh', '1'], cmdonly=True) == ['script.sh', '1']
+
+
 def test_dryrun():
 
     test_script = textwrap.dedent("""

tests/test_wrappers/test_wrapperutils.py

@@ -714,13 +714,15 @@ def test_fileOrThing_chained_outprefix():
         assert np.all(res['out_array'] == exparr)
 
 
-def test_fileOrThing_submit():
+def test_fileOrThing_submit_cmdonly():
 
     @wutils.fileOrImage('input', 'output')
-    def func(input, output, submit=False):
+    def func(input, output, submit=False, cmdonly=False):
 
         if submit:
             return 'submitted!'
+        if cmdonly:
+            return 'cmdonly!'
 
         img = nib.load(input)
         img = nib.nifti1.Nifti1Image(np.asanyarray(img.dataobj) * 2, np.eye(4))
@@ -735,7 +737,8 @@ def test_fileOrThing_submit():
         result = func(img, wutils.LOAD)
         assert np.all(np.asanyarray(result['output'].dataobj) == exp)
 
-        assert func('input.nii.gz', 'output.nii.gz', submit=True) == 'submitted!'
+        assert func('input.nii.gz', 'output.nii.gz', submit=True)  == 'submitted!'
+        assert func('input.nii.gz', 'output.nii.gz', cmdonly=True) == 'cmdonly!'
 
         with pytest.raises(ValueError):
             func(img, wutils.LOAD, submit=True)
@@ -753,15 +756,20 @@ def test_cmdwrapper():
     with run.dryrun():
         assert func(1, 2)[0] == 'func 1 2'
 
+    assert func(1, 2, cmdonly=True) == ['func', '1', '2']
+
 
 def test_fslwrapper():
     @wutils.fslwrapper
     def func(a, b):
         return ['func', str(a), str(b)]
 
-    with run.dryrun(), mockFSLDIR(bin=('func',)) as fsldir:
+    with mockFSLDIR(bin=('func',)) as fsldir:
         expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
-        assert func(1, 2)[0] == expected
+        with run.dryrun():
+            assert func(1, 2)[0] == expected
+
+        assert func(1, 2, cmdonly=True) == list(shlex.split(expected))
 
 
 _test_script = textwrap.dedent("""
@@ -835,3 +843,21 @@ def test_fslwrapper_submit():
 
         assert stdout.strip() == 'test_script running: 1 2'
         assert stderr.strip() == experr
+
+
+@pytest.mark.unixtest
+def test_cmdwrapper_fileorthing_cmdonly():
+
+    test_func = wutils.fileOrImage('a')(wutils.cmdwrapper(_test_script_func))
+    newpath   = op.pathsep.join(('.', os.environ['PATH']))
+    with tempdir.tempdir(), \
+         mock.patch.dict(os.environ, {'PATH' : newpath}):
+
+        with open('test_script', 'wt') as f:
+            f.write(_test_script)
+        os.chmod('test_script', 0o755)
+
+        ran = test_func('1', '2')
+        cmd = test_func('1', '2', cmdonly=True)
+        assert ran.stdout[0].strip() == 'test_script running: 1 2'
+        assert cmd                   == ['test_script', '1', '2']