Merge branch 'rel/2.6.2' into 'v2.6'

Rel/2.6.2

See merge request fsl/fslpy!170

.ci/test_template.sh

@@ -9,7 +9,7 @@ set -e
 # which gitlab CE does not currently do for us.
 if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
   git fetch upstream;
-  git merge --no-commit --no-ff upstream/master;
+  git merge --no-commit --no-ff -s recursive -X ours upstream/master;
 fi;
 
 source /test.venv/bin/activate

CHANGELOG.rst

@@ -2,6 +2,21 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+2.6.2 (Monday 7th October 2019)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Added a debugging hook in the :mod:`.idle` module.
+* The :func:`.fslsub.submit` function is now more flexible in the way it
+  accepts the command and input arguments.
+* The :func:`.run.prepareArgs` function has been renamed (from
+  ``_prepareArgs``).
+
+
 2.6.1 (Thursday 19th September 2019)
 ------------------------------------
 

doc/conf.py

@@ -62,7 +62,7 @@ copyright = u'{}, Paul McCarthy, University of Oxford, Oxford, UK'.format(
 # Links to other things
 rst_epilog = """
 .. |fsleyes_apidoc| replace:: FSLeyes
-.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes_apidoc/index.html
+.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/index.html
 """
 
 

doc/index.rst

@@ -4,7 +4,23 @@
 
 
 The ``fslpy`` package is a collection of utilities and data abstractions used
-by |fsleyes_apidoc|_.
+within `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki>`_ and by
+|fsleyes_apidoc|_.
+
+
+The top-level Python package for ``fslpy`` is called ``fsl``.  It is broadly
+split into the following sub-packages:
+
+
+.. autosummary::
+
+   fsl.data
+   fsl.utils
+   fsl.scripts
+   fsl.transform
+   fsl.version
+   fsl.wrappers
+
 
 .. toctree::
    :hidden:

fsl/utils/fslsub.py

@@ -55,7 +55,7 @@ import importlib
 log = logging.getLogger(__name__)
 
 
-def submit(command,
+def submit(*command,
            minutes=None,
            queue=None,
            architecture=None,
@@ -70,9 +70,12 @@ def submit(command,
            flags=False,
            multi_threaded=None,
            verbose=False):
-    """Submits a given command to the cluster
+    """
+    Submits a given command to the cluster
+
+    You can pass the command and arguments as a single string, or as a regular or unpacked sequence.
 
-    :arg command:        single string with the job command
+    :arg command:        string or regular/unpacked sequence of strings with the job command
     :arg minutes:        Estimated job length in minutes, used to auto-set
                          queue name
     :arg queue:          Explicitly sets the queue name
@@ -101,7 +104,7 @@ def submit(command,
     :return:             string of submitted job id
     """
 
-    from fsl.utils.run import runfsl
+    from fsl.utils.run import runfsl, prepareArgs
 
     base_cmd = ['fsl_sub']
 
@@ -132,7 +135,7 @@ def submit(command,
         base_cmd.append('-s')
         base_cmd.extend(multi_threaded)
 
-    base_cmd.append(command)
+    base_cmd.extend(prepareArgs(command))
 
     return runfsl(*base_cmd).strip()
 

fsl/utils/idle.py

@@ -196,6 +196,13 @@ _idleCallRate = 200
 """
 
 
+_idleAllowErrors = False
+"""Used for testing/debugging. If ``True``, and a function called on the idle
+loop raises an error, that error will not be caught, and the idle loop will
+stop.
+"""
+
+
 def idleReset():
     """Reset the internal :func:`idle` queue state.
 
@@ -211,6 +218,7 @@ def idleReset():
     global _idleQueueDict
     global _idleTimer
     global _idleCallRate
+    global _idleAllowErrors
 
     if _idleTimer is not None:
         _idleTimer.Stop()
@@ -221,11 +229,12 @@ def idleReset():
     if queue is not None: newQueue = queue.Queue()
     else:                 newQueue = None
 
-    _idleRegistered = False
-    _idleQueue      = newQueue
-    _idleQueueDict  = {}
-    _idleTimer      = None
-    _idleCallRate   = 200
+    _idleRegistered  = False
+    _idleQueue       = newQueue
+    _idleQueueDict   = {}
+    _idleTimer       = None
+    _idleCallRate    = 200
+    _idleAllowErrors = False
 
 
 # Call idleReset on exit, in
@@ -294,6 +303,7 @@ def _wxIdleLoop(ev):
     global _idleQueueDict
     global _idleTimer
     global _idleCallRate
+    global _idleAllowErrors
 
     ev.Skip()
 
@@ -342,6 +352,9 @@ def _wxIdleLoop(ev):
             log.warning('Idle task {} crashed - {}: {}'.format(
                 taskName, type(e).__name__, str(e)), exc_info=True)
 
+            if _idleAllowErrors:
+                raise e
+
         if task.name is not None:
             try:             _idleQueueDict.pop(task.name)
             except KeyError: pass

fsl/utils/run.py

@@ -72,7 +72,7 @@ def dryrun(*args):
         DRY_RUN = oldval
 
 
-def _prepareArgs(args):
+def prepareArgs(args):
     """Used by the :func:`run` function. Ensures that the given arguments is a
     list of strings.
     """
@@ -179,7 +179,7 @@ def run(*args, **kwargs):
     logStdout      = log   .get('stdout',   None)
     logStderr      = log   .get('stderr',   None)
     logCmd         = log   .get('cmd',      None)
-    args           = _prepareArgs(args)
+    args           = prepareArgs(args)
 
     if not bool(submit):
         submit = None
@@ -345,7 +345,7 @@ def runfsl(*args, **kwargs):
     if not prefixes:
         raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
 
-    args = _prepareArgs(args)
+    args = prepareArgs(args)
     for prefix in prefixes:
         cmdpath = op.join(prefix, args[0])
         if op.isfile(cmdpath):

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '2.6.1'
+__version__ = '2.6.2'
 """Current version number, as a string. """