Merge branch 'bf/submit' into 'main'

BF: Fix bug in the `fsl.utils.run.hold` function

See merge request fsl/fslpy!426

CHANGELOG.rst

@@ -2,8 +2,8 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
-3.16.0 (Under development)
---------------------------
+3.15.3 (Thursday 16th November 2023)
+------------------------------------
 
 
 Changed
@@ -15,6 +15,12 @@ Changed
   noisy components (!424, !425).
 
 
+Fixed
+^^^^^
+
+* Fixed a bug in the :func:`.run.hold` function (!426).
+
+
 3.15.2 (Wednesday 4th October 2023)
 -----------------------------------
 

fsl/utils/filetree/__init__.py

-"""
-Easy format to define input/output files in a python pipeline.
+"""Easy format to define input/output files in a python pipeline.
+
+.. warning::
+    File-tree is now an independent Python library, and will eventually be
+    removed from ``fslpy`` - visit the `file-tree` :ref:`API documentation
+    <https://open.win.ox.ac.uk/pages/fsl/file-tree/>`_ for more details.
 
 The goal is to separate the definition of the input/output filenames from the actual code
 by defining a directory tree (i.e., FileTree) in a separate file from the code.

fsl/utils/run.py

@@ -632,8 +632,8 @@ def hold(job_ids, hold_filename=None, timeout=10):
 
     submit = {
         'jobhold'  : _flatten_job_ids(job_ids),
-        'minutes'  : 1,
-        'job_name' : '.hold'
+        'jobtime'  : 1,
+        'name'     : '.hold'
     }
 
     run(f'touch {hold_filename}', submit=submit)

fsl/wrappers/__init__.py

@@ -19,14 +19,12 @@ For example, you can call BET like so::
 If you would like a command to be submitted as a cluster job, all wrappers
 accept a ``submit`` keyword argument, which may be given a value of ``True``
 indicating that the job should be submitted with default settings, or a
-dictionary with submission settings::
+dictionary with submission settings, which will be passed through to the
+``fsl_sub`` command (run ``fsl_sub --help`` for details on all options)::
 
     from fsl.wrappers import fnirt
     fnirt('srf', 'ref', 'out', submit=True)
-    fnirt('srf', 'ref', 'out', submit={'queue' : 'long.q', 'ram' : '4GB'})
-
-
-See the :mod:`.fslsub` module for more details.
+    fnirt('srf', 'ref', 'out', submit={'queue' : 'long.q', 'jobram' : '4'})
 
 
 Most of these wrapper functions strive to provide an interface which is as