From bc0c7431dd2c26caa126373f0323f47349d4e965 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 16 Nov 2023 10:56:50 +0000
Subject: [PATCH] BF: Wrong argument names to fsl_sub. Fix a few documentation
quirks
---
fsl/utils/filetree/__init__.py | 8 ++++++--
fsl/utils/run.py | 4 ++--
fsl/wrappers/__init__.py | 8 +++-----
3 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/fsl/utils/filetree/__init__.py b/fsl/utils/filetree/__init__.py
index 174b59cc6..636a4c7c2 100644
--- a/fsl/utils/filetree/__init__.py
+++ b/fsl/utils/filetree/__init__.py
@@ -1,5 +1,9 @@
-"""
-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.
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index e7feac04d..99187527d 100644
--- a/fsl/utils/run.py
+++ b/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)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 1458321ac..aa90bb456 100755
--- a/fsl/wrappers/__init__.py
+++ b/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
--
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