From 114bf373ff8af9b1c5bbc85a397b8ec3c7a4df57 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Jun 2020 11:46:12 +0100
Subject: [PATCH] DOC: fixes
---
fsl/data/gifti.py | 1 +
fsl/data/image.py | 2 +-
fsl/utils/fslsub.py | 6 +++---
fsl/wrappers/wrapperutils.py | 1 +
4 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 7dc0eca30..d75c73a79 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -314,6 +314,7 @@ def relatedFiles(fname, ftypes=None):
This function assumes that the GIFTI files are named according to a
standard convention - the following conventions are supported:
+
- HCP-style, i.e.: ``<subject>.<hemi>.<type>.<space>.<ftype>.gii``
- BIDS-style, i.e.:
``<source_prefix>_hemi-<hemi>[_space-<space>]*_<suffix>.<ftype>.gii``
diff --git a/fsl/data/image.py b/fsl/data/image.py
index a12f39b12..ce01645b4 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1005,7 +1005,7 @@ class Image(Nifti):
:arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image
- object, or an ``Image``object.
+ object, or an ``Image`` object.
:arg name: A name for the image.
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index 30ffc0b72..3796110d6 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -63,7 +63,7 @@ class SubmitParams(object):
Any command line script can be submitted by the parameters by calling the `SubmitParams` object:
- .. codeblock:: python
+ .. code-block:: python
submit = SubmitParams(minutes=1, logdir='log', wait_for=['108023', '108019'])
submit('echo finished')
@@ -71,14 +71,14 @@ class SubmitParams(object):
This will run "echo finished" with a maximum runtime of 1 minute after the jobs with IDs 108023 and 108019 are finished.
It is the equivalent of
- .. codeblock:: bash
+ .. code-block:: bash
fsl_sub -T 1 -l log -j 108023,108019 "echo finished"
For python scripts that submit themselves to the cluster, it might be useful to give the user some control
over at least some of the submission parameters. This can be done using:
- .. codeblock:: python
+ .. code-block:: python
import argparse
parser = argparse.ArgumentParser("my script doing awesome stuff")
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 150ef0ae9..7a58c0231 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -606,6 +606,7 @@ class FileOrThing(object):
:arg load: Function which is called to load items for arguments
that were set to :data:`LOAD`. Must accept the
following arguments:
+
- the name of the argument
- path to the file to be loaded
--
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