Merge pull request #778 from UNFmontreal/fix/pre-commit-all

run pre-commit on all files to avoid unrelated errors in other PRs.

docs/container.rst

@@ -4,7 +4,7 @@ Using heudiconv in a Container
 
 If heudiconv is :ref:`installed via a Docker container <install_container>`, you
 can run the commands in the following format::
-   
+
     docker run nipy/heudiconv:latest [heudiconv options]
 
 So a user running via container would check the version with this command::
@@ -46,4 +46,3 @@ We typically recommend users make use of the following flags to Docker and Podma
 
 * ``-it`` Interactive terminal
 * ``--rm`` Remove the changes to the container when it completes
-

docs/custom-heuristic.rst

@@ -316,4 +316,3 @@ Suppose you want to use the values in the field ``image_type``?  It is not a num
 Note that this differs from testing for a string because you cannot test for any substring (e.g., 'TEST' would not work).  String tests will not work on a tuple datatype.
 
 .. Note:: *image_type* is described in the `DICOM specification <https://dicom.innolitics.com/ciods/mr-image/general-image/00080008>`_
-

docs/index.rst

@@ -19,4 +19,3 @@ Contents
    commandline
    container
    api
-

docs/quickstart.rst

@@ -3,15 +3,15 @@ Quickstart
 
 This tutorial is based on `Dianne Patterson's University of Arizona tutorials <https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html#lesson-3-reproin-py>`_
 
-This guide assumes you have already :ref:`installed heudiconv and dcm2niix <install_local>` and 
+This guide assumes you have already :ref:`installed heudiconv and dcm2niix <install_local>` and
 demonstrates how to use the heudiconv tool with a provided `heuristic.py` to convert DICOMS into the BIDS data structure.
 
 .. _prepare_dataset:
 
 Prepare Dataset
 ***************
 
-Download and unzip `sub-219_dicom.zip <https://datasets.datalad.org/?dir=/repronim/heudiconv-tutorial-example/>`_. 
+Download and unzip `sub-219_dicom.zip <https://datasets.datalad.org/?dir=/repronim/heudiconv-tutorial-example/>`_.
 
 We will be working from a directory called MRIS. Under the MRIS directory is the *dicom* subdirectory: Under the subject number *219* the session *itbs* is nested.  Each dicom sequence folder is nested under the session::
 
@@ -29,7 +29,7 @@ We will be working from a directory called MRIS. Under the MRIS directory is the
             ├── field_mapping_21
             └── restingstate_18
     Nifti
-    └── code 
+    └── code
         └── heuristic1.py
 
 Basic Conversion
@@ -57,36 +57,36 @@ Run the following command::
 
 Output
 ******
-    
+
 The *Nifti* directory will contain a bids-compliant subject directory::
-    
-    
+
+
         └── sub-219
             └── ses-itbs
                 ├── anat
                 ├── dwi
                 ├── fmap
                 └── func
-    
+
 The following required BIDS text files are also created in the Nifti directory. Details for filling in these skeleton text files can be found under `tabular files <https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files>`_ in the BIDS specification::
-    
+
         CHANGES
         README
         dataset_description.json
         participants.json
         participants.tsv
         task-rest_bold.json
-    
+
 Validation
 **********
 
-Ensure that everything is according to spec by using `bids validator <https://bids-standard.github.io/bids-validator/>`_ 
+Ensure that everything is according to spec by using `bids validator <https://bids-standard.github.io/bids-validator/>`_
 
 Click `Choose File` and then select the *Nifti* directory.  There should be no errors (though there are a couple of warnings).
-    
+
       .. Note:: Your files are not uploaded to the BIDS validator, so there are no privacy concerns!
-    
-Next 
+
+Next
 ****
 
 In the following sections, you will modify *heuristic.py* yourself so you can test different options and understand how to work with your own data.