README.md

@@ -14,7 +14,7 @@
 
 junifer is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
 
-It is curently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
+It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
 
 The documentation is available at [https://juaml.github.io/junifer](https://juaml.github.io/junifer/main/index.html).
 

docs/changes/newsfragments/230.misc

@@ -0,0 +1 @@
+Improve ``codespell`` support by fixing typos in documentation by `Synchon Mandal`_

docs/contribution.rst

@@ -13,7 +13,7 @@ Setting up the local development environment
    <https://guides.github.com/activities/forking/>`_.
 #. Clone your fork locally as described in the same guide but also add the
    flag to sync the submodules as well by appending the following to the
-   clone commmand:
+   clone command:
 
    .. code-block:: bash
 

docs/extending/datagrabber.rst

@@ -36,7 +36,7 @@ c. the experiment included resting-stage fMRI and a task named *stroop*
 then the *element* should be composed of 3 items:
 
 * ``subject``: The subject IDs, e.g. `sub001`, `sub002`, ... `sub020`
-* ``session``: The sesion number, e.g. `ses1`, `ses2`
+* ``session``: The session number, e.g. `ses1`, `ses2`
 * ``task``: The task performed, e.g. `rest`, `stroop`
 
 If any of these items were not part of the element, then we will have more than
@@ -98,7 +98,7 @@ Option A: Extending from PatternDataGrabber
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The :class:`.PatternDataGrabber` class is an abstract class that has the
-functionality of understanding patterns embeded in it.
+functionality of understanding patterns embedded in it.
 
 Before creating the datagrabber, we need to define 3 variables:
 
@@ -385,7 +385,7 @@ Step 4: Optional: Adding *BOLD confounds*
 For some analyses, it is useful to have the confounds associated with the BOLD
 data. This corresponds to the ``BOLD_confounds`` item in the
 :ref:`Data Object <data_object>` (see :ref:`data_types`). However, the
-``BOLD_confounds`` element does not only consists of a ``path``, but it requries
+``BOLD_confounds`` element does not only consists of a ``path``, but it requires
 more information about the format of the confounds file. Thus, the
 ``BOLD_confounds`` element is a dictionary with the following keys:
 

docs/extending/marker.rst

@@ -76,7 +76,7 @@ The parameters of the marker are defined in the ``__init__`` method. The
    are allowed as parameters. This is because the parameters are stored in
    JSON format, and JSON only supports these types.
 
-In this example, only paramater required for the computation is the name of the
+In this example, only parameter required for the computation is the name of the
 parcellation to use. Thus, we can define the ``__init__`` method as follows:
 
 .. code-block:: python
@@ -109,7 +109,7 @@ arguments:
 
 * ``input``: a dictionary with the data to be used to compute the marker. This
   will be the corresponding element in the :ref:`Data Object<data_object>`
-  alredy indexed. Thus, the dictionary has at least two keys: ``data`` and
+  already indexed. Thus, the dictionary has at least two keys: ``data`` and
   ``path``. The first one contains the data, while the second one contains the
   path to the data. The dictionary can also contain other keys, depending on the
   data type.

docs/help.rst

@@ -21,7 +21,7 @@ While the song might have been written with another meaning in mind, it is a goo
 way to describe the situation of many researchers who are presented with a new
 toolbox. Indeed, the situation of many researchers is that the projects they are
 working on are becoming more and more complex in terms of methods and data. Thus,
-we *open up the doors* to new possibilites:
+we *open up the doors* to new possibilities:
 
     | When I was younger, so much younger than today
     | I never needed anybody's help in any way

docs/index.rst

@@ -11,7 +11,7 @@ junifer (JUelich NeuroImaging FEature extractoR) is a data handling and feature
 extraction library targeted towards neuroimaging data specifically functional
 MRI data.
 
-It is curently being developed and maintained at the Applied Machine Learning
+It is currently being developed and maintained at the Applied Machine Learning
 (`AML`_) group at Forschungszentrum Juelich, Germany. Although the library is
 designed for people working at Institute of Neuroscience and Medicine - Brain
 and Behaviour (`INM-7`_), it is designed to be as modular as possible thus

docs/installation.rst

@@ -113,7 +113,7 @@ the AFNI Docker container in your local system.
 
 Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
 
-Or, alternatively, you can exceute this command which will update the
+Or, alternatively, you can execute this command which will update the
 ``~/.bashrc`` for you:
 
 .. code-block:: bash

docs/maintaining.rst

@@ -50,7 +50,7 @@ before proceeding.
 to generate the proper changelog that should be reflected in
 ``docs/whats_new.rst``.
 
-#. Commit the chages, make a PR and merge via a merge commit.
+#. Commit the changes, make a PR and merge via a merge commit.
 
 #. Make sure you are in sync with the main branch.
 

docs/understanding/pipeline.rst

@@ -16,7 +16,7 @@ steps:
 4. :ref:`Marker Computation <marker>`: Compute the marker.
 5. :ref:`Storage <storage>`: Store the marker values.
 
-The element that is passed accross the pipeline is called the
+The element that is passed across the pipeline is called the
 :ref:`Data Object<data_object>`.
 
 The following is a graphical representation of the pipeline:

docs/understanding/preprocess.rst

@@ -94,7 +94,7 @@ The default value is to use all the *noise components* with the ``full`` *confou
 Other Parameters
 ~~~~~~~~~~~~~~~~
 
-Additionaly, the :class:`.fMRIPrepConfoundRemover` supports the following
+Additionally, the :class:`.fMRIPrepConfoundRemover` supports the following
 parameters:
 
 .. list-table::

docs/using/queueing.rst

@@ -11,7 +11,7 @@ computational clusters. This is done by adding the ``queue`` section in the
 
 While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing
 using `GNU Parallel`_, only HTCondor is currently supported. This will be
-implemented in future relases of junifer. If you are in immediate need of any of
+implemented in future releases of junifer. If you are in immediate need of any of
 these schedulers, please create an issue on the `junifer github`_ repository.
 
 The ``queue`` section of the :ref:`codeless` must start by defining the
@@ -45,17 +45,17 @@ When using HTCondor, junifer will use a DAG to queue one job per element
 (``junifer collect``) to collect the results once all of the individual element
 jobs are finished.
 
-The following parameters are avilable for HTCondor:
+The following parameters are available for HTCondor:
 
-* ``env``: Definition of the Python enviroment. It must provide two variables:
+* ``env``: Definition of the Python environment. It must provide two variables:
 
   * ``kind``: This is the kind of virtual environment to use:
 
     * ``conda``
     * ``virtualenv`` (not yet supported)
-    * ``local`` (no virtual enviroment)
+    * ``local`` (no virtual environment)
 
-  * ``name``: This is the name of the enviroment to use in case a virtual
+  * ``name``: This is the name of the environment to use in case a virtual
     environment is used.
 
 * ``mem``: Memory to be used by the job. It must be provided as a string with

docs/whats_new.rst

@@ -18,7 +18,7 @@ Bugfixes
   and not to the location of the YAML file by `Fede Raimondo`_. (:gh:`127`)
 - Fix ``junifer run`` to respect preprocess step specified in the pipeline by
   `Synchon Mandal`_ (:gh:`159`)
-- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in
+- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accessed in
   :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede
   Raimondo`_ (:gh:`183`)
 - Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a
@@ -41,7 +41,7 @@ Bugfixes
   `Fede Raimondo`_ (:gh:`194`)
 - Fix a bug in which :func:`.count` will not be correctly applied across an
   axis by `Fede Raimondo`_ (:gh:`195`)
-- Fix an issue with datalad cache and locks in which the overriden settings in
+- Fix an issue with datalad cache and locks in which the overridden settings in
   Junifer were not propagated to subprocesses, resulting in using the default
   settings by `Fede Raimondo`_ (:gh:`199`)
 - Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase

ignore_words.txt

@@ -1 +1,4 @@
-master
+master
+nin
+chang
+sepulcre

pyproject.toml

@@ -95,6 +95,14 @@ extend-exclude = """
 )
 """
 
+[tool.codespell]
+skip = "*/auto_examples/*,*.html,.git/,*.pyc,*/_build/*,*/h5io/*"
+count = ""
+quiet-level = 3
+ignore-words = "ignore_words.txt"
+interactive = 0
+builtin = "clear,rare,informal,names,usage,code"
+
 [tool.pytest.ini_options]
 minversion = "7.0"
 addopts = "--ignore=junifer/external/h5io -vv"
@@ -140,4 +148,4 @@ showcontent = true
 # Add custom towncrier fragment for API changes
 [tool.towncrier.fragment.change]
 name = "API Changes"
-showcontent = true
+showcontent = true

tox.ini

@@ -63,8 +63,9 @@ commands =
 skip_install = true
 deps =
     codespell
+    tomli
 commands =
-    codespell --config tox.ini examples/ junifer/ scratch/ tools/
+    codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ {toxinidir}/README.md
 
 ################
 # Tool configs #
@@ -150,12 +151,4 @@ exclude_lines =
     if TYPE_CHECKING:
     # Don't complain if non-runnable code isn't run:
     if __name__ == .__main__.:
-precision = 2
+precision = 2
-
-[codespell]
-skip = docs/auto_*,*.html,.git/,*.pyc,docs/_build,junifer/external/h5io/
-count =
-quiet-level = 3
-ignore-words = ignore_words.txt
-interactive = 0
-builtin = clear,rare,informal,names,usage