Merge pull request netneurolab#112 from yarikoptic/enh-codespell

codespell: action (to prevent typos in the future), config + typos fixed

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

docs/api.rst

@@ -126,7 +126,7 @@ Reference API
 
 .. _ref_points:
 
-:mod:`neuromaps.points` - Triangle mesh utilites
+:mod:`neuromaps.points` - Triangle mesh utilities
 ------------------------------------------------
 .. automodule:: neuromaps.points
     :no-members:

docs/installation.rst

@@ -11,7 +11,7 @@ Requirements
 
 In order to effectively use ``neuromaps`` you must have the `Connectome
 Workbench <https://www.humanconnectome.org/software/connectome-workbench>`_
-installed and accesible on your computer. Large portions of the functionality
+installed and accessible on your computer. Large portions of the functionality
 of the ``neuromaps`` toolbox rely on a few of the functions from the
 Connectome Workbench. You can follow `instructions here
 <https://www.humanconnectome.org/software/get-connectome-workbench>`_ for

docs/user_guide/comparisons.rst

@@ -50,7 +50,7 @@ There are four options for the ``resampling`` parameters:
 
 The default ('downsample_only') specifies that the higher-resolution map will
 be transformed to the space of the lower-resolution map. This ensures that we
-are never artifically "creating" (i.e., upsampling) data that does not exist.
+are never artificially "creating" (i.e., upsampling) data that does not exist.
 
 .. note::
 

docs/user_guide/transformations.rst

@@ -17,7 +17,7 @@ system is involved), which we discuss below.
 Transforming from volumetric spaces
 -----------------------------------
 
-Curently ``neuromaps`` only supports transforming brain annotations *from*
+Currently ``neuromaps`` only supports transforming brain annotations *from*
 MNI152 volumetric space to one of the other three surface-based coordinate
 systems (though work in ongoing to integrate transformations in the other
 direction!). This transformation is achieved through a process known as

examples/plot_fetch_datasets.py

@@ -72,7 +72,7 @@
 print(tags)
 
 ###############################################################################
-# Tags can be used as a keyword argumnet with :func:`~.available_annotations`.
+# Tags can be used as a keyword argument with :func:`~.available_annotations`.
 # You can supply either a single tag or a list of tags. Note that supplying a
 # list will only return those annotations that match ALL supplied tags:
 

neuromaps/_version.py

@@ -270,7 +270,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%s'"
                                % describe_out)
             return pieces

neuromaps/datasets/annotations.py

@@ -118,7 +118,7 @@ def available_annotations(source=None, desc=None, space=None, den=None,
         Values on which to match annotations. If not specified annotations with
         any value for the relevant key will be matched. Default: None
     return_restricted : bool, optional
-        Whether to return restricted annotations. These will only be accesible
+        Whether to return restricted annotations. These will only be accessible
         with a valid OSF token. Default: True
 
     Returns
@@ -142,7 +142,7 @@ def available_tags(return_restricted=False):
     Parameters
     ----------
     return_restricted : bool, optional
-        Whether to return restricted annotations. These will only be accesible
+        Whether to return restricted annotations. These will only be accessible
         with a valid OSF token. Default: True
 
 
@@ -213,7 +213,7 @@ def fetch_annotation(*, source=None, desc=None, space=None, den=None, res=None,
                         source=source, desc=desc, space=space, den=den,
                         res=res, hemi=hemi, tags=tags, format=format)
     if verbose > 1:
-        print(f'Identified {len(info)} datsets matching specified parameters')
+        print(f'Identified {len(info)} datasets matching specified parameters')
 
     # get session for requests
     session = _get_session(token=token)

neuromaps/datasets/utils.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 """
-Utilites for loading / creating datasets
+Utilities for loading / creating datasets
 """
 
 import json
@@ -21,7 +21,7 @@ def _osfify_urls(data, return_restricted=True):
     data : object
         If dict with a `url` key, will format OSF_API with relevant values
     return_restricted : bool, optional
-        Whether to return restricted annotations. These will only be accesible
+        Whether to return restricted annotations. These will only be accessible
         with a valid OSF token. Default: True
 
     Returns
@@ -65,7 +65,7 @@ def get_dataset_info(name, return_restricted=True):
     name : str
         Name of dataset
     return_restricted : bool, optional
-        Whether to return restricted annotations. These will only be accesible
+        Whether to return restricted annotations. These will only be accessible
         with a valid OSF token. Default: True
 
     Returns

neuromaps/nulls/spins.py

@@ -219,10 +219,11 @@ def gen_spinsamples(coords, hemiid, n_rotate=1000, check_duplicates=True,
         True may increase the runtime of this function! Default: True
     method : {'original', 'vasa', 'hungarian'}, optional
         Method by which to match non- and rotated coordinates. Specifying
-        'original' will use the method described in [ST1]_. Specfying 'vasa'
-        will use the method described in [ST4]_. Specfying 'hungarian' will use
-        the Hungarian algorithm to minimize the global cost of reassignment
-        (will dramatically increase runtime). Default: 'original'
+        'original' will use the method described in [ST1]_. Specifying 'vasa'
+        will use the method described in [ST4]_. Specifying 'hungarian' will
+        use the Hungarian algorithm to minimize the global cost of
+        reassignment (will dramatically increase runtime).
+        Default: 'original'
     seed : {int, np.random.RandomState instance, None}, optional
         Seed for random number generation. Default: None
     verbose : bool, optional

neuromaps/plotting.py

@@ -116,7 +116,7 @@ def _fix_facecolors(ax, facecolors, vertices, faces, view, hemi):
     Returns
     -------
     colors : (F,) array_like
-        Updated facecolors with approriate shading
+        Updated facecolors with appropriate shading
     """
 
     hemi_view = {'R': {'lateral': 'medial', 'medial': 'lateral'}}

pyproject.toml

@@ -1,3 +1,8 @@
 [build-system]
 requires = ["setuptools >= 38.3.0", "wheel", "versioneer-518"]
 build-backend = "setuptools.build_meta"
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,versioneer.py'
+#
+# ignore-words-list = ''