ENH+FIX: codespell - config, workflow and typos fixed

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+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@v1

CODE_OF_CONDUCT.rst

@@ -4,7 +4,7 @@ Code of Conduct
 ===============
 
 We value the participation of every member of our community and want to
-ensure an that every contributer has an enjoyable and fulfilling
+ensure an that every contributor has an enjoyable and fulfilling
 experience. Accordingly, everyone who participates in the NiBetaSeries
 project is expected to show respect and courtesy to other community
 members at all time.
@@ -86,7 +86,7 @@ Enforcement
 Members of the community who violate these rules - no matter how much
 they have contributed to the NiBetaSeries, or how specialised their
 skill set - will be approached by Peer or Rita. If inappropriate
-behaviour persists after this discussion, the contributer will be asked
+behaviour persists after this discussion, the contributor will be asked
 to discontinue their participation in the project.
 
 **To report an issue you have with community interactions** please

CONTRIBUTING.rst

@@ -403,7 +403,7 @@ If you want your git configurations inside the container, so you do not need to
 your email or username, you can add the following option to your Docker command: 
 ``-v ${HOME}/.gitconfig:/home/neuro/.gitconfig``.
 
-Furthermore, if you do not want to type your password everytime you push changes to
+Furthermore, if you do not want to type your password every time you push changes to
 Github, you can store your credentials in a file named ``.git-credentials``.
 Github has wonderful `instructions to create a personal access token
 <https://help.github.com/en/articles/creating-a-personal-access-token-for-the-command-line>`_ to store

docs/development/roadmap.rst

@@ -11,7 +11,7 @@ Goals
 
 1. Flexibly generate beta series maps for the user.
 2. Provide analyses of beta series maps for the user.
-3. Keep code test coverage at least at 70% because this allows for decent expections
+3. Keep code test coverage at least at 70% because this allows for decent exceptions
    towards what the software claims to do, while maintaining enough wiggle room for code
    that cannot reasonably be tested at that time.
    Please read `testivus <https://www.artima.com/weblogs/viewpost.jsp?thread=204677>`_

examples/plot_run_nibetaseries.py

@@ -32,7 +32,7 @@
 # :cite:`n-Verstynen2014`.
 # The atlas data came from a `recently published parcellation
 # <https://www.ncbi.nlm.nih.gov/pubmed/28981612>`_
-# in a publically accessible github repository.
+# in a publicly accessible github repository.
 
 # atlas github repo for reference:
 """https://github.com/ThomasYeoLab/CBIG/raw/master/stable_projects/\
@@ -76,7 +76,7 @@ def list_files(startpath):
 list_files(data_dir)
 
 #############################################################################
-# Manipulate events file so it satifies assumptions
+# Manipulate events file so it satisfies assumptions
 # =================================================
 # 1. the correct column has 1's and 0's corresponding to correct and incorrect,
 # respectively.
@@ -263,7 +263,7 @@ def list_files(startpath):
 # Graph beta map standard deviation
 # =================================
 # We can find where the betas have the highest standard deviation for each trial type.
-# Unsuprisingly, the largest deviations are near the edge of the brain mask and
+# Unsurprisingly, the largest deviations are near the edge of the brain mask and
 # the subcortical regions.
 
 # standard deviations for each trial type

pyproject.toml

@@ -1,2 +1,6 @@
 [build-system]
-requires = ["setuptools >= 40.8.0", "wheel", "cython"]
+requires = ["setuptools >= 40.8.0", "wheel", "cython"]
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,versioneer.py'
+#
+# ignore-words-list = ''

src/nibetaseries/_version.py

@@ -268,7 +268,7 @@ 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

src/nibetaseries/cli/run.py

@@ -137,7 +137,7 @@ def get_parser():
     bids_opts.add_argument('--exclude-description-label', action='store_true',
                            default=False, help='exclude this `desc` label from nibetaseries')
     bids_opts.add_argument('--database-path', action='store', default=None,
-                           help="Path to directory containing SQLite database indicies "
+                           help="Path to directory containing SQLite database indices "
                                 "for this BIDS dataset. "
                                 "If a value is passed and the file already exists, "
                                 "indexing is skipped.")

src/nibetaseries/interfaces/nilearn.py

@@ -169,7 +169,7 @@ def is_outlier(points, thresh=3.5):
 
     Returns
     -------
-        A bolean mask, of size numobservations-length array.
+        A boolean mask, of size numobservations-length array.
 
     .. note:: References
         Boris Iglewicz and David Hoaglin (1993), "Volume 16: How to Detect and

versioneer.py

@@ -180,7 +180,7 @@
   `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
   distributions (and upload multiple independently-installable tarballs).
 * Source trees whose main purpose is to contain a C library, but which also
-  provide bindings to Python (and perhaps other langauges) in subdirectories.
+  provide bindings to Python (and perhaps other languages) in subdirectories.
 
 Versioneer will look for `.git` in parent directories, and most operations
 should get the right version string. However `pip` and `setuptools` have bugs
@@ -688,7 +688,7 @@ 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]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%%s'"
                                %% describe_out)
             return pieces
@@ -1080,7 +1080,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', 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