Merge pull request #71 from yarikoptic/enh-codespell

Add codespell support (config, workflow to detect/not fix) and make it fix few typos

Author: effigies

.codespellrc

@@ -0,0 +1,7 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+# ./labguide/research is generated from .md
+skip = .git*,*.pdf,*.css,*.min.*,.codespellrc,site_libs,search.json,publications.html,additional_pubs.csv,./docs/labguide/*/*.html,./academicdb/*.csv
+check-hidden = true
+ignore-regex = \bNichols TE\b
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+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@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

labguide/environment/code_of_conduct.md

@@ -12,7 +12,7 @@ Conduct](https://adminguide.stanford.edu/chapter-1/subchapter-1/policy-1-1-1).
 For definitions of an act of intolerance & hate crime escalation policy
 please see this page on University [AOI](https://deanofstudents.stanford.edu/acts-intolerance-protocol/overview/definitions).
 If you wish to speak with someone outside of the lab regarding an
-incident that occured in or outside of the lab, the university has
+incident that occurred in or outside of the lab, the university has
 this[ list of
 resources.](https://deanofstudents.stanford.edu/acts-intolerance-protocol/talk-someone)
 

labguide/research/intellectual_property.md

@@ -4,7 +4,7 @@ All products of research at Stanford (including data and code) are the property
 
 As discussed in the section on [data management and sharing](https://poldracklab.github.io/research/data_management.html), all data collected within our laboratory is meant to be shared upon submission of the related paper.  In cases where these data can be deidentified they will be shared under a public domain dedication (CC0), which places no restrictions on their use by other researchers.  Thus, any researcher can continue to use those data once they leave the lab. In other cases it may be necessary to restrict data sharing (e.g. when the data cannot be deidentified), in which case researchers will need to obtain a data use agreement from Stanford in order to access those data at their new institution. Dr. Poldrack commits to supporting any such requests, unless they violate other obligations of his or the University.
 
-In many cases we use data within the lab under Data Use Agreements (such as the ABCD or HCP datasets), and any researcher wishing to use such datasets must be explcitly listed on the DUA.  Once a researcher is no longer included in the Stanford DUA for a particular dataset, they must no longer access the dataset via Stanford computer systems.
+In many cases we use data within the lab under Data Use Agreements (such as the ABCD or HCP datasets), and any researcher wishing to use such datasets must be explicitly listed on the DUA.  Once a researcher is no longer included in the Stanford DUA for a particular dataset, they must no longer access the dataset via Stanford computer systems.
 
 ## Research ideas
 

labguide/research/statistical_methods.md

@@ -12,7 +12,7 @@
     the preregistration document.
 - The nature of grouping for
     multiple testing corrections (e.g., parameter within single models,
-    sets ot models, etc) should be pre-specified.
+    sets of models, etc) should be pre-specified.
 - For fMRI data, if using
     cluster-based thresholding the cluster forming threshold must be Z ≥
     3.1 if using parametric thresholding.  There are no restrictions on