Merge pull request #17 from con/enh-codespell

Add codespell and use it to fix typos

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git,.codespellrc
+check-hidden = true
+ignore-regex = \bths=true\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

conboarding.md

@@ -66,14 +66,14 @@ How much does it cost to run things?
       $SOME_PORT`
    1. login to `typhon`: `ssh -i /path/to/key me@typhon.dartmouth.edu -p
       $SOME_PORT`
-      Note: When loging in from campus (use `eduroam`), SSH does not always work on
+      Note: When logging in from campus (use `eduroam`), SSH does not always work on
       `typhon`. Instead it is recommended to use `ssh-agent` and forward the authentication connection using `-A`
          1. (Assuming `ssh-agent` is running) `ssh-add -t 3600 /path/to/key`
          1. `ssh-add -l` should now show your fingerprint.
          1. SSH into `smaug` with connection forwarding: `ssh -A me@smaug.dartmouth.edu -p $SOME_PORT`
          1. Once on `smaug` `ssh-add -l` should now show the same fingerprint.
          1. From `smaug`, proceed to `typhon` with `ssh me@typhon.dartmouth.edu -p $SOME_PORT`
-   1. You might benefit from specifying some details withing your
+   1. You might benefit from specifying some details within your
       `~/.ssh/config` for the given host(s):
          1. `SOME_PORT` so you don't need to enter it every time
          1. `AgentForward` is equivalent to `-A`
@@ -141,7 +141,7 @@ How much does it cost to run things?
       If are using `xtightvncviewer` which has builtin SSH tunneling, you can connect to
       a VNC session directly.
 
-      ```xtightvncviewer -via <username>@<server name>.dartmouth.edu localhost:<VNC assgined port number>```
+      ```xtightvncviewer -via <username>@<server name>.dartmouth.edu localhost:<VNC assigned port number>```
 
       If you are using a VNC client that does not have builtin SSH tunneling, you will
       need to create an SSH tunnel to the VNC server and then connect to the VNC session
@@ -154,7 +154,7 @@ How much does it cost to run things?
       2. Connect to the VNC session through the SSH tunnel using the VNC client on your
          local machine at `localhost:<local port number>`
 
-      Where `<VNC assgined port number>` is the port number assigned to the VNC session
+      Where `<VNC assigned port number>` is the port number assigned to the VNC session
       on the server and `<local port number>` is the port number on your local machine
       that you want to use for the SSH tunnel. `<server name>` is the name of the server
       where the VNC session is running.

definitions.md

@@ -4,7 +4,7 @@
 : AWS Launch, run, and scale feature-rich and highly-performant file systems with just a few clicks
 
 [ANCP-bids](https://github.com/ANCPLabOldenburg/ancp-bids)
-: A Python package to read/write/query/validate BIDS datasets. Ligher weight than PyBids.
+: A Python package to read/write/query/validate BIDS datasets. Lighter weight than PyBids.
 
 [Apptainer](https://apptainer.org/)
 : Apptainer/Singularity is the most widely used container system for HPC. It is designed to execute applications at bare-metal performance while being secure, portable, and 100% reproducible. Apptainer is an open-source project with a friendly community of developers and users. The user base continues to expand, with Apptainer/Singularity now used across industry and academia in many areas of work.
@@ -162,7 +162,7 @@ PBS
 : with a collection of popular neuroscience computational tools provided within ready to use containerized environmentshttps://github.com/CenterForOpenScience/modular-file-renderer
 
 [RN/reproin](https://github.com/ReproNim/reproin)
-: Its goal is to provide a turnkey flexible setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners. Provids heuristic for HeudiConv  and convention for naming exam cards and sequences in the MRI scanner.
+: Its goal is to provide a turnkey flexible setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners. Provides heuristic for HeudiConv  and convention for naming exam cards and sequences in the MRI scanner.
 
 [RN/reprostim](https://github.com/ReproNim/reprostim)
 : ReproStim is a video capture and recording suite for neuroimaging and psychology experiments. Its goal is to provide experimenters with a complete record of audio and visual stimulation for every data collection session by making it possible to easily collect high fidelity copies of the actual stimuli shown to each subject in the form of video files that can be stored alongside behavioral or neuroimaging data in public repositories.