From b080a7e199baa19b489448e0c94becb99870ad66 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 24 Mar 2023 14:01:08 -0400
Subject: [PATCH 1/3] Add github action to codespell master on push and PRs

---
 .github/workflows/codespell.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 .github/workflows/codespell.yml

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 0000000..5768d7c
--- /dev/null
+++ b/.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

From 7554111df71c18237d8c70601ffdc3fcd01a90b7 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 24 Mar 2023 14:01:08 -0400
Subject: [PATCH 2/3] Add rudimentary .codespellrc

---
 .codespellrc | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 .codespellrc

diff --git a/.codespellrc b/.codespellrc
new file mode 100644
index 0000000..5aa4b5e
--- /dev/null
+++ b/.codespellrc
@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+# ignore-words-list = 

From 0e74a7b62644e0e62f5d240934601c45a18e99ec Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 24 Mar 2023 14:01:16 -0400
Subject: [PATCH 3/3] [DATALAD RUNCMD] run codespell throughout

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 preprocessing/step1_preproc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/preprocessing/step1_preproc.sh b/preprocessing/step1_preproc.sh
index 50783c1..dd607c3 100755
--- a/preprocessing/step1_preproc.sh
+++ b/preprocessing/step1_preproc.sh
@@ -47,7 +47,7 @@ cat $raw_dir/check_volumes/$output
 
 # STEP 3: unzip dicoms
 # NOTE: Look at your dcm folder and check that your dicoms end in .gz. If they end in .gz, you need to run this line.
-# Otherwise, don't run. If they have mutliple .gz.gz endings, you will have to run multiple times until they are no longer
+# Otherwise, don't run. If they have multiple .gz.gz endings, you will have to run multiple times until they are no longer
 # zipped!
 echo "unzipping session $session dicoms"
 gunzip $raw_dir/$subj_dir/dcm/*.gz # NOTE: you may have to do this multiple times if your files are double zipped