Staging

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg, */student/*, */instructor/*
+# ignore embedded images or javascript in notebooks
+ignore-regex = (^\s*("image/\S+": ".*|"!function.*"|"[^\s]{30,100}\\\\n"|"  <source src=\S+;base64.*"|"!\[.*\]\(data:.*;base64,.*))|'t Hart|Chater, N\.|\bChristina Savin\b
+# ignore all kinds of short up to 3 letter variables found to be used throughout
+ignore-words-list = 3nd,4rd,aci,acn,afe,ags,als,bu,bui,caf,cna,daa,ede,esy,fle,fo,fof,fwe,hax,hge,hte,hve,iif,inh,ist,ket,mis,mor,mot,nam,nax,nce,nd,ned,nin,nwe,nwo,oce,ofo,ois,oly,onl,onw,ot,oyu,siz,tbe,te,teh,tha,tht,thw,ue,wee,wew,wih,wll,wqs,wth,yau,yse,zar,

.github/workflows/codespell.yml

@@ -0,0 +1,20 @@
+---
+name: Codespell
+
+on:
+  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

.github/workflows/notebook-pr.yaml

@@ -94,6 +94,8 @@ jobs:
         id: process_notebooks
         run: |
           branch=${{ github.event.pull_request.head.ref }}
+          # nbs="projects/ECoG/*.ipynb projects/neurons/*.ipynb";
+          # nbs="tutorials/Bonus_Autoencoders/*Tutorial*.ipynb";
           nbs=`python ci/select_notebooks.py ${{ steps.changed-files.outputs.all_changed_files }}`
           if ${{ contains(env.COMMIT_MESSAGE, 'ci:check') }}; then
             execflag="--check-execution";

projects/ECoG/exploreAJILE12.ipynb

@@ -298,7 +298,7 @@
    },
    "source": [
     "### Access to data on cloud\n",
-    "The data is hosted on [AMAZON AWS](https://aws.amazon.com) in **S3** buckets. The following steps guide you to locate the data based on the **dandiset** information, setup streaming and reading the data from the cloud. Alternatively, you can access the data on **[DANDI](https://dandiarchive.org/dandiset/000055?search=ajile12&pos=1)**. If you choose to directly download from DANDI, you will need a github account. The following code will be sufficient to programatically download/stream data (either for colab notebook or for your own personal machine)."
+    "The data is hosted on [AMAZON AWS](https://aws.amazon.com) in **S3** buckets. The following steps guide you to locate the data based on the **dandiset** information, setup streaming and reading the data from the cloud. Alternatively, you can access the data on **[DANDI](https://dandiarchive.org/dandiset/000055?search=ajile12&pos=1)**. If you choose to directly download from DANDI, you will need a github account. The following code will be sufficient to programmatically download/stream data (either for colab notebook or for your own personal machine)."
    ]
   },
   {
@@ -857,7 +857,7 @@
     "execution": {}
    },
    "source": [
-    "Each subject has multiple experimental sessions. You can check that programatically."
+    "Each subject has multiple experimental sessions. You can check that programmatically."
    ]
   },
   {

projects/ECoG/load_ECoG_motor_imagery.ipynb

@@ -127,7 +127,7 @@
     "\n",
     "`dat1` and `dat2` are data from the two blocks performed in each subject. The first one was the actual movements, the second one was motor imagery. For the movement task, from the original dataset instructions:\n",
     "\n",
-    "*Patients performed simple, repetitive, motor tasks of hand (synchronous flexion and extension of all fingers, i.e., clenching and releasing a fist at a self-paced rate of ~1-2 Hz) or tongue (opening of mouth with protrusion and retraction of the tongue, i.e., sticking the tongue in and out, also at ~1-2 Hz). These movements were performed in an interval-based manner, alternating between movement and rest, and the side of move- ment was always contralateral to the side of cortical grid placement.*\n",
+    "*Patients performed simple, repetitive, motor tasks of hand (synchronous flexion and extension of all fingers, i.e., clenching and releasing a fist at a self-paced rate of ~1-2 Hz) or tongue (opening of mouth with protrusion and retraction of the tongue, i.e., sticking the tongue in and out, also at ~1-2 Hz). These movements were performed in an interval-based manner, alternating between movement and rest, and the side of move- meant was always contralateral to the side of cortical grid placement.*\n",
     "\n",
     "<br>\n",
     "\n",