MNT add codespell (#14)

* Add github action to codespell master on push and PRs

* Add rudimentary codespell config

* MNT fix spelling

* Add readme

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg,.codespellrc
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+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

README.md

@@ -39,7 +39,7 @@ In this case, the intermediate files will be stored in the working directory and
 - `01cleaned.ply` for the cleaned head model, and 
 - `02aligned.stl` for the aligned head model
 
-To manually refine the alignement, `02aligned.stl` can be loaded in blender with the desired headcase model (stored under the `stls` directory of this repository).
+To manually refine the alignment, `02aligned.stl` can be loaded in blender with the desired headcase model (stored under the `stls` directory of this repository).
 Finally, the headcase can be generated with
 
 ```bash

autocase3d/fmin_autograd.py

@@ -136,7 +136,7 @@ def _compute_log_det_cholesky(matrix_chol, covariance_type, n_features):
 
 
 def _load_gmm_model():
-    """Load GMM model by loading the parameters and instatiating a GMM object."""
+    """Load GMM model by loading the parameters and instantiating a GMM object."""
     here = os.path.dirname(os.path.abspath(__file__))
     model_file = os.path.join(here, "gmm_params.npz")
     params = np.load(model_file)

docs/glab_headcase_pipeline.md

@@ -34,7 +34,7 @@ Once you have a good scan, send the file to an email you can access.
 1. Create an [Ultimaker account](https://ultimaker.com/software/ultimaker-cura) and ask a senior lab member to add you to the Gallant Lab group. 
 2. Download the [Ultimaker Cura software](https://ultimaker.com/software/ultimaker-cura) and sign in to your account.
 3. Upload both the front and back headcase stl files. Rotate and set the front to x=70mm. Set the back to x=-70mm. The two should be touching.
-4. In the `PREPARE` page, select the correct filament type and set the folloing print settings:
+4. In the `PREPARE` page, select the correct filament type and set the following print settings:
     - Profiles
       - Default = 0.2
       - Visual = 0.15

stls/default_customizations.stl

@@ -0,0 +1 @@
+default_customizations_v2.stl