Add codespell: config, workflow (to alert when new typos added) and get typos fixed (#19)

* do not git ignore .github -- useful to keep under Git

* Add github action to codespell main on push and PRs

* Add rudimentary codespell config

* [DATALAD RUNCMD] run codespell throughout but ignore fail

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w || :",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] Do interactive fixing of some ambigous typos

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* Update app_utils.py

* Update pyproject.toml

---------

Co-authored-by: Mackenzie Mathis <[email protected]>

Author: yarikoptic

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+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@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.gitignore

@@ -7,7 +7,6 @@ __pycache__
 .env
 .DS_Store
 /examples
-.github
 
 ## gitignore for Python
 ## Source: https://raw.githubusercontent.com/github/gitignore/master/Python.gitignore

README.md

@@ -34,7 +34,7 @@ make app
 - arXiv preprint version **[AmadeusGPT: a natural language interface for interactive animal behavioral analysis](https://arxiv.org/abs/2307.04858)** by [Shaokai Ye](https://github.com/yeshaokai), [Jessy Lauer](https://github.com/jeylau), [Mu Zhou](https://github.com/zhoumu53), [Alexander Mathis](https://github.com/AlexEMG) & [Mackenzie W. Mathis](https://github.com/MMathisLab).
 
 ### Install tips
-- *Make a new conda env: `conda create --name amadeusGPT python=3.9` then run `conda activate amadeusGPT` or you can also use our supplied conda if you git cloned the repo (navigate into the conda directory): `conda env create -f amadesuGPT.yml` then pip install amadeusGPT once created/lauched.
+- *Make a new conda env: `conda create --name amadeusGPT python=3.9` then run `conda activate amadeusGPT` or you can also use our supplied conda if you git cloned the repo (navigate into the conda directory): `conda env create -f amadesuGPT.yml` then pip install amadeusGPT once created/launched.
 - **Git clone this repo: so please open a terminal, we recommend to download into Documents (so type `cd Documents`) and run `git clone https://github.com/AdaptiveMotorControlLab/AmadeusGPT.git` Then go into the dir (`cd AmadeusGPT`)
 - If you want to use SAM, you need to download the weights. Otherwise you will see the following message in the app: `Cannot find SAM checkpoints. Skipping SAM`. Download them and add to "static" directory: wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth
 

amadeusgpt/app_utils.py

@@ -370,7 +370,7 @@ def update_roi(result_json, ratios):
             count += 1
         AnimalBehaviorAnalysis.set_roi_objects(roi_objects)
 
-        AmadeusLogger.debug("User just drawed roi")
+        AmadeusLogger.debug("User just drew an roi")
 
 
 def finish_drawing(canvas_result, ratio):

amadeusgpt/brains/base.py

@@ -103,7 +103,7 @@ def connect_gpt(cls, messages, functions=None, function_call=None, **kwargs):
             if "gpt_model" in st.session_state:
                 gpt_model = st.session_state["gpt_model"]
 
-        # allow kwargs to overrite gpt_model. This is to make sure child class of BaseBrain can use different option
+        # allow kwargs to override gpt_model. This is to make sure child class of BaseBrain can use different option
         if "gpt_model" in kwargs:
             gpt_model = kwargs["gpt_model"]
 

amadeusgpt/interface.txt

@@ -115,7 +115,7 @@ class AnimalBehaviorAnalysis:
         return the orientation vector of the vector connecting bodypart_name1 and bodypart_name2 for all animals
 
     plot_ethogram(events: AnimalEvent) -> Tuple[plt.Figure, plt.Axes, plot_caption]  
-        get ethogram for correpsonding AnimalEvent    
+        get ethogram for corresponding AnimalEvent    
 
     animals_social_events(inter_individual_animal_state_query_list, 
                                 inter_individual_animal_state_comparison_list,

amadeusgpt/main.py

@@ -159,7 +159,7 @@ def magic_command(cls, user_input):
 
     @classmethod
     def save_state(cls):
-        # save the class attirbutes of all classes that are under state_list.
+        # save the class attributes of all classes that are under state_list.
         def get_class_variables(_class):
             return {
                 k: v

amadeusgpt/modules/implementation/visualization/occupancy_plot.py

@@ -35,7 +35,7 @@ def plot_occupancy_heatmap_per_animal(
     print("xmin,ymin, xmax,ymax")
     print(xmin, ymin, xmax, ymax)
 
-    # Peform the kernel density estimate
+    # Perform the kernel density estimate
     bins = complex(bins)
     xx, yy = np.mgrid[xmin:xmax:bins, ymin:ymax:bins]
     pos = np.vstack([xx.ravel(), yy.ravel()])

pyproject.toml

@@ -14,3 +14,9 @@ packages = ["amadeusgpt"]
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["setup.cfg"]}
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,go.sum,*.css,*.txt'
+check-hidden = true
+# ignore-regex = ''
+ignore-words-list = 'mabe,missings,nd,tread'