add codespell config, workflow (just to detect typos) and have some typos fixed

.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

CONTRIBUTING.md

@@ -79,7 +79,7 @@ For more reference see:
 ### Testing
 Testing is done via [`pytest`](https://docs.pytest.org/).
 
-Tests should be created in the [`tests/`](tests) subfolder following the convention `test_{MODULE_NAME}.py` which mimicks the main module organization.
+Tests should be created in the [`tests/`](tests) subfolder following the convention `test_{MODULE_NAME}.py` which mimics the main module organization.
 
 It is highly recommended checking out other existing tests for reference on how these are structured.
 

pyproject.toml

@@ -57,3 +57,9 @@ line-length = 88
 [pydocstyle]
 convention = "google"
 match-dir = "sleap_io"
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg'
+check-hidden = true
+# ignore-regex = ''
+# ignore-words-list = ''

sleap_io/io/labelstudio.py

@@ -2,7 +2,7 @@
 
 Some important nomenclature:
   - `tasks`: typically maps to a single frame of data to be annotated, closest
-    correspondance is to `LabeledFrame`
+    correspondence is to `LabeledFrame`
   - `annotations`: collection of points, polygons, relations, etc. corresponds to
     `Instance`s and `Point`s, but a flattened hierarchy
 

sleap_io/io/nwb.py

@@ -174,7 +174,7 @@ def write_nwb(
             e.g. pose_estimation_metadata["video_timestamps"] = np.array(timestamps)
             or   pose_estimation_metadata["video_sample_rate] = 15  # In Hz
 
-            2) The other use of this dictionary is to ovewrite sleap-io default
+            2) The other use of this dictionary is to overwrite sleap-io default
             arguments for the PoseEstimation container.
             see https://github.com/rly/ndx-pose for a full list or arguments.
     """
@@ -221,7 +221,7 @@ def append_nwb_data(
             e.g. pose_estimation_metadata["video_timestamps"] = np.array(timestamps)
             or   pose_estimation_metadata["video_sample_rate"] = 15  # In Hz
 
-            2) The other use of this dictionary is to ovewrite sleap-io default
+            2) The other use of this dictionary is to overwrite sleap-io default
             arguments for the PoseEstimation container.
             see https://github.com/rly/ndx-pose for a full list or arguments.
 
@@ -366,7 +366,7 @@ def build_pose_estimation_container_for_track(
     timestamps = pose_estimation_metadata_copy.pop("video_timestamps", None)
     sample_rate = pose_estimation_metadata_copy.pop("video_sample_rate", 1.0)
     if timestamps is None:
-        # Keeps backward compatbility.
+        # Keeps backward compatibility.
         timestamps = np.arange(track_data_df.shape[0]) * sample_rate
     else:
         timestamps = np.asarray(timestamps)

sleap_io/model/instance.py

@@ -26,9 +26,9 @@ class Point:
         complete: Has the point been verified by the user labeler.
 
     Class variables:
-        eq_atol: Controls absolute tolerence allowed in `x` and `y` when comparing two
+        eq_atol: Controls absolute tolerance allowed in `x` and `y` when comparing two
             `Point`s for equality.
-        eq_rtol: Controls relative tolerence allowed in `x` and `y` when comparing two
+        eq_rtol: Controls relative tolerance allowed in `x` and `y` when comparing two
             `Point`s for equality.
 
     """
@@ -166,7 +166,7 @@ def _compare_points(
     Returns:
         True if `a` and `b` are considered equal, otherwise False
     """
-    # First check we are speaking the same languague of nodes
+    # First check we are speaking the same language of nodes
     if not set(a.keys()) == set(b.keys()):
         return False
 

tests/io/test_nwb.py

@@ -206,7 +206,7 @@ def test_complex_case_append_with_timestamps_metadata(nwbfile, centered_pair):
             extracted_starting_time = pose_estimation_series.starting_time
             assert extracted_starting_time == 0
 
-        # Other store timestamps and the timestmaps should be a subset of the videotimestamps
+        # Other store timestamps and the timestamps should be a subset of the videotimestamps
         else:
             extracted_timestamps = pose_estimation_series.timestamps
             assert np.in1d(

tests/model/test_instance.py

@@ -72,7 +72,7 @@ def test_predicted_point():
     ppt2 = PredictedPoint(x=1.2, y=3.4, visible=True, complete=False, score=0.9)
     assert ppt1 == ppt2
 
-    # Test equivelance of Point and PredictedPoint
+    # Test equivalence of Point and PredictedPoint
     pt3 = Point(x=1.2, y=3.4, visible=True, complete=False)
     assert not ppt1 == pt3  # PredictedPoint is not equivalent to Point
     assert not pt3 == ppt1  # Point is not equivalent to PredictedPoint