Fix tips and add jupyter lab to the environment (#75)

* lint

* fix test for tips to return expected values

* clean README

* update codecov-action version

* bump release version

* add codecov token

.github/workflows/ci.yml

@@ -103,8 +103,9 @@ jobs:
           pytest --cov=sleap_roots --cov-report=xml tests/
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }}
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           verbose: false

README.md

@@ -139,19 +139,16 @@ convex_hull = sr.convhull.get_convhull(pts)
 Jupyter notebooks are located in this repo at `sleap-roots/notebooks`.
 
 To use them, activate your conda environment which includes JupyterLab (recommended):
-
 ```
 conda activate sleap-roots
 ```
 
 Clone this repository if you haven't already:
-
 ```
 git clone https://github.com/talmolab/sleap-roots.git && cd sleap-roots
 ```
 
 Then you can change directories to the location of the notebooks, and open Jupyter Lab:
-
 ```
 cd notebooks
 jupyter lab

sleap_roots/__init__.py

@@ -23,4 +23,4 @@
 
 # Define package version.
 # This is read dynamically by setuptools in pyproject.toml to determine the release version.
-__version__ = "0.0.7"
+__version__ = "0.0.8"

sleap_roots/tips.py

@@ -76,4 +76,3 @@ def get_tip_ys(tip_pts: np.ndarray) -> np.ndarray:
         return tip_ys[0]
 
     return tip_ys
-

tests/test_tips.py

@@ -146,11 +146,16 @@ def test_get_tip_ys_standard(pts_standard):
 
 # test get_tip_ys with no tips
 def test_get_tip_ys_no_tip(pts_no_tips):
+    # `pts_no_tips` is a 2x2x2 array with the second point in each frame being `np.nan`
+    # Get the tips from the no tips points
+    # `tips` should be [[np.nan, np.nan], [np.nan, np.nan]]
     tips = get_tips(pts_no_tips)
+    assert tips.shape == (2, 2)
+    np.testing.assert_array_equal(tips, [[np.nan, np.nan], [np.nan, np.nan]])
+    # Get the tip y-coordinates
+    # `tip_ys` should be [np.nan, np.nan]
     tip_ys = get_tip_ys(tips)
     assert tip_ys.shape[0] == 2
     np.testing.assert_almost_equal(tip_ys[1], np.nan, decimal=3)
-    assert type(tip_ys) == np.ndarray
-
-    tip_ys = get_tip_ys(tips[[0]])
+    np.testing.assert_almost_equal(tip_ys[0], np.nan, decimal=3)
     assert type(tip_ys) == np.ndarray