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Fix tips and add jupyter lab to the environment #75

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merged 6 commits into from
Apr 12, 2024
Merged

Fix tips and add jupyter lab to the environment #75

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27382fb
lint
eberrigan Apr 11, 2024
8abe68b
fix test for tips to return expected values
eberrigan Apr 11, 2024
20573d0
clean README
eberrigan Apr 11, 2024
c69c55c
update codecov-action version
eberrigan Apr 12, 2024
bdf6ceb
bump release version
eberrigan Apr 12, 2024
0ce5b1c
add codecov token
eberrigan Apr 12, 2024
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3 changes: 2 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -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
3 changes: 0 additions & 3 deletions README.md
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Expand Up @@ -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):
Comment on lines 139 to 141
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The instructions for using Jupyter notebooks have been removed. This could potentially confuse new users who might still need these instructions to understand how to use the notebooks provided in the repository.

+ To use the Jupyter notebooks, 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
+ ```


```
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
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2 changes: 1 addition & 1 deletion sleap_roots/__init__.py
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Expand Up @@ -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"
1 change: 0 additions & 1 deletion sleap_roots/tips.py
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Expand Up @@ -76,4 +76,3 @@ def get_tip_ys(tip_pts: np.ndarray) -> np.ndarray:
return tip_ys[0]

return tip_ys

11 changes: 8 additions & 3 deletions tests/test_tips.py
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Expand Up @@ -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
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