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Merged
jkanche merged 1 commit into from
Mar 3, 2025
Merged

Preparing the package for release #2

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13 changes: 8 additions & 5 deletions .github/workflows/publish-pypi.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,11 @@ on:
jobs:
build:
runs-on: ubuntu-latest
permissions:
id-token: write
repository-projects: write
contents: write
pages: write

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -45,8 +50,6 @@ jobs:
run: |
python -m tox -e clean,build

- name: Publish package
uses: pypa/[email protected]
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
# This uses the trusted publisher workflow so no token is required.
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
28 changes: 24 additions & 4 deletions README.md
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Expand Up @@ -5,10 +5,6 @@

A Python package for storing and analyzing spatial-omics experimental data. This package provide the `SpatialFeatureExperiment` class, based on the [R package and class](https://github.com/pachterlab/SpatialFeatureExperiment).

> [!NOTE]
>
> This package is not published to PyPI.

## Install

To get started, install the package from [PyPI](https://pypi.org/project/SpatialFeatureExperiment/)
Expand All @@ -17,6 +13,30 @@ To get started, install the package from [PyPI](https://pypi.org/project/Spatial
pip install spatialfeatureexperiment
```

## Quick Usage

This package uses shapely and geopandas to support the `*_geometries` slots.

```python
from spatialexperiment import SpatialFeatureExperiment
import numpy as np
import geopandas as gpd
from shapely.geometry import Polygon

nrows = 200
ncols = 500
counts = np.random.rand(nrows, ncols)
polys = gpd.GeoSeries(
[
Polygon([(1, -1), (1, 0), (0, 0)]),
Polygon([(3, -1), (4, 0), (3, 1)]),
]
)

colgeoms = {"polygons" : gpd.GeoDataFrame({"geometry": polys})}
tspe = SpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)
```

<!-- biocsetup-notes -->

## Note
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14 changes: 7 additions & 7 deletions tests/test_pSFE.py
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@@ -1,6 +1,6 @@
import pytest
from PIL import Image
from spatialexperiment import ProxySpatialFeatureExperiment
from spatialfeatureexperiment import SpatialFeatureExperiment
import numpy as np
import geopandas as gpd
from shapely.geometry import Polygon
Expand All @@ -13,14 +13,14 @@ def test_init_basic():
nrows = 200
ncols = 500
counts = np.random.rand(nrows, ncols)
tspe = ProxySpatialFeatureExperiment(assays={"spots": counts})
tspe = SpatialFeatureExperiment(assays={"spots": counts})

assert isinstance(tspe, ProxySpatialFeatureExperiment)
assert isinstance(tspe, SpatialFeatureExperiment)

def test_init_empty():
tspe = ProxySpatialFeatureExperiment()
tspe = SpatialFeatureExperiment()

assert isinstance(tspe, ProxySpatialFeatureExperiment)
assert isinstance(tspe, SpatialFeatureExperiment)

def test_init_with_col_geoms():
nrows = 200
Expand All @@ -34,6 +34,6 @@ def test_init_with_col_geoms():
)

colgeoms = {"polygons" : gpd.GeoDataFrame({"geometry": polys})}
tspe = ProxySpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)
tspe = SpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)

assert isinstance(tspe, ProxySpatialFeatureExperiment)
assert isinstance(tspe, SpatialFeatureExperiment)