From 2d1b06c85306d86f42c17b9ac7e62cbb7f104b54 Mon Sep 17 00:00:00 2001
From: Brian Long <brianl@alleninstitute.org>
Date: Sat, 23 Nov 2024 15:35:05 -0800
Subject: [PATCH 1/2] add mock test for SpatialCompare

---
 tests/test_spatial_compare.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/tests/test_spatial_compare.py b/tests/test_spatial_compare.py
index 87922dc..0ebfa09 100644
--- a/tests/test_spatial_compare.py
+++ b/tests/test_spatial_compare.py
@@ -1,13 +1,17 @@
 from spatial_compare import SpatialCompare, get_column_ordering
 import pandas as pd
+import anndata as ad
 import pathlib
 
 SC_DIR = pathlib.Path().absolute()
 print(SC_DIR)
 
-XENIUM_STEM = "xenium.h5ad"
+DATA_STEMS = ["CJ_BG_mini1.h5ad", "CJ_BG_mini2.h5ad", "CJ_BG_mini3.h5ad", "CJ_BG_mini4.h5ad"]
+
 TEST_DIR = SC_DIR.joinpath("tests").joinpath("data")
-XENIUM_DIR = TEST_DIR.joinpath(XENIUM_STEM)
+
+TEST_ANNDATAS = [ad.read_h5ad(TEST_DIR.joinpath(DATA_STEM)) for DATA_STEM in DATA_STEMS] 
+
 TEST_DF_RECORDS = [dict(a=1, b=0.5, c=0.1), dict(a=.5, b=.8, c=.9), dict(a=0.1, b=1., c=0.1)]
 TEST_DF = pd.DataFrame.from_records(TEST_DF_RECORDS)
 TEST_DF.index  = ["a", "b", "c"]
@@ -16,4 +20,9 @@
 def test_get_column_ordering():
     ordered_columns = get_column_ordering(TEST_DF, ordered_rows=["a", "b", "c"])
     print(ordered_columns)
-    assert ordered_columns == ["a", "c", "b"]
\ No newline at end of file
+    assert ordered_columns == ["a", "c", "b"]
+
+def test_SpatialCompare():
+    # mock up test
+    sc = SpatialCompare(TEST_ANNDATAS[0], TEST_ANNDATAS[1])
+    assert all(sc.ad_0[0].obs.columns == sc.ad_1[1].obs.columns)
\ No newline at end of file

From 40dbb690fb3cab4f81fb2507fbc70f8522d840cc Mon Sep 17 00:00:00 2001
From: Brian Long <brianl@alleninstitute.org>
Date: Sat, 23 Nov 2024 15:36:09 -0800
Subject: [PATCH 2/2] bump

---
 .github/workflows/test.yml | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..b7ba42b
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,32 @@
+name: Test
+
+on: [ pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: pyproject.toml
+        lfs: true
+    - name: Git LFS Pull
+      run: |
+        git lfs pull
+    - name: Install dependencies
+      run: |
+        pip install '.[test]'
+    - name: Run tests
+      run: |
+        pytest -rP
+