Added pedigree.py specific test

.github/workflows/check-pedigree.yml

@@ -0,0 +1,31 @@
+name: Test Pedigree
+on:
+  push:
+    paths:
+    - 'robustocs/pedigree.py'
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python: ["3.10", "3.12"]
+        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install -e .
+
+    - name: Testing pedigree functions
+      run: |
+        cd examples/ped/
+        python3 test.py

examples/ped/example.ped

@@ -0,0 +1,8 @@
+i,p,q
+1,0,0
+2,0,0
+3,1,0
+4,1,2
+5,3,4
+6,1,4
+7,5,6

examples/ped/test.py

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+import numpy as np
+import robustocs as rocs
+from time import time
+
+
+ped = rocs.load_ped("example.ped")
+
+
+def printMatrix(matrix, description="ans =", precision=3):
+    """Quick function for nicely printing a matrix"""
+    print(f"{description}\n", np.round(matrix, precision))
+
+
+# test constructing a WNRM
+# ========================
+
+tic = time()
+A = rocs.makeA(ped)
+printMatrix(A, f"\n{time()-tic:.2E} secs for makeA")
+
+A_true = np.array([
+    [1., 0., 0.5, 0.5, 0.5, 0.75, 0.625],
+    [0., 1., 0., 0.5, 0.25, 0.25, 0.25],
+    [0.5, 0., 1., 0.25, 0.625, 0.375, 0.5],
+    [0.5, 0.5, 0.25, 1., 0.625, 0.75, 0.6875],
+    [0.5, 0.25, 0.625, 0.625, 1.125, 0.5625, 0.84375],
+    [0.75, 0.25, 0.375, 0.75, 0.5625, 1.25, 0.90625],
+    [0.625, 0.25, 0.5, 0.6875, 0.84375, 0.90625, 1.28125]
+])
+
+# check makeA produced correct answer
+assert np.all(np.abs(A-A_true) < 1e-7)
+
+
+# test inverting a WNRM
+# =====================
+
+tic = time()
+B = rocs.makeA(ped)
+invA1 = np.linalg.inv(B)
+printMatrix(invA1, f"\n{time()-tic:.2E} secs for np.linalg.inv")
+
+tic = time()
+invA2 = rocs.make_invA(ped)
+printMatrix(invA2, f"\n{time()-tic:.2E} secs for make_invA")
+
+tic = time()
+invA3 = rocs.pedigree.make_invA_decomposition(ped)
+printMatrix(invA3, f"\n{time()-tic:.2E} secs for make_invA_decomposition")
+
+# all three inverses should be mutually within tolerance of each other
+assert np.all(np.abs(invA1-invA2) < 1e-7)
+assert np.all(np.abs(invA2-invA3) < 1e-7)
+assert np.all(np.abs(invA1-invA3) < 1e-7)