Merge pull request #2 from BlockScience/dev

debug

Author: mzargham

.github/workflows/ci.yml

@@ -21,8 +21,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install package and dev dependencies
-        run: pip install -e ".[dev]"
+      - name: Install package with all dependencies
+        run: pip install -e ".[dev,analysis,viz,viz-interactive]"
 
       - name: Run tests
         run: python -m pytest tests/ -v --tb=short

pyproject.toml

@@ -11,6 +11,7 @@ dependencies = [
     "pyshacl>=0.25",
     "owlrl>=6.0",
     "pandas>=2.0",
+    "pyyaml>=6.0",
 ]
 
 [project.optional-dependencies]

tests/test_analysis.py

@@ -11,7 +11,10 @@
 """
 
 import pytest
-import numpy as np
+
+np = pytest.importorskip("numpy")
+scipy = pytest.importorskip("scipy")
+
 from numpy.testing import assert_allclose
 
 from knowledgecomplex.schema import SchemaBuilder, vocab

tests/test_partition.py

@@ -12,7 +12,10 @@
 """
 
 import pytest
-import numpy as np
+
+np = pytest.importorskip("numpy")
+scipy = pytest.importorskip("scipy")
+
 from numpy.testing import assert_allclose
 
 from knowledgecomplex.schema import SchemaBuilder, vocab

tests/test_stress.py

@@ -255,6 +255,7 @@ def test_from_function_all_same_value(self):
 class TestAnalysisEdgeCases:
 
     def test_betti_single_vertex(self):
+        pytest.importorskip("scipy")
         from knowledgecomplex.analysis import betti_numbers
         sb = SchemaBuilder(namespace="test")
         sb.add_vertex_type("N")
@@ -263,13 +264,15 @@ def test_betti_single_vertex(self):
         assert betti_numbers(kc) == [1, 0, 0]
 
     def test_betti_no_elements(self):
+        pytest.importorskip("scipy")
         from knowledgecomplex.analysis import betti_numbers
         sb = SchemaBuilder(namespace="test")
         sb.add_vertex_type("N")
         kc = KnowledgeComplex(schema=sb)
         assert betti_numbers(kc) == [0, 0, 0]
 
     def test_boundary_matrices_vertices_only(self):
+        pytest.importorskip("scipy")
         from knowledgecomplex.analysis import boundary_matrices
         sb = SchemaBuilder(namespace="test")
         sb.add_vertex_type("N")

tests/test_topology.py

@@ -1,4 +1,4 @@
-"""
+r"""
 tests/test_topology.py
 
 Tests for topological query methods on KnowledgeComplex: