Restructure folder for generators and linalg (#321)

* refact: new folder structure for linalg * refact: new folder structure for generators step 1g * fix: imports * fix: add missing files * updated codecov params to avoid annoying warnings * refact: moved more generators around * refact: merged (non)uniform random_hypergraph() and remove nonuniform file * fix: tests * PR review comments * minor adjustments * minor adjustments * docs: added missing documentation * added the uniform Erdos-Renyi back in --------- Co-authored-by: Nicholas Landry <[email protected]>
xgi-org · Apr 5, 2023 · 3435409 · 3435409
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diff --git a/codecov.yml b/codecov.yml
@@ -8,7 +8,5 @@ coverage:
         # basic
         target: auto
         threshold: 0.1
-    patch:
-      default:
-        # basic
-        target: 0
+        removed_code_behavior: removals_only # off, removals_only, adjust_base
+    patch: off
diff --git a/docs/source/api/generators.rst b/docs/source/api/generators.rst
@@ -8,5 +8,9 @@ generators package
    :toctree: generators
 
    ~xgi.generators.classic
-   ~xgi.generators.nonuniform
-   ~xgi.generators.uniform
+   ~xgi.generators.simple
+   ~xgi.generators.lattice
+   ~xgi.generators.random
+   ~xgi.generators.uniform
+   ~xgi.generators.simplicial_complexes
+
diff --git a/docs/source/api/generators/xgi.generators.classic.rst b/docs/source/api/generators/xgi.generators.classic.rst
@@ -8,9 +8,4 @@
    .. rubric:: Functions
 
    .. autofunction:: empty_hypergraph
-   .. autofunction:: empty_simplicial_complex
-   .. autofunction:: flag_complex
-   .. autofunction:: flag_complex_d2
-   .. autofunction:: star_clique
-   .. autofunction:: sunflower
-   .. autofunction:: ring_lattice
+   .. autofunction:: empty_simplicial_complex
diff --git a/docs/source/api/generators/xgi.generators.lattice.rst b/docs/source/api/generators/xgi.generators.lattice.rst
@@ -0,0 +1,10 @@
+xgi.generators.lattice
+======================
+
+.. currentmodule:: xgi.generators.lattice
+
+.. automodule:: xgi.generators.lattice
+
+    .. rubric:: Functions
+
+    .. autofunction:: ring_lattice
diff --git a/docs/source/api/generators/xgi.generators.nonuniform.rst b/docs/source/api/generators/xgi.generators.nonuniform.rst
diff --git a/docs/source/api/generators/xgi.generators.random.rst b/docs/source/api/generators/xgi.generators.random.rst
@@ -0,0 +1,13 @@
+xgi.generators.random
+=====================
+
+.. currentmodule:: xgi.generators.random
+
+.. automodule:: xgi.generators.random
+
+    .. rubric:: Functions
+
+    .. autofunction:: chung_lu_hypergraph
+    .. autofunction:: dcsbm_hypergraph
+    .. autofunction:: random_hypergraph
+    .. autofunction:: watts_strogatz_hypergraph
diff --git a/docs/source/api/generators/xgi.generators.simple.rst b/docs/source/api/generators/xgi.generators.simple.rst
@@ -0,0 +1,11 @@
+xgi.generators.simple
+=====================
+
+.. currentmodule:: xgi.generators.simple
+
+.. automodule:: xgi.generators.simple
+
+    .. rubric:: Functions
+
+    .. autofunction:: star_clique
+    .. autofunction:: sunflower
diff --git a/docs/source/api/generators/xgi.generators.simplicial_complexes.rst b/docs/source/api/generators/xgi.generators.simplicial_complexes.rst
@@ -0,0 +1,14 @@
+xgi.generators.simplicial_complex
+=================================
+
+.. currentmodule:: xgi.generators.simplicial_complex
+
+.. automodule:: xgi.generators.simplicial_complex
+
+    .. rubric:: Functions
+
+    .. autofunction:: flag_complex
+    .. autofunction:: flag_complex_d2
+    .. autofunction:: random_flag_complex
+    .. autofunction:: random_flag_complex_d2
+    .. autofunction:: random_simplicial_complex
diff --git a/docs/source/api/linalg.rst b/docs/source/api/linalg.rst
@@ -7,4 +7,6 @@ linalg package
 .. autosummary::
    :toctree: linalg
 
-   ~xgi.linalg.matrix
+   ~xgi.linalg.hypergraph_matrix
+   ~xgi.linalg.laplacian_matrix
+   ~xgi.linalg.hodge_matrix
diff --git a/docs/source/api/linalg/xgi.linalg.hodge_matrix.rst b/docs/source/api/linalg/xgi.linalg.hodge_matrix.rst
@@ -0,0 +1,11 @@
+xgi.linalg.hodge_matrix
+=======================
+
+.. currentmodule:: xgi.linalg.hodge_matrix
+
+.. automodule:: xgi.linalg.hodge_matrix
+
+   .. rubric:: Functions
+
+   .. autofunction:: boundary_matrix
+   .. autofunction:: hodge_laplacian
diff --git a/docs/source/api/linalg/xgi.linalg.hypergraph_matrix.rst b/docs/source/api/linalg/xgi.linalg.hypergraph_matrix.rst
@@ -0,0 +1,14 @@
+xgi.linalg.hypergraph_matrix
+============================
+
+.. currentmodule:: xgi.linalg.hypergraph_matrix
+
+.. automodule:: xgi.linalg.hypergraph_matrix
+
+   .. rubric:: Functions
+
+   .. autofunction:: adjacency_matrix
+   .. autofunction:: clique_motif_matrix
+   .. autofunction:: degree_matrix
+   .. autofunction:: incidence_matrix
+   .. autofunction:: intersection_profile
diff --git a/docs/source/api/linalg/xgi.linalg.laplacian_matrix.rst b/docs/source/api/linalg/xgi.linalg.laplacian_matrix.rst
@@ -0,0 +1,11 @@
+xgi.linalg.laplacian_matrix
+===========================
+
+.. currentmodule:: xgi.linalg.laplacian_matrix
+
+.. automodule:: xgi.linalg.laplacian_matrix
+
+   .. rubric:: Functions
+
+   .. autofunction:: laplacian
+   .. autofunction:: normalized_hypergraph_laplacian
diff --git a/docs/source/api/linalg/xgi.linalg.matrix.rst b/docs/source/api/linalg/xgi.linalg.matrix.rst
diff --git a/tests/generators/test_classic.py b/tests/generators/test_classic.py
@@ -1,8 +1,4 @@
-import networkx as nx
-import pytest
-
 import xgi
-from xgi.exception import XGIError
 
 
 def test_empty_hypergraph():
@@ -13,110 +9,3 @@ def test_empty_hypergraph():
 def test_empty_hypergraph():
     SC = xgi.empty_simplicial_complex()
     assert (SC.num_nodes, SC.num_edges) == (0, 0)
-
-
-def test_star_clique():
-    with pytest.raises(ValueError):
-        H = xgi.star_clique(-1, 7, 3)
-    with pytest.raises(ValueError):
-        H = xgi.star_clique(6, -1, 3)
-    with pytest.raises(ValueError):
-        H = xgi.star_clique(6, 7, -1)
-    with pytest.raises(ValueError):
-        H = xgi.star_clique(6, 7, 7)
-
-    H = xgi.star_clique(6, 7, 3)
-    assert H.num_nodes == 13
-    assert H.num_edges == 97
-    assert xgi.max_edge_order(H) == 3
-
-
-def test_flag_complex():
-    edges = [[0, 1], [1, 2], [2, 0], [0, 3]]
-    G = nx.Graph(edges)
-
-    S = xgi.flag_complex(G)
-
-    simplices_2 = [
-        frozenset({0, 1}),
-        frozenset({0, 2}),
-        frozenset({0, 3}),
-        frozenset({1, 2}),
-    ]
-
-    simplices_3 = simplices_2 + [frozenset({0, 1, 2})]
-
-    assert S.edges.members() == simplices_3
-
-    S1 = xgi.flag_complex(G, ps=[1], seed=42)
-    S2 = xgi.flag_complex(G, ps=[0.5], seed=42)
-    S3 = xgi.flag_complex(G, ps=[0], seed=42)
-
-    assert S1.edges.members() == simplices_3
-    assert S2.edges.members() == simplices_2
-    assert S3.edges.members() == simplices_2
-
-    G1 = nx.complete_graph(4)
-    S4 = xgi.flag_complex(G1)
-    S5 = xgi.flag_complex(G1, ps=[1])
-    assert S4.num_nodes == S5.num_nodes
-    assert S4.num_edges == S5.num_edges
-    assert set(S4.edges.members()) == set(S5.edges.members())
-
-
-def test_flag_complex_d2():
-    G = nx.erdos_renyi_graph(15, 0.3, seed=3)
-
-    S = xgi.flag_complex(G, max_order=2)
-    S2 = xgi.flag_complex_d2(G)
-
-    assert set(S.edges.members()) == set(S2.edges.members())
-
-
-def test_ring_lattice():
-    H = xgi.ring_lattice(5, 2, 2, 0)
-    assert H.num_nodes == 5
-    assert H.num_edges == 5
-    assert xgi.unique_edge_sizes(H) == [2]
-
-    H = xgi.ring_lattice(5, 3, 4, 1)
-    edges = H.edges.members()
-    for i in range(H.num_edges - 1):
-        assert len(set(edges[i]).intersection(set(edges[i + 1]))) == 2  # d-l
-    assert xgi.unique_edge_sizes(H) == [3]
-
-    # k < 2 test
-    with pytest.warns(Warning):
-        H = xgi.ring_lattice(5, 2, 1, 0)
-    assert H.num_nodes == 5
-    assert H.num_edges == 0
-
-    # k % 2 != 0 test
-    with pytest.warns(Warning):
-        xgi.ring_lattice(5, 2, 3, 0)
-
-    # k < 0 test
-    with pytest.raises(XGIError):
-        xgi.ring_lattice(5, 2, -1, 0)
-
-
-def test_sunflower():
-    with pytest.raises(XGIError):
-        H = xgi.sunflower(3, 4, 2)
-
-    H = xgi.sunflower(3, 1, 5)
-
-    assert H.nodes.memberships(0) == {0, 1, 2}
-    assert set(H.nodes) == set(range(13))
-    assert H.num_edges == 3
-    for n in range(1, H.num_nodes):
-        assert len(H.nodes.memberships(n)) == 1
-
-    H = xgi.sunflower(4, 3, 6)
-    for i in range(3):
-        H.nodes.memberships(i) == {0, 1, 2, 3}
-
-    assert H.num_nodes == 15
-
-    for i in range(3, 15):
-        assert len(H.nodes.memberships(i)) == 1
diff --git a/tests/generators/test_lattice.py b/tests/generators/test_lattice.py
@@ -0,0 +1,31 @@
+import pytest
+
+import xgi
+from xgi.exception import XGIError
+
+
+def test_ring_lattice():
+    H = xgi.ring_lattice(5, 2, 2, 0)
+    assert H.num_nodes == 5
+    assert H.num_edges == 5
+    assert xgi.unique_edge_sizes(H) == [2]
+
+    H = xgi.ring_lattice(5, 3, 4, 1)
+    edges = H.edges.members()
+    for i in range(H.num_edges - 1):
+        assert len(set(edges[i]).intersection(set(edges[i + 1]))) == 2  # d-l
+    assert xgi.unique_edge_sizes(H) == [3]
+
+    # k < 2 test
+    with pytest.warns(Warning):
+        H = xgi.ring_lattice(5, 2, 1, 0)
+    assert H.num_nodes == 5
+    assert H.num_edges == 0
+
+    # k % 2 != 0 test
+    with pytest.warns(Warning):
+        xgi.ring_lattice(5, 2, 3, 0)
+
+    # k < 0 test
+    with pytest.raises(XGIError):
+        xgi.ring_lattice(5, 2, -1, 0)
diff --git a/tests/generators/test_nonuniform.py b/tests/generators/test_nonuniform.py
@@ -47,19 +47,27 @@ def test_dcsbm_hypergraph():
 
 def test_random_hypergraph():
     # seed
-    H1 = xgi.random_hypergraph(10, [0.1, 0.001], seed=1)
-    H2 = xgi.random_hypergraph(10, [0.1, 0.001], seed=2)
-    H3 = xgi.random_hypergraph(10, [0.1, 0.001], seed=2)
+    H1 = xgi.random_hypergraph(10, [0.1, 0.01], seed=1)
+    H2 = xgi.random_hypergraph(10, [0.1, 0.01], seed=2)
+    H3 = xgi.random_hypergraph(10, [0.1, 0.01], seed=2)
 
     assert H1._edge != H2._edge
     assert H2._edge == H3._edge
 
+    assert H1.num_nodes == 10
+    assert xgi.unique_edge_sizes(H1) == [2, 3]
+
     # wrong input
     with pytest.raises(ValueError):
         H1 = xgi.random_hypergraph(10, [1, 1.1])
     with pytest.raises(ValueError):
         H1 = xgi.random_hypergraph(10, [1, -2])
 
+    # uniform
+    H4 = xgi.random_hypergraph(10, [0.1], order=2, seed=1)
+    assert H4.num_nodes == 10
+    assert xgi.unique_edge_sizes(H4) == [3]
+
 
 def test_random_simplicial_complex():
     # seed