Fix random hypergraph (#597)

* Add ability to generate ER hypergraphs without multiedges

* update

* Remove bad characters

* Fix #361

* Revert "Fix #361"

This reverts commit 28cbbf3.

* Fix #361

* Update test.yml

* fix non-multi-edge probability

* formatting

* Update random.py

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update using-xgi.rst

* Response to review

* Update uniform.py

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/uniform.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* updates

* Conditional API note (#595)

* Conditional API note

* Update api_reference.rst

* Remove bad characters

* Update random.py

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* response to review

* updates

* Update random.py

* format

* Update random.py

* update docs

* add unit tests

* Fix test

* test different version

* fix test

* updates

* last additions

* update

* fix error

* unnecessary import

* add unit tests

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

* Update xgi/generators/random.py

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

---------

Co-authored-by: Maxime Lucas <maximelucas@users.noreply.github.com>

.github/workflows/coverage.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - name: Install packages
         run: |
           pip install --upgrade pip

.github/workflows/publish_xgi.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
 
     - name: Install dependencies
       run: |

docs/source/api/generators/xgi.generators.random.rst

@@ -9,5 +9,6 @@ xgi.generators.random
 
     .. autofunction:: chung_lu_hypergraph
     .. autofunction:: dcsbm_hypergraph
+    .. autofunction:: fast_random_hypergraph
     .. autofunction:: random_hypergraph
     .. autofunction:: watts_strogatz_hypergraph

pytest.ini

@@ -1,7 +1,7 @@
 [pytest]
 # always run doctests
-addopts = --doctest-modules
+addopts = --doctest-modules --ignore=docs
 # custom markers
 markers =
     webtest: mark test as an online test.
-    slow: mark test as slow.
+    slow: mark test as slow.

tests/algorithms/test_simpliciality.py

@@ -68,7 +68,18 @@ def test_edit_simpliciality(
     mf = 3
     assert np.allclose(es, (s - mf) / (m + s - mf))
 
-    H = xgi.Hypergraph([[1, 2, 3, 4], [3, 4, 5, 6], [2, 3, 6, 7], [1, 2], [3, 4], [2, 3], [3, 6], [3, 4]])
+    H = xgi.Hypergraph(
+        [
+            [1, 2, 3, 4],
+            [3, 4, 5, 6],
+            [2, 3, 6, 7],
+            [1, 2],
+            [3, 4],
+            [2, 3],
+            [3, 6],
+            [3, 4],
+        ]
+    )
     es = xgi.edit_simpliciality(H, exclude_min_size=False)
     assert np.allclose(es, 0.1785714285714286)
 

tests/drawing/test_draw.py

@@ -717,6 +717,7 @@ def test_draw_undirected_dyads(edgelist8):
         ax, dyad_collection = xgi.draw_undirected_dyads(H, dyad_lw=-1, ax=ax)
 
     fig, ax = plt.subplots()
+    np.random.seed(0)
     ax, dyad_collection = xgi.draw_undirected_dyads(
         H, dyad_color=np.random.random(H.num_edges), ax=ax
     )

tests/generators/test_random.py

@@ -0,0 +1,131 @@
+import random
+
+import numpy as np
+import pytest
+from scipy.special import comb
+
+import xgi
+
+
+def test_chung_lu_hypergraph():
+    k1 = {1: 1, 2: 2, 3: 3, 4: 4}
+    k2 = {1: 2, 2: 2, 3: 3, 4: 3}
+    H = xgi.chung_lu_hypergraph(k1, k2)
+    assert H.num_nodes == 4
+
+    # seed
+    H1 = xgi.chung_lu_hypergraph(k1, k2, seed=1)
+    H2 = xgi.chung_lu_hypergraph(k1, k2, seed=2)
+    H3 = xgi.chung_lu_hypergraph(k1, k2, seed=2)
+    assert H1._edge != H2._edge
+    assert H2._edge == H3._edge
+
+    with pytest.warns(Warning):
+        _ = xgi.chung_lu_hypergraph({1: 1, 2: 2}, {1: 2, 2: 2})
+
+
+def test_dcsbm_hypergraph():
+    n = 50
+    k1 = {i: random.randint(1, n) for i in range(n)}
+    k2 = {i: sorted(k1.values())[i] for i in range(n)}
+    g1 = {i: random.choice([0, 1]) for i in range(n)}
+    g2 = {i: random.choice([0, 1]) for i in range(n)}
+    omega = np.array([[n // 2, 10], [10, n // 2]])
+
+    H = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega)
+
+    assert H.num_nodes == 50
+
+    # seed
+    H1 = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=1)
+    H2 = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=2)
+    H3 = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega, seed=2)
+    assert H1._edge != H2._edge
+    assert H2._edge == H3._edge
+
+
+def test_random_hypergraph():
+    # seed
+    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 inputs
+    # p > 1
+    with pytest.raises(ValueError):
+        H1 = xgi.random_hypergraph(10, [1, 1.1])
+    # p < 0
+    with pytest.raises(ValueError):
+        H1 = xgi.random_hypergraph(10, [1, -2])
+    # p list and order number
+    with pytest.raises(ValueError):
+        H1 = xgi.random_hypergraph(10, [0.1, 0.1], order=3)
+    # different lengths
+    with pytest.raises(ValueError):
+        H1 = xgi.random_hypergraph(10, [0.1, 0.1], order=[3])
+
+    # uniform
+    H4 = xgi.random_hypergraph(10, 0.1, order=2, seed=1)
+    assert H4.num_nodes == 10
+    assert xgi.unique_edge_sizes(H4) == [3]
+
+    H5 = xgi.random_hypergraph(10, [0.1, 0.1], order=[1, 3], seed=1)
+    assert H5.num_nodes == 10
+    assert xgi.unique_edge_sizes(H5) == [2, 4]
+
+
+def test_fast_random_hypergraph():
+    # seed
+    H1 = xgi.fast_random_hypergraph(10, [0.1, 0.01], seed=1)
+    H2 = xgi.fast_random_hypergraph(10, [0.1, 0.01], seed=2)
+    H3 = xgi.fast_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 inputs
+    # p > 1
+    with pytest.raises(ValueError):
+        H1 = xgi.fast_random_hypergraph(10, [1, 1.1])
+    # p < 0
+    with pytest.raises(ValueError):
+        H1 = xgi.fast_random_hypergraph(10, [1, -2])
+    # p list and order number
+    with pytest.raises(ValueError):
+        H1 = xgi.fast_random_hypergraph(10, [0.1, 0.1], order=3)
+    # different lengths
+    with pytest.raises(ValueError):
+        H1 = xgi.fast_random_hypergraph(10, [0.1, 0.1], order=[3])
+
+    # uniform
+    H4 = xgi.fast_random_hypergraph(10, 0.1, order=2, seed=1)
+    assert H4.num_nodes == 10
+    assert xgi.unique_edge_sizes(H4) == [3]
+
+    H5 = xgi.fast_random_hypergraph(10, [0.1, 0.1], order=[1, 3], seed=1)
+    assert H5.num_nodes == 10
+    assert xgi.unique_edge_sizes(H5) == [2, 4]
+
+    H5 = xgi.fast_random_hypergraph(10, [1, 1])
+    assert H5.num_edges == comb(10, 2) + comb(10, 3)
+
+    with pytest.raises(ValueError):
+        xgi.fast_random_hypergraph(10, 0.1)
+
+    with pytest.raises(ValueError):
+        xgi.fast_random_hypergraph(10, 0.1, order=[1, 2])
+
+    with pytest.raises(ValueError):
+        xgi.fast_random_hypergraph(10, [1.1, 1])
+
+    with pytest.raises(ValueError):
+        xgi.fast_random_hypergraph(10, [-0.1, 1])

xgi/algorithms/connected.py

@@ -220,7 +220,7 @@ def largest_connected_hypergraph(H, in_place=False):
     >>> H = xgi.random_hypergraph(10, [0.1, 0.01], seed=1)
     >>> H_gcc = xgi.largest_connected_hypergraph(H)
     >>> print(H_gcc.num_nodes)
-    8
+    6
 
     """
     connected_nodes = max(connected_components(H), key=len)

xgi/algorithms/simpliciality.py

@@ -16,7 +16,7 @@
 
 
 def edit_simpliciality(H, min_size=2, exclude_min_size=True):
-    """Computes the edit simpliciality.
+    r"""Computes the edit simpliciality.
 
     The fraction of sub-edges contained when compared to a simplicial complex.
 
@@ -78,7 +78,7 @@ def edit_simpliciality(H, min_size=2, exclude_min_size=True):
 
 
 def simplicial_edit_distance(H, min_size=2, exclude_min_size=True, normalize=True):
-    """Computes the simplicial edit distance.
+    r"""Computes the simplicial edit distance.
 
     The number (or fraction) of sub-edges needed to be added
     to a hypergraph to make it a simplicial complex.
@@ -150,7 +150,7 @@ def simplicial_edit_distance(H, min_size=2, exclude_min_size=True, normalize=Tru
     )
     if not maxH.edges:
         return np.nan
-    
+
     id_to_num = dict(zip(maxH.edges, range(maxH.num_edges)))
 
     ms = 0
@@ -184,7 +184,7 @@ def simplicial_edit_distance(H, min_size=2, exclude_min_size=True, normalize=Tru
 
 
 def face_edit_simpliciality(H, min_size=2, exclude_min_size=True):
-    """Computes the face edit simpliciality.
+    r"""Computes the face edit simpliciality.
 
     The average fraction of sub-edges contained in a hyperedge
     relative to a simplex.
@@ -247,7 +247,7 @@ def face_edit_simpliciality(H, min_size=2, exclude_min_size=True):
 
 
 def mean_face_edit_distance(H, min_size=2, exclude_min_size=True, normalize=True):
-    """Computes the mean face edit distance
+    r"""Computes the mean face edit distance
 
     The average number (or fraction) of sub-edges needed to be added to make
     a hyperedge a simplex.
@@ -324,7 +324,7 @@ def mean_face_edit_distance(H, min_size=2, exclude_min_size=True, normalize=True
 
 
 def simplicial_fraction(H, min_size=2, exclude_min_size=True):
-    """Computing the simplicial fraction for a hypergraph.
+    r"""Computing the simplicial fraction for a hypergraph.
 
     What fraction of the hyperedges are simplices?
 

xgi/core/dihypergraph.py

@@ -599,7 +599,7 @@ def add_edges_from(self, ebunch_to_add, **attr):
             i.e. you cannot mix different formats.  The iterables containing edge
             members cannot be strings.
 
-        attr : \*\*kwargs, optional
+        **attr : kwargs, optional
             Additional attributes to be assigned to all edges. Attribues specified via
             `ebunch_to_add` take precedence over `attr`.
 

xgi/core/hypergraph.py

@@ -633,7 +633,7 @@ def add_edges_from(self, ebunch_to_add, **attr):
             the same length, i.e. you cannot mix different formats.  The iterables
             containing edge members cannot be strings.
 
-        attr : \*\*kwargs:, optional
+        **attr : kwargs, optional
             Additional attributes to be assigned to all edges. Attribues specified via
             `ebunch_to_add` take precedence over `attr`.
 

xgi/core/simplicialcomplex.py

@@ -400,7 +400,7 @@ def add_simplices_from(self, ebunch_to_add, max_order=None, **attr):
             Maximal dimension of simplices to add. If None (default), adds all
             simplices.  If int, and `ebunch_to_add` contains simplices of order >
             `max_order`, creates and adds all its subfaces up to `max_order`.
-        attr : \*\*kwargs, optional
+        **attr : kwargs, optional
             Additional attributes to be assigned to all simplices. Attribues specified
             via `ebunch_to_add` take precedence over `attr`.