[Test GH Actions changes]

.github/workflows/tests.yml

@@ -7,16 +7,38 @@ on:
     branches: [main]
     paths:
       - ts2vg/**
+      - tests/**
   pull_request:
     branches: [main]
 
 jobs:
+  type-check:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[dev]"
+
+      - name: Run type checks
+        run: |
+          mypy
+
   build-and-test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
       - name: Checkout

docs/source/_static/custom.css

@@ -10,24 +10,6 @@
     font-size: 0.8rem;
 }
 
-/* hidden block / drop down */
-/* https://stackoverflow.com/questions/2454577/sphinx-restructuredtext-show-hide-code-snippets */
-/* https://stackoverflow.com/questions/59679797/show-hide-part-of-text-question-answer-in-sphinx-file */
-
-.toggle {
-    background: none repeat scroll 0 0 #e7f2fa;
-}
-
-.toggle.admonition {
-    padding: 0 .6rem 0!important;
-}
-
-.toggle .admonition-title {
-    display: block;
-    clear: both;
-    cursor: pointer;
-}
-
 /* logo-like */
 
 .ts2vg, .navbar-brand p.title {

docs/source/conf.py

@@ -35,6 +35,8 @@
     "sphinx.ext.linkcode",
     "sphinx.ext.autosummary",
     "sphinx.ext.autosectionlabel",
+    "sphinx_favicon",
+    "sphinx_togglebutton",
 ]
 
 autoclass_content = "class"
@@ -70,21 +72,9 @@
 html_copy_source = False
 html_show_sourcelink = False
 
-html_favicon = "_static/favicon-32x32.png"
+html_title = f"{project} v{version}"
 
 html_theme_options = {
-    "favicons": [
-        {
-            "rel": "icon",
-            "sizes": "16x16",
-            "href": "favicon-16x16.png",
-        },
-        {
-            "rel": "icon",
-            "sizes": "32x32",
-            "href": "favicon-32x32.png",
-        },
-    ],
     "icon_links": [
         {
             "name": "GitHub",
@@ -101,6 +91,11 @@
     "navigation_with_keys": False,
 }
 
+favicons = [
+    "favicon-16x16.png",
+    "favicon-32x32.png",
+]
+
 # svg math output
 # mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js"
 

docs/source/examples.rst

@@ -74,7 +74,7 @@ This example illustrates different options for the ``directed`` parameter when b
 
 
 .. admonition:: Code for :meth:`plot_nvg`
-   :class: toggle
+   :class: dropdown
 
     .. literalinclude:: examples/plot_utils.py
         :language: python
@@ -99,7 +99,7 @@ See :ref:`Weighted graphs` for a complete list of available values for ``weighte
 
 
 .. admonition:: Code for :meth:`plot_weighted_nvg`
-   :class: toggle
+   :class: dropdown
 
     .. literalinclude:: examples/plot_utils.py
         :language: python
@@ -124,7 +124,7 @@ Note that horizontal visibility graphs can also be directed and/or weighted.
 
 
 .. admonition:: Code for :meth:`plot_utils`
-   :class: toggle
+   :class: dropdown
 
     .. literalinclude:: examples/plot_utils.py
         :language: python
@@ -156,7 +156,7 @@ Note that when ``penetrable_limit`` is 0, the behavior is exactly the same as a
 
 
 .. admonition:: Code for :meth:`plot_nvg`, :meth:`plot_hvg`
-   :class: toggle
+   :class: dropdown
 
     .. literalinclude:: examples/plot_utils.py
         :language: python

docs_requirements.txt

@@ -1,25 +1,29 @@
+accessible-pygments==0.0.4
 alabaster==0.7.13
-Babel==2.11.0
-beautifulsoup4==4.11.1
+Babel==2.12.1
+beautifulsoup4==4.12.2
 certifi==2023.7.22
-charset-normalizer==3.0.1
-docutils==0.16
+charset-normalizer==3.2.0
+docutils==0.20.1
 idna==3.4
 imagesize==1.4.1
-Jinja2==3.0.3
-MarkupSafe==2.1.2
+Jinja2==3.1.2
+MarkupSafe==2.1.3
 packaging==23.0
-pydata-sphinx-theme==0.6.3
+pydata-sphinx-theme==0.13.3
 Pygments==2.15.0
 pytz==2022.7.1
 requests==2.31.0
 snowballstemmer==2.2.0
 soupsieve==2.3.2.post1
-Sphinx==3.5.4
+Sphinx==7.2.5
+sphinx-favicon==1.0.1
+sphinx-togglebutton==0.3.2
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.9
 sphinxcontrib.applehelp==1.0.3
-urllib3==1.26.14
+typing_extensions==4.7.1
+urllib3==2.0.4

pyproject.toml

@@ -51,3 +51,19 @@ build-backend = "setuptools.build_meta"
 #     "pytest",
 # ]
 
+
+[tool.mypy]
+packages = ["ts2vg"]
+disallow_untyped_defs = true
+
+[[tool.mypy.overrides]]
+module = [
+    "igraph",
+    "networkx",
+    "snap",
+    "ts2vg.graph._natural",
+    "ts2vg.graph._natural_penetrable",
+    "ts2vg.graph._horizontal",
+    "ts2vg.graph._horizontal_penetrable",
+]
+ignore_missing_imports = true

setup.cfg

@@ -41,8 +41,10 @@ install_requires    =
 include             = ts2vg*
 
 [options.extras_require]
+dev                 =
+    mypy==1.5.1
 tests               =
-    pytest
+    pytest==7.4.2
 
 [options.entry_points]
 console_scripts     = ts2vg=ts2vg.cli:main

tests/fixtures.py

@@ -58,9 +58,9 @@ def linear_ts_small():
 
 @pytest.fixture
 def linear_ts_large():
-    return 99999999 + np.arange(0, 1_000, 0.1, dtype="float64")
+    return 99999999 + np.arange(0, 1_000, 0.1, dtype=np.float64)
 
 
 @pytest.fixture
 def linear_ts_large_negative():
-    return -99999999 - np.arange(0, 1_000, 0.1, dtype="float64")
+    return -99999999 - np.arange(0, 1_000, 0.1, dtype=np.float64)

tests/test_horizontal.py

@@ -352,7 +352,7 @@ def test_degrees(sample_ts):
     np.testing.assert_array_equal(out_got, out_truth)
 
 
-def test_not_built():
+def test_unbuilt():
     with pytest.raises(ts2vg.graph.base.NotBuiltError):
         ts2vg.HorizontalVG().edges
 

tests/test_horizontal_penetrable.py

@@ -808,7 +808,7 @@ def test_penetrable_100_floating_point_linear_large_num_penetrations(linear_ts_l
     m = 100
 
     vg = ts2vg.HorizontalVG(penetrable_limit=m, weighted="num_penetrations")
-    out_got = vg.build(linear_ts_large).weights.sum()
+    out_got = sum(vg.build(linear_ts_large).weights)
 
     # sum of num_penetrations =  0 * (n - 1) + 1 * (n - 2) + ... + m * (n - (m + 1))
     out_truth = sum((i * (n - (i + 1))) for i in range(m + 1))
@@ -833,7 +833,7 @@ def test_penetrable_100_floating_point_linear_large_negative_num_penetrations(li
     m = 100
 
     vg = ts2vg.HorizontalVG(penetrable_limit=m, weighted="num_penetrations")
-    out_got = vg.build(linear_ts_large_negative).weights.sum()
+    out_got = sum(vg.build(linear_ts_large_negative).weights)
 
     out_truth = sum((i * (n - (i + 1))) for i in range(m + 1))
 

tests/test_natural.py

@@ -401,6 +401,34 @@ def test_adjacency_matrix_both(sample_ts):
     np.testing.assert_array_equal(out_got, out_truth)
 
 
+def test_adjacency_matrix_use_weights(sample_ts):
+    vg = ts2vg.NaturalVG(weighted="distance").build(sample_ts)
+    out_got = vg.adjacency_matrix(triangle="both", use_weights=True)
+
+    out_truth = [
+        [np.nan,    sqrt(2.0),  np.nan,     np.nan      ],
+        [sqrt(2.0), np.nan,     sqrt(5.0),  sqrt(13.0)  ],
+        [np.nan,    sqrt(5.0),  np.nan,     sqrt(2.0)   ],
+        [np.nan,    sqrt(13.0), sqrt(2.0),  np.nan      ],
+    ]
+
+    np.testing.assert_allclose(out_got, out_truth)
+
+
+def test_adjacency_matrix_use_weights_no_weight_value(sample_ts):
+    vg = ts2vg.NaturalVG(weighted="distance").build(sample_ts)
+    out_got = vg.adjacency_matrix(triangle="both", use_weights=True, no_weight_value=-1)
+
+    out_truth = [
+        [-1,        sqrt(2.0),  -1,         -1          ],
+        [sqrt(2.0), -1,         sqrt(5.0),  sqrt(13.0)  ],
+        [-1,        sqrt(5.0),  -1,         sqrt(2.0)   ],
+        [-1,        sqrt(13.0), sqrt(2.0),  -1          ],
+    ]
+
+    np.testing.assert_allclose(out_got, out_truth)
+
+
 def test_adjacency_matrix_directed_upper(sample_ts):
     vg = ts2vg.NaturalVG(directed="left_to_right").build(sample_ts)
 
@@ -429,8 +457,8 @@ def test_adjacency_matrix_directed_both(sample_ts):
     np.testing.assert_array_equal(out_got, out_truth)
 
 
-def test_adjacency_matrix_directed_lower(sample_ts):
-    vg = ts2vg.NaturalVG(directed="left_to_right")
+def test_adjacency_matrix_unbuilt():
+    vg = ts2vg.NaturalVG()
 
     with pytest.raises(ts2vg.graph.base.NotBuiltError):
         vg.adjacency_matrix()
@@ -492,9 +520,95 @@ def test_degrees_out_ttb(sample_ts):
     np.testing.assert_array_equal(out_got, out_truth)
 
 
-def test_not_built():
+def test_degrees_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG().build(sample_ts, only_degrees=True)
+    out_got = vg.degrees
+
+    out_truth = [1, 3, 2, 2]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_in_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG().build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_in
+
+    out_truth = [0, 1, 1, 2]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_out_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG().build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_out
+
+    out_truth = [1, 2, 1, 0]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_in_ltr_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG(directed="left_to_right").build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_in
+
+    out_truth = [0, 1, 1, 2]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_out_ltr_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG(directed="left_to_right").build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_out
+
+    out_truth = [1, 2, 1, 0]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_in_ttb_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG(directed="top_to_bottom").build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_in
+
+    out_truth = [1, 0, 1, 2]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degrees_out_ttb_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG(directed="top_to_bottom").build(sample_ts, only_degrees=True)
+    out_got = vg.degrees_out
+
+    out_truth = [0, 3, 1, 0]
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+
+def test_degree_counts(sample_ts):
+    out_got = ts2vg.NaturalVG().build(sample_ts).degree_counts
+
+    out_truth = ([1, 2, 3], [1, 2, 1])
+
+    np.testing.assert_array_equal(out_got, out_truth)
+
+def test_degree_distribution(sample_ts):
+    out_got = ts2vg.NaturalVG().build(sample_ts).degree_distribution
+
+    out_truth = ([1, 2, 3], [0.25, 0.5, 0.25])
+
+    np.testing.assert_allclose(out_got, out_truth)
+
+def test_unbuilt():
+    vg = ts2vg.NaturalVG()
+
+    with pytest.raises(ts2vg.graph.base.NotBuiltError):
+        vg.edges
+
+
+def test_unbuilt_only_degrees(sample_ts):
+    vg = ts2vg.NaturalVG().build(sample_ts, only_degrees=True)
+
     with pytest.raises(ts2vg.graph.base.NotBuiltError):
-        ts2vg.NaturalVG().edges
+        vg.edges
 
 
 def test_empty_ts(empty_ts):