Bump ton of dependencies (#92)

* Bump everything

* Fix labeled free scale graph generation

In newer versions create_using argument is missing

* Fix number of edges for fast binomial graph

networkx/networkx@dc3c486 changed
algorithm in NetworkX 2.7

* Change sphinx theme activation

html_theme_path no longer needed as of their tutorial

.github/workflows/coverage.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ 3.9 ]
     steps:
       - uses: actions/checkout@v3
 

.github/workflows/deploy_docs.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ 3.9 ]
     steps:
       - uses: actions/checkout@v3
 

.github/workflows/lint.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ 3.9 ]
     steps:
       - uses: actions/checkout@v3
 
@@ -18,7 +18,7 @@ jobs:
 
       - name: Install pre-commit
         run: |
-          python -m pip install pre-commit==2.20.0
+          python -m pip install pre-commit==3.6.2
           pre-commit install
 
       - name: Run pre-commit

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
             macos-latest,
             windows-latest,
         ]
-        python-version: [ 3.8, 3.9 ]
+        python-version: [ 3.9 ]
     steps:
       - uses: actions/checkout@v3
 

cfpq_data/graphs/generators/fast_labeled_binomial_graph.py

@@ -46,7 +46,7 @@ def fast_labeled_binomial_graph(
     >>> g.number_of_nodes()
     42
     >>> g.number_of_edges()
-    722
+    711
 
     Returns
     -------

cfpq_data/graphs/generators/labeled_scale_free_graph.py

@@ -90,7 +90,6 @@ def labeled_scale_free_graph(
         delta_in=delta_in,
         delta_out=delta_out,
         seed=seed,
-        create_using=nx.MultiDiGraph,
     )
 
     random.seed(seed)

docs/conf.py

@@ -16,8 +16,6 @@
 import sys
 from datetime import date
 
-from pydata_sphinx_theme import get_html_theme_path
-
 sys.path.insert(0, os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
@@ -123,7 +121,6 @@
 # a list of builtin themes.
 #
 html_theme = "pydata_sphinx_theme"
-html_theme_path = get_html_theme_path()
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

requirements/default.txt

@@ -1,5 +1,5 @@
-networkx==2.6.2
-pandas==1.3.4
-pyformlang==1.0.1
-rdflib==6.0.0
-requests==2.26.0
+networkx==3.2.1
+pandas==2.2.1
+pyformlang==1.0.7
+rdflib==7.0.0
+requests==2.31.0

requirements/developer.txt

@@ -1,3 +1,3 @@
-black==22.10
-pre-commit==2.20
-pytest==6.2.4
+black==24.2.0
+pre-commit==3.6.2
+pytest==8.0.1

requirements/docs.txt

@@ -1,5 +1,5 @@
-nb2plots==0.6
-numpydoc==1.1.0
-pydata_sphinx_theme==0.6.3
-sphinx==4.1.2
-sphinx-copybutton==0.4.0
+nb2plots==0.7.2
+numpydoc==1.6.0
+pydata_sphinx_theme==0.15.2
+sphinx==7.2.6
+sphinx-copybutton==0.5.2

setup.py

@@ -48,7 +48,6 @@
     "Operating System :: Unix",
     "Operating System :: Microsoft :: Windows",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3 :: Only",
     "Topic :: Software Development :: Libraries :: Python Modules",

tests/graphs/generators/test_fast_labeled_binomial_graph.py

@@ -12,7 +12,7 @@
 
 
 @pytest.mark.parametrize(
-    "graph,expected_nodes,expected_edges", [(g1, 29, 91), (g2, 42, 182)]
+    "graph,expected_nodes,expected_edges", [(g1, 29, 85), (g2, 42, 177)]
 )
 def test_fast_labeled_binomial_graph(graph, expected_nodes, expected_edges):
     assert graph.number_of_nodes() == expected_nodes