Merge remote-tracking branch 'origin/master'

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/build_and_upload_pypi.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/python-package-conda.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: Add conda to system path

.github/workflows/test_ubuntu.yml

@@ -8,6 +8,9 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
+  workflow_dispatch:
+  schedule:
+    - cron: "0 6 1 * *"  # The 1st day of each month at 06:00 UTC
 
 jobs:
   build:
@@ -16,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -48,4 +51,4 @@ jobs:
         pytest --cov-config=.coveragerc --cov=./ --cov-report=xml
 
     - name: codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3

README.md

@@ -17,7 +17,7 @@ DyNetx provides implementations of dynamic networks in python (it is built upon
 
 The project documentation can be found on [ReadTheDocs](http://dynetx.readthedocs.io).
 
-If you would like to test ``DyNetx`` functionalities withouth installing anything on your machine consider using the preconfigured Jupyter Hub instances offered by [SoBigData++](https://sobigdata.d4science.org/group/sobigdata-gateway/explore?siteId=20371853).
+If you would like to test ``DyNetx`` functionalities without installing anything on your machine consider using the preconfigured Jupyter Hub instances offered by [SoBigData++](https://sobigdata.d4science.org/group/sobigdata-gateway/explore?siteId=20371853).
 
 
 ## Citation

docs/installing.rst

@@ -50,7 +50,7 @@ Run python setup.py install to build and install
 ------
 GitHub
 ------
-Clone the DyNetx repostitory (see GitHub_ for options)
+Clone the DyNetx repository (see GitHub_ for options)
 
 .. code-block:: python
 

dynetx/algorithms/assortativity.py

@@ -217,7 +217,7 @@ def sliding_delta_conformity(dg, delta: int, alphas: list, labels: list, profile
     :param profile_size:
     :param hierarchies: label hierarchies
     :param path_type: time respecting path type. String among: shortest, fastest, foremost, fastest_shortest and shortest_fastest (default: shortest)
-    :param progress_bar: wheter to show the progress bar, default false
+    :param progress_bar: whether to show the progress bar, default false
     :return: conformity trend value for each node
 
     -- Example --

dynetx/classes/dyndigraph.py

@@ -321,7 +321,7 @@ def number_of_nodes(self, t=None):
             return nds
 
     def avg_number_of_nodes(self):
-        """Return the number of nodes in the t snpashot of a dynamic graph.
+        """Return the number of nodes in the t snapshot of a dynamic graph.
 
 
             Returns

dynetx/test/test_algorithms.py

@@ -4,7 +4,7 @@
 import dynetx.algorithms as al
 
 
-def get_netowrk():
+def get_network():
     g = dn.DynGraph()
     g.add_interaction("A", "B", 1, 4)
     g.add_interaction("B", "D", 2, 5)
@@ -19,7 +19,7 @@ def get_netowrk():
 class AlgorithmsTestCase(unittest.TestCase):
 
     def test_DAG(self):
-        g = get_netowrk()
+        g = get_network()
         DAG, sources, targets, _, _ = al.temporal_dag(g, "D", "C", start=1, end=9)
         self.assertIsInstance(DAG, nx.DiGraph)
         self.assertIsInstance(sources, list)
@@ -59,7 +59,7 @@ def test_ping_pong(self):
         self.assertIsInstance(ressa, dict)
 
     def test_time_respecting_paths(self):
-        g = get_netowrk()
+        g = get_network()
         pts = al.time_respecting_paths(g, "A", "D", start=1, end=9)
 
         for p in pts:
@@ -73,14 +73,14 @@ def test_time_respecting_paths(self):
             self.assertIsInstance(p, tuple)
 
     def test_all_time_respecting_paths(self):
-        g = get_netowrk()
+        g = get_network()
         pts = al.all_time_respecting_paths(g, start=1, end=9)
 
         for p in pts:
             self.assertIsInstance(p, tuple)
 
     def test_annotated_paths(self):
-        g = get_netowrk()
+        g = get_network()
         pts = al.time_respecting_paths(g, "D", "C", start=2, end=9)
 
         for _, ap in pts.items():

dynetx/utils/decorators.py

@@ -3,7 +3,6 @@
 
 import networkx as nx
 from decorator import decorator
-from networkx.utils import is_string_like
 
 __all__ = [
     'open_file',
@@ -22,14 +21,14 @@ def not_implemented():
 
     Raises
     ------
-    NetworkXNotImplemnted
+    NetworkXNotImplemented
     If any of the packages cannot be imported
 
     Examples
     --------
     Decorate functions like this::
 
-       @not_implemnted()
+       @not_implemented()
        def sp_function():
            pass
 
@@ -167,7 +166,7 @@ def _open_file(func, *args, **kwargs):
         # Now we have the path_arg. There are two types of input to consider:
         #   1) string representing a path that should be opened
         #   2) an already opened file object
-        if is_string_like(path):
+        if isinstance(path, str):
             ext = splitext(path)[1]
             fobj = _dispatch_dict[ext](path, mode=mode)
             close_fobj = True

requirements.txt

@@ -1,5 +1,5 @@
 numpy
 future
 tqdm
-networkx>=2.4
+networkx
 decorator

setup.py

@@ -21,7 +21,7 @@
 
 
 setup(name='dynetx',
-      version='0.3.1',
+      version='0.3.2',
       license='BSD-2-Clause',
       description='Dynamic Network library',
       url='https://github.com/GiulioRossetti/dynetx',