changes for 1.6.0 (#279)

* changes for 1.6.0

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: a-r-j

.requirements/docs.in

@@ -12,3 +12,4 @@ sphinxext-opengraph
 sphinxcontrib-gtagjs
 ipython
 watermark
+sphinx_codeautolink

docs/source/conf.py

@@ -55,6 +55,7 @@
     "nbsphinx",
     "nbsphinx_link",
     "sphinx.ext.napoleon",
+    "sphinx_codeautolink",
     # "sphinx_autorun",
 ]
 
@@ -63,9 +64,9 @@
 nbsphinx_require_js_path = (
     "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"
 )
-nbsphinx_kernel_name = "graphein-wip"
-# nbsphinx_execute = "always"
-nbsphinx_execute = "never"
+nbsphinx_kernel_name = "graphein"
+nbsphinx_execute = "always"
+# nbsphinx_execute = "never"
 
 ogp_site_url = "https://graphein.ai/"
 ogp_image = "https://graphein.ai/_static/graphein.png"

graphein/protein/utils.py

@@ -90,7 +90,7 @@ def read_fasta(file_path: str) -> Dict[str, str]:
 
 def download_pdb_multiprocessing(
     pdb_codes: List[str],
-    out_dir: Union[str, Path],
+    out_dir: Union[str, Path],  # type: ignore
     overwrite: bool = False,
     strict: bool = False,
     max_workers: int = 16,

graphein/protein/visualisation.py

@@ -195,7 +195,7 @@ def plotly_protein_structure_graph(
     figsize: Tuple[int, int] = (620, 650),
     node_alpha: float = 0.7,
     node_size_min: float = 20.0,
-    node_size_multiplier: float = 20.0,
+    node_size_multiplier: float = 1.0,
     node_size_feature: str = "degree",
     label_node_ids: bool = True,
     node_colour_map=plt.cm.plasma,
@@ -217,7 +217,7 @@ def plotly_protein_structure_graph(
     :param node_size_min: Specifies node minimum size. Defaults to ``20.0``.
     :type node_size_min: float
     :param node_size_multiplier: Scales node size by a constant. Node sizes
-        reflect degree. Defaults to ``20.0``.
+        reflect degree. Defaults to ``1.0``.
     :type node_size_multiplier: float
     :param node_size_feature: Which feature to scale the node size by. Defaults
         to ``degree``.
@@ -378,7 +378,7 @@ def plot_protein_structure_graph(
     figsize: Tuple[int, int] = (10, 7),
     node_alpha: float = 0.7,
     node_size_min: float = 20.0,
-    node_size_multiplier: float = 20.0,
+    node_size_multiplier: float = 1.0,
     label_node_ids: bool = True,
     node_colour_map=plt.cm.plasma,
     edge_color_map=plt.cm.plasma,
@@ -402,10 +402,10 @@ def plot_protein_structure_graph(
     :type figsize: Tuple[int, int]
     :param node_alpha: Controls node transparency, defaults to ``0.7``.
     :type node_alpha: float
-    :param node_size_min: Specifies node minimum size, defaults to ``20``.
+    :param node_size_min: Specifies node minimum size, defaults to ``20.0``.
     :type node_size_min: float
     :param node_size_multiplier: Scales node size by a constant. Node sizes
-        reflect degree. Defaults to ``20``.
+        reflect degree. Defaults to ``1.0``.
     :type node_size_multiplier: float
     :param label_node_ids: bool indicating whether or not to plot ``node_id``
         labels. Defaults to ``True``.
@@ -629,15 +629,15 @@ def plot_distance_matrix(
         raise ValueError("Must provide either a graph or a distance matrix.")
 
     if dist_mat is None:
-        dist_mat = g.graph["dist_mat"]
+        dist_mat = g.graph["dist_mat"]  # type: ignore
     if g is not None:
         x_range = list(g.nodes)
         y_range = list(g.nodes)
         if not title:
             title = g.graph["name"] + " - Distance Matrix"
     else:
-        x_range = list(range(dist_mat.shape[0]))
-        y_range = list(range(dist_mat.shape[1]))
+        x_range = list(range(dist_mat.shape[0]))  # type: ignore
+        y_range = list(range(dist_mat.shape[1]))  # type: ignore
         if not title:
             title = "Distance matrix"
 
@@ -743,7 +743,7 @@ def asteroid_plot(
     use_plotly: bool = True,
     show_edges: bool = False,
     show_legend: bool = True,
-    node_size_multiplier: float = 10,
+    node_size_multiplier: float = 10.0,
 ) -> Union[plotly.graph_objects.Figure, matplotlib.figure.Figure]:
     # sourcery skip: remove-unnecessary-else, swap-if-else-branches
     """Plots a k-hop subgraph around a node as concentric shells.
@@ -778,12 +778,12 @@ def asteroid_plot(
     :type use_plotly: bool
     :param show_edges: Whether to show edges in the plot. Defaults to ``False``.
     :type show_edges: bool
-    :param show_legend: Whether to show the legend of the edges. Fefaults to
+    :param show_legend: Whether to show the legend of the edges. Defaults to
         `True``.
     :type show_legend: bool
     :param node_size_multiplier: Multiplier for the size of the nodes. Defaults
-        to ``10``.
-    :type node_size_multiplier: float.
+        to ``10.0``.
+    :type node_size_multiplier: float
     :returns: Plotly figure or matplotlib figure.
     :rtpye: Union[plotly.graph_objects.Figure, matplotlib.figure.Figure]
     """

setup.py

@@ -134,13 +134,19 @@ def run(self):
 
 setup(
     name="graphein",
-    version="1.5.2",
+    version="1.6.0",
     description="Protein & Interactomic Graph Construction for Machine Learning",
     long_description=long_description,
     long_description_content_type="text/markdown",
     author="Arian Jamasb",
     author_email="arian@jamasb.io",
     url="https://github.com/a-r-j/graphein",
+    project_urls={
+        "homepage": "https://github.com/a-r-j/graphein",
+        "changelog": "https://github.com/a-r-j/graphein/blob/master/CHANGELOG.md",
+        "issue": "https://github.com/a-r-j/graphein/issues",
+        "documentation": "https://graphein.ai/",
+    },
     packages=find_packages(),
     package_data={
         "": ["LICENSE.txt", "README.md", "requirements.txt", "*.csv"]