towards v1.0

.gitignore

@@ -133,3 +133,4 @@ _version.py
 
 #IDE
 .idea
+.vscode

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black

pyproject.toml

@@ -16,16 +16,6 @@ authors=[
     {name="Mike Henry", email="[email protected]"},
     {name="Richard J Gowers", email="[email protected]"},
 ]
-dependencies = [
-  'scipy',
-  'numpy',
-  'networkx',
-  'gufe',
-  'rdkit',
-  'scikit-mol',
-  'scikit-learn',
-  'ipycytoscape'
-]
 description="Konnektor is a package for calculating networks."
 readme="README.md"
 requires-python = ">=3.9"
@@ -35,6 +25,26 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 
+dependencies = [
+  'gufe',
+  'numpy',
+  'rdkit',
+  'networkx',
+  'scikit-mol',
+  'scikit-learn',
+  'ipycytoscape',
+]
+
+[project.optional-dependencies]
+test = [
+  'pytest',
+  'pytest-cov[all]',
+]
+dev = [
+  'black',
+  'pre-commit',
+]
+
 [project.urls]
 "Homepage" = "https://github.com/OpenFreeEnergy/konnektor"
 
@@ -50,7 +60,7 @@ dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.versioningit.vcs]
-method = "git" 
+method = "git"
 match = ["*"]
 default-tag = "0.0.0"
 

src/konnektor/__init__.py

@@ -1,21 +1,29 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/konnektor
 
-from .network_planners import (MaximalNetworkGenerator,
-                               HeuristicMaximalNetworkGenerator,
-                               RadialLigandNetworkPlanner,
-                               NNodeEdgesNetworkGenerator,
-                               MinimalSpanningTreeNetworkGenerator,
-                               CyclicNetworkGenerator,
-                               ClusteredNetworkGenerator,
-                               StarrySkyNetworkGenerator,
-                               MstConcatenator,
-                               )
+from .network_planners import (
+    MaximalNetworkGenerator,
+    HeuristicMaximalNetworkGenerator,
+    RadialLigandNetworkPlanner,
+    NNodeEdgesNetworkGenerator,
+    MinimalSpanningTreeNetworkGenerator,
+    CyclicNetworkGenerator,
+    ClusteredNetworkGenerator,
+    StarrySkyNetworkGenerator,
+    MstConcatenator,
+)
 
-from .network_tools import concatenate_networks, merge_networks, append_component, \
-    delete_transformation
-from .network_tools import ChargeClusterer, ScaffoldClusterer, \
-    ComponentsDiversityClusterer
+from .network_tools import (
+    concatenate_networks,
+    merge_networks,
+    append_component,
+    delete_transformation,
+)
+from .network_tools import (
+    ChargeClusterer,
+    ScaffoldClusterer,
+    ComponentsDiversityClusterer,
+)
 
 from . import network_analysis
 

src/konnektor/data/__init__.py

@@ -10,8 +10,10 @@
 root_path = os.path.dirname(__file__)
 benzenes_sdf_path = f"{root_path}/benzenes_RHFE.sdf"
 hif2a_sdf_path = f"{root_path}/hif2a_ligands.sdf"
+charged_ligands_path = f"{root_path}/charged_ligands.sdf"
 
-def get_benzene_ligands()->list[SmallMoleculeComponent]:
+
+def get_benzene_ligands() -> list[SmallMoleculeComponent]:
     """
     get the benzene test dataset parsed as SmallMoleculeComponents.
 
@@ -21,9 +23,29 @@
         a list of the benzene compounds.
 
     """
-    return [SmallMoleculeComponent.from_rdkit(rdm) for rdm in Chem.SDMolSupplier(benzenes_sdf_path, removeHs=False)]
+    return [
+        SmallMoleculeComponent.from_rdkit(rdm)
+        for rdm in Chem.SDMolSupplier(benzenes_sdf_path, removeHs=False)
+    ]
+
+
+def get_hif2a_ligands() -> list[SmallMoleculeComponent]:
+    """
+    get the benzene test dataset parsed as SmallMoleculeComponents.
+
+    Returns
+    -------
+    list[SmallMoleculeComponent]
+        a list of the benzene compounds.
+
+    """
+    return [
+        SmallMoleculeComponent.from_rdkit(rdm)
+        for rdm in Chem.SDMolSupplier(hif2a_sdf_path, removeHs=False)
+    ]
+
 
-def get_hif2a_ligands()->list[SmallMoleculeComponent]:
+def get_charged_ligands() -> list[SmallMoleculeComponent]:
     """
     get the benzene test dataset parsed as SmallMoleculeComponents.
 
@@ -33,4 +55,7 @@
         a list of the benzene compounds.
 
     """
-    return [SmallMoleculeComponent.from_rdkit(rdm) for rdm in Chem.SDMolSupplier(hif2a_sdf_path, removeHs=False)]
+    return [
+        SmallMoleculeComponent.from_rdkit(rdm)
+        for rdm in Chem.SDMolSupplier(charged_ligands_path, removeHs=False)
+    ]