GraphAtoms 1.2.0__tar.gz → 1.2.1__tar.gz

{graphatoms-1.2.0 → graphatoms-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 1.2.0
+Version: 1.2.1
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong

graphatoms-1.2.1/pyproject.toml

@@ -0,0 +1,156 @@
+[build-system]
+requires = ["uv_build>=0.11.15,<0.12"]
+build-backend = "uv_build"
+
+[project]
+name = "graphatoms"
+version = "1.2.1"
+readme = "README.md"
+description = "The Chemical Core Class for Graph Theory Analysis."
+license-files = ["src/LICENSE"]
+license = "GPL-3.0-or-later"
+requires-python = ">=3.12"
+keywords = [
+    "chemistry",
+    "graph theory",
+    "reaction",
+    "event",
+    "KMC",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Intended Audience :: Science/Research",
+]
+dependencies = [
+    "ase",
+    "pymatgen>2023.6",
+    "rdkit>=2025",
+    "scikit-learn>=1.5",
+    "array-api-compat>=1.10",
+    "array_api-extra>=0.10",
+    "pyarrow",
+    "igraph>=0.11",
+    "h5py>=3.16",
+    "hydra-core",
+    "numpy>=2.0.0,<3",
+    "numpydantic",
+    "ovld",
+    "pydantic>=2.10",
+    "python-snappy>=0.7.3",
+    "tomli; python_version < '3.11'",
+    "tomli-w",
+    "typing-extensions",
+    "loguru",
+]
+
+[project.urls]
+Homepage = "https://github.com/LiuGaoyong/GraphAtoms"
+Repository = "https://github.com/LiuGaoyong/GraphAtoms"
+Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
+
+[[project.authors]]
+name = "LiuGaoyong"
+email = "liugaoyong_88@163.com"
+
+[dependency-groups]
+dev = [
+    "ruff>=0.11",
+    "array-api-strict",
+    "pytest>=8.3",
+    "pytest-xdist",
+    "jupyter",
+    "sqlmodel",
+    "openbabel-wheel",
+]
+
+[tool.uv]
+package = true
+
+[[tool.uv.index]]
+url = "https://mirrors.cernet.edu.cn/pypi/web/simple"
+default = true
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore::RuntimeWarning",
+    "ignore::DeprecationWarning",
+]
+addopts = "--maxfail=1 -rf"
+testpaths = ["src/tests"]
+
+[tool.ruff]
+line-length = 80
+indent-width = 4
+unsafe-fixes = true
+
+[tool.ruff.lint]
+select = [
+    "F",
+    "E",
+    "W",
+    "UP",
+    "TID",
+]
+ignore = [
+    "F722",
+    "D100",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.pixi.package.build.backend]
+name = "pixi-build-python"
+version = "*"
+
+[tool.pixi.workspace]
+preview = ["pixi-build"]
+channels = ["conda-forge"]
+platforms = [
+    "linux-64",
+    "osx-arm64",
+]
+
+[tool.pixi.pypi-dependencies.graphatoms]
+path = "."
+editable = true
+
+[tool.pixi.environments.default]
+solve-group = "default"
+
+[tool.pixi.environments.dev]
+features = ["dev"]
+solve-group = "default"
+
+[tool.pixi.tasks]
+test = "pytest -s -vv"
+benchmark = "pytest -s src/tests-benchmark/*.py"
+
+[tool.pixi.dependencies]
+python = ">=3.12"
+pytest = ">=9.0.3,<10"
+array-api-compat = ">=1.15.0,<2"
+array-api-extra = ">=0.11.0,<0.12"
+array-api-strict = ">=2.5,<3"
+ase = ">=3.28.0,<4"
+pymatgen = ">=2026.5.4,<2027"
+rdkit = ">=2025.9.5,<2027"
+openbabel = ">=3.1.1,<4"
+pyarrow = ">=21.0.0,<25"
+scikit-learn = ">=1.8.0,<2"
+python-igraph = ">=0.11.9,<0.12"
+numpy = ">=2.0.0,<3"
+pydantic = ">=2.10.0,<3"
+numpydantic = ">=1.8.1,<2"
+python-snappy = ">=0.7.3,<0.8"
+h5py = ">=3.16.0,<4"
+hydra-core = ">=1.3.2,<2"
+tomli-w = ">=1.2.0,<2"
+loguru = ">=0.7.3,<0.8"
+pytorch = ">=2.10.0,<3"
+jax = ">=0.9.0,<0.10"
+jupyterlab = ">=4.5.8,<5"
+ovld = ">=0.5.15,<0.6"
+pytest-xdist = ">=3.8.0,<4"

graphatoms-1.2.0/pyproject.toml → graphatoms-1.2.1/pyproject.toml.orig

@@ -9,7 +9,7 @@ Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
 
 [project]
 name = "graphatoms"
-version = "1.2.0"
+version = "1.2.1"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
@@ -49,7 +49,7 @@ dependencies = [
     "hydra-core",
     "numpy>=2.0.0,<3",
     "numpydantic",
-    "ovld", # singledispatch which works for multiple arguments.
+    "ovld",                           # singledispatch which works for multiple arguments.
     "pydantic>=2.10",
     "python-snappy>=0.7.3",           # More Fase Data Compression
     "tomli; python_version < '3.11'", # use tomllib in python>=3.11
@@ -64,7 +64,7 @@ dev = [
     "pytest>=8.3",
     "pytest-xdist",
     "jupyter",
-    "sqlmodel",        # SQL + pydantic
+    "sqlmodel",         # SQL + pydantic
     'openbabel-wheel',
 ]
 

{graphatoms-1.2.0 → graphatoms-1.2.1}/src/graphatoms/system/bonds.py

@@ -64,7 +64,7 @@ class BondGraph(Matter, OurFrozenModel):
                             f"Invalid shape for `{k}`: Len({k})="
                             f"{len(v)} but nbonds={self.nbonds}."
                         )
-            # assert self.__IGRAPH.is_simple(), "The graph should be simple."
+            assert self.__IGRAPH.is_simple(), "The graph should be simple."
         return self
 
     @override
@@ -112,7 +112,9 @@ class BondGraph(Matter, OurFrozenModel):
     @cached_property
     def __IGRAPH(self) -> IGraph:
         edges = np.column_stack([self.source, self.target])
-        g = IGraph(n=self.natoms, edges=edges, directed=False)
+        g = IGraph(n=self.natoms, edges=edges, directed=True)
+        # use directed graph for compatibility of full neighbor list
+        assert not g.has_multiple(), "This graph has multiple edges."
         return g.as_undirected()  # make sure it is undirected
 
     @cached_property
@@ -165,7 +167,7 @@ class BondGraph(Matter, OurFrozenModel):
 
     def get_match_mode(
         self,
-        pattern: Self,  # big graph
+        pattern: "BondGraph",
         algorithm: Literal["lad", "vf2"] = "lad",
         return_match_target: bool = True,
         only_number_color: bool = False,

{graphatoms-1.2.0 → graphatoms-1.2.1}/src/graphatoms/system/graph.py

@@ -425,7 +425,12 @@ class SysGraph(BondGraph, Structure, AtomTag, GasMixin):
             df_bonds["order"] = self.order
         if self.distance is not None:
             df_bonds["distance"] = self.distance
-        G = IGraph.DataFrame(df_bonds, False, df_atoms, True)
+        G = IGraph.DataFrame(
+            edges=df_bonds,
+            directed=True,  # use directed graph to avoid duplicate edges
+            vertices=df_atoms,
+            use_vids=True,
+        )
         for k in (
             Box.__pydantic_fields__.keys()
             | Energetics.__pydantic_fields__.keys()