GraphAtoms 1.1.3__tar.gz → 1.2.0__tar.gz

{graphatoms-1.1.3 → graphatoms-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 1.1.3
+Version: 1.2.0
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong
@@ -14,12 +14,16 @@ Requires-Dist: ase
 Requires-Dist: pymatgen>2023.6
 Requires-Dist: rdkit>=2025
 Requires-Dist: scikit-learn>=1.5
+Requires-Dist: array-api-compat>=1.10
+Requires-Dist: array-api-extra>=0.10
 Requires-Dist: pyarrow
 Requires-Dist: igraph>=0.11
 Requires-Dist: h5py>=3.16
 Requires-Dist: hydra-core
+Requires-Dist: numpy>=2.0.0,<3
 Requires-Dist: numpydantic
-Requires-Dist: pydantic>=2.11
+Requires-Dist: ovld
+Requires-Dist: pydantic>=2.10
 Requires-Dist: python-snappy>=0.7.3
 Requires-Dist: tomli ; python_full_version < '3.11'
 Requires-Dist: tomli-w
@@ -35,45 +39,62 @@ Description-Content-Type: text/markdown
 
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)    [![Pypi version](https://img.shields.io/pypi/v/graphatoms)](https://pypi.org/project/graphatoms/) [![PyPI Downloads](https://static.pepy.tech/badge/graphatoms)](https://pepy.tech/projects/graphatoms)
 
-
-The Chemical Core Class for Graph Theory Analysis & Graph Neural Network.
+The Chemical Core Class for Graph Theory Analysis.
 
 ## Overview
 
-The `graphatoms` is a Python library designed for chemical graph theory analysis and graph neural network applications. It provides core classes for representing chemical systems and reactions with graph-based data structures.
+The `graphatoms` is a Python library designed for chemical graph theory analysis. It provides core classes for representing chemical systems and reactions with graph-based data structures.
 
 ## Features
 
 - **Graph-based Chemical System Representation**: Represent chemical systems, clusters, and gas molecules using graph theory
 - **Reaction Modeling**: Support for reaction classes, KMC (Kinetic Monte Carlo) events, and MC (Monte Carlo) moves
-- **Geometry Operations**: Bond lists, distance calculations, neighbor lists, rotations, and sampling
+- **Geometry Operations**: Bond lists, distance calculations, neighbor lists, rotations, MIC (Minimum Image Convention), and sampling
 - **Data Storage**: Support for HDF5 and SQLite databases for efficient data persistence
 - **Dataclasses**: Pydantic-based data models for type-safe data handling
+- **Array API Compatibility**: Full support for array API standard for cross-framework compatibility (NumPy, PyTorch, JAX, CuPy, etc.)
+- **Subgraph Operations**: Backend-agnostic subgraph extraction with relabeling support using array-api-compat and array-api-extra
 
 ## Module Structure
 
 ```
 src/graphatoms/
+├── arrayapi/        # Array API compatibility layer
 ├── dataclasses/     # Pydantic-based data models
 ├── geometry/        # Geometric operations
 ├── reaction/        # Reaction classes and KMC events
-├── system/          # Core system classes (System, Cluster, Gas)
+│   ├── base/        # Abstract base classes
+│   ├── event/       # KMC events (adsorption, desorption, reaction)
+│   ├── mcmove/      # Monte Carlo moves
+│   ├── mdwarpper/   # MD wrapper
+│   └── network/     # Reaction network
+├── system/          # Core system classes
+│   ├── atoms/       # Atomic structure handling
+│   ├── database/    # Database storage backends
+│   └── graph/       # Graph-based system representation
 └── utils/           # Utility functions
+    └── subgraph.py  # Array API compatible subgraph operations
 ```
 
 ## Requirements
 
-- Python >= 3.10
+- Python >= 3.12
 - ase
 - pymatgen > 2023.6
 - rdkit >= 2025
 - scikit-learn >= 1.5
+- array-api-compat >= 1.15.0
+- array-api-extra >= 0.11.0
 - pyarrow
 - igraph >= 0.11
 - h5py >= 3.16
 - hydra-core
+- numpy >= 2.0.0
 - numpydantic
-- pydantic >= 2.11
+- ovld
+- pydantic >= 2.10
+- python-snappy >= 0.7.3
+- loguru
 
 ## Installation
 
@@ -81,6 +102,12 @@ src/graphatoms/
 pip install graphatoms
 ```
 
+Or with conda:
+
+```bash
+conda install -c conda-forge graphatoms
+```
+
 ## Development
 
 For development setup with pixi:
@@ -90,6 +117,27 @@ pixi install
 pixi run test
 ```
 
+## Running Tests
+
+# Run all tests
+
+pytest src/tests/ -v
+
+# Run benchmark tests
+
+pytest src/tests-benchmark/ -v
+
+## Array API Compatibility
+
+The library leverages `array-api-compat` and `array-api-extra` for backend-agnostic array operations. Key utilities include:
+
+- `subgraph()`: Extracts induced subgraphs from edge indices
+- `map_index()`: Maps indices across arrays
+- `index_to_mask()`: Converts index arrays to boolean masks
+- `maybe_num_nodes()`: Determines the number of nodes from edge indices
+
+These functions work seamlessly with NumPy, PyTorch, JAX, and other array API compliant libraries.
+
 ## License
 
 GPL-3.0-or-later

graphatoms-1.2.0/README.md

@@ -0,0 +1,116 @@
+# graphatoms
+
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)    [![Pypi version](https://img.shields.io/pypi/v/graphatoms)](https://pypi.org/project/graphatoms/) [![PyPI Downloads](https://static.pepy.tech/badge/graphatoms)](https://pepy.tech/projects/graphatoms)
+
+The Chemical Core Class for Graph Theory Analysis.
+
+## Overview
+
+The `graphatoms` is a Python library designed for chemical graph theory analysis. It provides core classes for representing chemical systems and reactions with graph-based data structures.
+
+## Features
+
+- **Graph-based Chemical System Representation**: Represent chemical systems, clusters, and gas molecules using graph theory
+- **Reaction Modeling**: Support for reaction classes, KMC (Kinetic Monte Carlo) events, and MC (Monte Carlo) moves
+- **Geometry Operations**: Bond lists, distance calculations, neighbor lists, rotations, MIC (Minimum Image Convention), and sampling
+- **Data Storage**: Support for HDF5 and SQLite databases for efficient data persistence
+- **Dataclasses**: Pydantic-based data models for type-safe data handling
+- **Array API Compatibility**: Full support for array API standard for cross-framework compatibility (NumPy, PyTorch, JAX, CuPy, etc.)
+- **Subgraph Operations**: Backend-agnostic subgraph extraction with relabeling support using array-api-compat and array-api-extra
+
+## Module Structure
+
+```
+src/graphatoms/
+├── arrayapi/        # Array API compatibility layer
+├── dataclasses/     # Pydantic-based data models
+├── geometry/        # Geometric operations
+├── reaction/        # Reaction classes and KMC events
+│   ├── base/        # Abstract base classes
+│   ├── event/       # KMC events (adsorption, desorption, reaction)
+│   ├── mcmove/      # Monte Carlo moves
+│   ├── mdwarpper/   # MD wrapper
+│   └── network/     # Reaction network
+├── system/          # Core system classes
+│   ├── atoms/       # Atomic structure handling
+│   ├── database/    # Database storage backends
+│   └── graph/       # Graph-based system representation
+└── utils/           # Utility functions
+    └── subgraph.py  # Array API compatible subgraph operations
+```
+
+## Requirements
+
+- Python >= 3.12
+- ase
+- pymatgen > 2023.6
+- rdkit >= 2025
+- scikit-learn >= 1.5
+- array-api-compat >= 1.15.0
+- array-api-extra >= 0.11.0
+- pyarrow
+- igraph >= 0.11
+- h5py >= 3.16
+- hydra-core
+- numpy >= 2.0.0
+- numpydantic
+- ovld
+- pydantic >= 2.10
+- python-snappy >= 0.7.3
+- loguru
+
+## Installation
+
+```bash
+pip install graphatoms
+```
+
+Or with conda:
+
+```bash
+conda install -c conda-forge graphatoms
+```
+
+## Development
+
+For development setup with pixi:
+
+```bash
+pixi install
+pixi run test
+```
+
+## Running Tests
+
+# Run all tests
+
+pytest src/tests/ -v
+
+# Run benchmark tests
+
+pytest src/tests-benchmark/ -v
+
+## Array API Compatibility
+
+The library leverages `array-api-compat` and `array-api-extra` for backend-agnostic array operations. Key utilities include:
+
+- `subgraph()`: Extracts induced subgraphs from edge indices
+- `map_index()`: Maps indices across arrays
+- `index_to_mask()`: Converts index arrays to boolean masks
+- `maybe_num_nodes()`: Determines the number of nodes from edge indices
+
+These functions work seamlessly with NumPy, PyTorch, JAX, and other array API compliant libraries.
+
+## License
+
+GPL-3.0-or-later
+
+## Authors
+
+- LiuGaoyong (liugaoyong_88@163.com)
+
+## Links
+
+- Homepage: https://github.com/LiuGaoyong/GraphAtoms
+- Repository: https://github.com/LiuGaoyong/GraphAtoms
+- Issues: https://github.com/LiuGaoyong/GraphAtoms/issues/

{graphatoms-1.1.3 → graphatoms-1.2.0}/pyproject.toml

@@ -9,7 +9,7 @@ Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
 
 [project]
 name = "graphatoms"
-version = "1.1.3"
+version = "1.2.0"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
@@ -37,6 +37,8 @@ dependencies = [
     # Scientific Computing
     # numpy pandas, scipy
     "scikit-learn>=1.5",
+    "array-api-compat>=1.10",
+    "array_api-extra>=0.10",
     "pyarrow",
 
     # Graph Theory
@@ -45,8 +47,10 @@ dependencies = [
     # Data Model
     "h5py>=3.16",
     "hydra-core",
+    "numpy>=2.0.0,<3",
     "numpydantic",
-    "pydantic>=2.11",
+    "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
     "tomli-w",                        # TOML writer
@@ -56,6 +60,7 @@ dependencies = [
 [dependency-groups]
 dev = [
     "ruff>=0.11",
+    "array-api-strict",
     "pytest>=8.3",
     "pytest-xdist",
     "jupyter",
@@ -84,6 +89,7 @@ filterwarnings = [
     # ignore the following warnings that matching a regex
     # example: 'ignore:function ham\(\) is deprecated:DeprecationWarning',
     "ignore::RuntimeWarning",
+    "ignore::DeprecationWarning",
 
 ]
 addopts = '--maxfail=1 -rf' # exit after 1 failures, report fail info
@@ -93,7 +99,9 @@ testpaths = ['src/tests']
 [tool.ruff]
 line-length = 80
 indent-width = 4
-select = ["F", "E", "W", "UP", "D"]
+unsafe-fixes = true
+[tool.ruff.lint]
+select = ["F", "E", "W", "UP", "TID"]
 ignore = ["F722", "D100"]
 [tool.ruff.lint.pydocstyle]
 convention = "google"
@@ -106,7 +114,7 @@ backend = { name = "pixi-build-python", version = "*" }
 [tool.pixi.workspace]
 preview = ["pixi-build"]
 channels = ["conda-forge"]
-platforms = ["win-64", "linux-64", "osx-arm64"]
+platforms = ["linux-64", "osx-arm64"]
 
 [tool.pixi.pypi-dependencies]
 graphatoms = { path = ".", editable = true }
@@ -117,11 +125,14 @@ dev = { features = ["dev"], solve-group = "default" }
 
 [tool.pixi.tasks]
 test = "pytest -s -vv"
-benchmark = 'pytest -s src/benchmark/*.py'
+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"
@@ -129,9 +140,16 @@ 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/src/graphatoms/arrayapi/__init__.py

@@ -0,0 +1,11 @@
+"""The array api wrapper of this packages."""
+
+from graphatoms.arrayapi.compat import get_namespace
+from graphatoms.arrayapi.typing import Array, ArrayNamespace, LinalgNamespace
+
+__all__ = [
+    "get_namespace",
+    "ArrayNamespace",
+    "LinalgNamespace",
+    "Array",
+]

graphatoms-1.2.0/src/graphatoms/arrayapi/compat.py

@@ -0,0 +1,15 @@
+from array_api_compat import array_namespace
+from array_api_compat.common._typing import Namespace
+
+from graphatoms.arrayapi.typing import Array, ArrayNamespace
+
+
+def get_namespace(
+    *xs: Array | complex | None,
+    use_compat: bool | None = None,
+) -> ArrayNamespace | Namespace:
+    return array_namespace(
+        *xs,  # type: ignore[reportOptionalMemberAccess]
+        use_compat=use_compat,
+        # api_version="2024.12",
+    )  # type: ignore[reportOptionalMemberAccess]