Mordern py

.github/workflows/Build.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     # Skip CI if 'skip ci' is contained in latest commit message
     if: "!contains(github.event.head_commit.message, 'skip ci')"
@@ -34,7 +34,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest --cov=SFC_Torch --cov-report=xml
+        pytest
 
     - name: Upload coverage to Codecov  
       uses: codecov/codecov-action@v3

.github/workflows/Publish.yml

@@ -8,15 +8,15 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Install Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build packaging setuptools twine wheel
+        pip install build twine
     - name: Build package
       run: |
         python -m build

SFC_Torch/VERSION

@@ -1 +1 @@
-0.2.5
+0.3.0

SFC_Torch/__init__.py

@@ -1,20 +1,49 @@
 def getVersionNumber():
-    import pkg_resources
-    version = pkg_resources.require("SFcalculator_torch")[0].version
-    return version
+    try:
+        from importlib.metadata import version
+    except ImportError:
+        # Fallback for Python < 3.8
+        from importlib_metadata import version
+    return version("SFcalculator_torch")
 
 __author__ = "Minhuan Li"
-__email__ = "minhuanli@g.harvard.edu"
+__email__ = "minhuanli41@gmail.com"
 __version__ = getVersionNumber()
 
-# Top level API
-from .Fmodel import SFcalculator
-from .io import PDBParser, fetch_pdb, fetch_pdbredo
-from .symmetry import get_polar_axis
+# Lazy loading to speed up imports while maintaining API compatibility
+_LAZY_IMPORTS = {
+    'SFcalculator': 'Fmodel',
+    'PDBParser': 'io',
+    'fetch_pdb': 'io',
+    'fetch_pdbredo': 'io',
+    'get_polar_axis': 'symmetry',
+    'utils': 'utils',
+    'patterson': 'patterson',
+    'packingscore': 'packingscore',
+}
 
-# Submodules
-from . import utils
-from . import patterson
-from . import packingscore
+def __getattr__(name):
+    """Lazy import mechanism for top-level API"""
+    if name in _LAZY_IMPORTS:
+        module_name = _LAZY_IMPORTS[name]
+        import importlib
+
+        # Import the module
+        if name in ['utils', 'patterson', 'packingscore']:
+            # These are submodule imports
+            module = importlib.import_module(f'.{module_name}', __name__)
+            globals()[name] = module
+            return module
+        else:
+            # These are specific objects from modules
+            module = importlib.import_module(f'.{module_name}', __name__)
+            obj = getattr(module, name)
+            globals()[name] = obj
+            return obj
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+def __dir__():
+    """Support for dir() to show available lazy imports"""
+    return list(globals().keys()) + list(_LAZY_IMPORTS.keys())
 
 

pyproject.toml

@@ -0,0 +1,70 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sfcalculator_torch"
+dynamic = ["version"]
+description = "A differentiable pipeline connecting molecule models and scattering data"
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "MIT"}
+authors = [
+    {name = "Minhuan Li", email = "minhuanli@g.harvard.edu"}
+]
+keywords = ["pytorch", "structure-factors", "differentiable", "crystallography", "cryoEM"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+dependencies = [
+    "gemmi>=0.5.6,<=0.6.7",
+    "reciprocalspaceship>=0.9.18,<=1.0.3",
+    "numpy<2.0.0",
+    "tqdm",
+    "loguru",
+]
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-cov"]
+dev = ["pytest", "pytest-cov", "build", "twine"]
+
+[project.urls]
+Homepage = "https://github.com/Hekstra-Lab/SFcalculator_torch"
+Documentation = "https://hekstra-lab.github.io/SFcalculator_torch/"
+Repository = "https://github.com/Hekstra-Lab/SFcalculator_torch"
+"Bug Tracker" = "https://github.com/Hekstra-Lab/SFcalculator_torch/issues"
+
+[tool.setuptools]
+packages = ["SFC_Torch"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+SFC_Torch = ["VERSION"]
+
+[tool.setuptools.dynamic]
+version = {file = "SFC_Torch/VERSION"}
+
+[tool.pytest.ini_options]
+addopts = "--cov=SFC_Torch --cov-report xml --cov-report term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+source = ["SFC_Torch"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+]
+