move version to mellon/version.py

Author: katosh

CHANGELOG.md

@@ -3,7 +3,8 @@
  - use [PyNNDescent](https://github.com/lmcinnes/pynndescent) for faster nearest neighbor distance computation
  - update deprecated `tol` argument of `jax.numpy.linalg.matrix_rank` to `rtol`
  - forward random state to k-means to compute landmarks
- - modernize build system using pyproject.toml instead of setup.py
+ - modernize build system using `pyproject.toml` instead of setup.py
+ - centralize version in `mellon/version.py` with dynamic versioning in pyproject.toml
 
 # v1.5.0
 

docs/source/conf.py

@@ -35,7 +35,7 @@ def get_version(rel_path):
 author = "Setty Lab"
 
 # The full version, including alpha/beta/rc tags
-release = get_version("../../mellon/__init__.py")
+release = get_version("../../mellon/version.py")
 
 
 # -- General configuration ---------------------------------------------------

mellon/__init__.py

@@ -18,8 +18,7 @@
 from . import _conditional as conditional
 from . import _derivatives as derivatives
 from . import validation
-
-__version__ = "1.6.0"
+from .version import __version__
 
 __all__ = [
     "DensityEstimator",
@@ -37,13 +36,30 @@
     "decomposition",
     "derivatives",
     "__version__",
+    "setup_jax",
+    "setup_logging",
 ]
 
-# Set default configuration at import time
-jaxconfig.update("jax_enable_x64", True)
-jaxconfig.update("jax_platform_name", "cpu")
 
-# configure logging
+def setup_jax(enable_x64=True, platform="cpu"):
+    """Set up JAX configuration.
+
+    Parameters
+    ----------
+    enable_x64 : bool, default=True
+        Whether to enable 64-bit precision.
+    platform : str, default="cpu"
+        Platform to use for JAX computation.
+    """
+    jaxconfig.update("jax_enable_x64", enable_x64)
+    jaxconfig.update("jax_platform_name", platform)
+
+
+# Default JAX configuration
+setup_jax()
+
+
+# Logging configuration
 LOGGING_CONFIG = {
     "version": 1,
     "disable_existing_loggers": False,
@@ -69,5 +85,21 @@
     },
 }
 
-logging.config.dictConfig(LOGGING_CONFIG)
-logger = logging.getLogger("mellon")
+
+def setup_logging(config=None):
+    """Set up logging configuration.
+
+    Parameters
+    ----------
+    config : dict, optional
+        Logging configuration dictionary. If None, the default
+        configuration is used.
+    """
+    if config is None:
+        config = LOGGING_CONFIG
+    logging.config.dictConfig(config)
+    return logging.getLogger("mellon")
+
+
+# Configure default logging
+logger = setup_logging()

mellon/version.py

@@ -0,0 +1,3 @@
+"""Version information."""
+
+__version__ = "1.6.0"

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>=42", "wheel"]
+requires = ["setuptools>=61.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "mellon"
-version = "1.6.0"
+dynamic = ["version"]
 description = "Non-parametric density estimator."
 authors = [
     {name = "Setty Lab", email = "dominik.otto@gmail.com"}
@@ -29,6 +29,9 @@ Homepage = "https://github.com/settylab/mellon"
 [tool.setuptools]
 packages = ["mellon"]
 
+[tool.setuptools.dynamic]
+version = {attr = "mellon.version.__version__"}
+
 [project.optional-dependencies]
 dev = [
     "black",