Update logging and unpin numpy and cython versions in pyproject.toml

docs/conf.py

@@ -25,9 +25,9 @@
 author = "Jason D. McEwen, Christopher G. R. Wallis, Matthew A. Price, Matthew M. Docherty, Alicja Polanska"
 
 # The short X.Y version
-version = "1.2.2"
+version = "1.2.3"
 # The full version, including alpha/beta/rc tags
-release = "1.2.2"
+release = "1.2.3"
 
 
 # -- General configuration  ---------------------------------------------------

logs/logging.yaml → harmonic/default-logging-config.yaml

@@ -1,5 +1,5 @@
 # ==================================================
-# Logging setup for Harmonic Software package (2018)
+# Logging setup for Harmonic Software package (2024)
 # ==================================================
 
 version: 1
@@ -29,21 +29,21 @@ handlers:
         class: logging.FileHandler
         level: INFO
         formatter: simple
-        filename: /logs/info.log
+        filename: info.log
         encoding: utf8
 
     debug_file_handler:
         class: logging.FileHandler
         level: DEBUG
         formatter: simple
-        filename: /logs/debug.log
+        filename: debug.log
         encoding: utf8
 
     critical_file_handler:
         class: logging.FileHandler
         level: CRITICAL
         formatter: simple
-        filename: /logs/critical.log
+        filename: critical.log
         encoding: utf8
 
 loggers:

harmonic/logs.py

@@ -1,15 +1,16 @@
 import os
 import logging.config
 import logging
+from pathlib import Path
 import yaml
 import harmonic
-import colorlog
+
 
 def setup_logging(custom_yaml_path=None, default_level=logging.DEBUG):
     """initialise and configure logging.
-    
-    Should be called at the beginning of code to initialise and configure the 
-    desired logging level. Logging levels can be ints in [0,50] where 10 is 
+
+    Should be called at the beginning of code to initialise and configure the
+    desired logging level. Logging levels can be ints in [0,50] where 10 is
     debug logging and 50 is critical logging.
 
     Args:
@@ -24,35 +25,21 @@ def setup_logging(custom_yaml_path=None, default_level=logging.DEBUG):
         ValueError: Raised if logging.yaml is not in ./logs/ directory.
 
     """
-    if custom_yaml_path == None:
-        path = os.path.join(os.path.dirname(os.path.dirname(
-            os.path.realpath(harmonic.__file__))) + '/logs/logging.yaml')
-    if custom_yaml_path != None:
-        path = custom_yaml_path
-    value = os.getenv('LOG_CFG', None)
-    if value:
-        path = value
-    if os.path.exists(path):
-        with open(path, 'rt') as f:
-            config = yaml.safe_load(f.read())
-        if custom_yaml_path == None:
-            config['handlers']['info_file_handler']['filename'] = os.path.join(
-                os.path.dirname(os.path.dirname(
-                    os.path.realpath(harmonic.__file__))) + '/logs/info.log')
-            config['handlers']['debug_file_handler']['filename'] = os.path.join(
-                os.path.dirname(os.path.dirname(
-                    os.path.realpath(harmonic.__file__))) + '/logs/debug.log')
-            config['handlers']['critical_file_handler']['filename'] = os.path.join(
-                os.path.dirname(os.path.dirname(
-                    os.path.realpath(harmonic.__file__))) + '/logs/critical.log')
-            config['handlers']['info_file_handler']['filename'] = os.path.join(
-                os.path.dirname(os.path.dirname(
-                    os.path.realpath(harmonic.__file__))) + '/logs/info.log')
-        logging.config.dictConfig(config)
+    if "LOG_CFG" in os.environ:
+        path = Path(os.environ["LOG_CFG"])
+    elif custom_yaml_path is None:
+        path = Path(harmonic.__file__).parent / "default-logging-config.yaml"
     else:
-        logging.basicConfig(level=default_level)
-        raise ValueError("Logging config pathway incorrect.")
-        critical_log('Using custom config from {}'.format(path))
+        path = Path(custom_yaml_path)
+    if not path.exists():
+        raise ValueError(f"Logging config path {path} does not exist.")
+    with open(path, "rt") as f:
+        config = yaml.safe_load(f.read())
+    if custom_yaml_path is None:
+        config["handlers"]["info_file_handler"]["filename"] = "info.log"
+        config["handlers"]["debug_file_handler"]["filename"] = "debug.log"
+        config["handlers"]["critical_file_handler"]["filename"] = "critical.log"
+    logging.config.dictConfig(config)
 
 
 def debug_log(message):
@@ -63,21 +50,23 @@ def debug_log(message):
         message: Message to log.
 
     """
-    logger = logging.getLogger('Harmonic')
+    logger = logging.getLogger("Harmonic")
     logger.debug(message)
 
+
 def warning_log(message):
-    """Log a warning (e.g. for internal code warnings such as large dynamic 
+    """Log a warning (e.g. for internal code warnings such as large dynamic
     ranges).
 
     Args:
 
         message: Warning to log.
 
     """
-    logger = logging.getLogger('Harmonic')
+    logger = logging.getLogger("Harmonic")
     logger.warning(message)
 
+
 def critical_log(message):
     """Log a critical message (e.g. core code failures etc).
 
@@ -86,18 +75,18 @@ def critical_log(message):
         message: Message to log.
 
     """
-    logger = logging.getLogger('Harmonic')
+    logger = logging.getLogger("Harmonic")
     logger.critical(message)
 
+
 def info_log(message):
-    """Log an information message (e.g. evidence value printing, run completion 
+    """Log an information message (e.g. evidence value printing, run completion
     etc).
 
     Args:
 
         message: Message to log.
 
     """
-    logger = logging.getLogger('Harmonic')
+    logger = logging.getLogger("Harmonic")
     logger.info(message)
-

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy==1.23.1", "Cython==0.29.30"]
+requires = ["setuptools", "wheel", "numpy", "Cython"]
 build-backend = "setuptools.build_meta"

setup.py

@@ -1,7 +1,5 @@
-import sys
 import os
 import shutil
-import setuptools
 from setuptools import setup, Extension
 from Cython.Distutils import build_ext
 from Cython.Build import cythonize
@@ -48,7 +46,7 @@ def read_file(file):
         "Intended Audience :: Science/Research",
     ],
     name="harmonic",
-    version="1.2.2",
+    version="1.2.3",
     prefix=".",
     url="https://github.com/astro-informatics/harmonic",
     author="Jason D. McEwen, Alicja Polanska, Christopher G. R. Wallis, Matthew A. Price, Matthew M. Docherty & Contributors",
@@ -59,6 +57,8 @@ def read_file(file):
     long_description_content_type="text/x-rst",
     long_description=long_description,
     packages=["harmonic"],
+    include_package_data=True,
+    package_data={"harmonic": ["default-logging-config.yaml"]},
     cmdclass={"build_ext": build_ext},
     ext_modules=cythonize(
         [