First try at changing the logging facilities

autotest/utils_tests.py

@@ -2099,10 +2099,15 @@ def run_sp_capture_output_test(tmp_path):
     else:
         shell = False
     log_file = os.path.join(tmp_path, "pyemu.log")
-    pyemu.os_utils.run("echo Hello World", 
-                       verbose=False, use_sp=True, 
-                       shell=shell, cwd=tmp_path, logfile=True)
-
+    pyemu.os_utils.run(
+        "echo Hello World",
+        verbose=False,
+        use_sp=True,
+        shell=shell,
+        cwd=tmp_path,
+        logfile=log_file,
+    )
+
     with open(log_file, 'r') as f:
         content = f.read()
     assert "Hello World" in content

pyemu/utils/log_utils.py

@@ -0,0 +1,71 @@
+"""Utilities to help with logging."""
+
+import logging
+import sys
+from typing import Any, Optional, Union
+
+FILE_HANDLER = logging.FileHandler("pyemu.log", delay=True)
+STREAM_HANDLER = logging.StreamHandler(sys.stdout)
+
+LOGGER: Optional[logging.Logger] = None
+
+
+def set_logger(
+    logger: Optional[logging.Logger] = None,
+    /,
+    **basic_config: Any,
+) -> None:
+    """Set the global logger to be used by pyemu.
+
+    Args:
+        logger (logging.Logger): the logger to be used.
+        **basic_config (Any): keyword arguments to `logging.basicConfig`
+    """
+    global LOGGER
+    if logger is not None:
+        if basic_config:
+            raise ValueError(
+                "If a logger is passed no extra keyword arguments should be passed as well."
+            )
+    else:
+        if not basic_config:
+            raise ValueError(
+                "If no logger is passed then keyword arguments for logging.basicConfig should be passed."
+            )
+        logging.basicConfig(**basic_config)
+        logger = logging.getLogger("pyemu")
+    LOGGER = logger
+
+
+def get_logger(
+    name: Optional[str] = "pyemu",
+    verbose: bool = False,
+    logfile: Union[bool , str] = False,
+) -> logging.Logger:
+    """Get a logger instance.
+
+    Used to either get
+    Args:
+        name (`str`): name of the logger (default: "pyemu")
+        logger (`bool` or `logging.Logger`): either a boolean indicating to write to
+            "pyemu.log" or a logger to return as is.
+
+    Returns:
+        logging.Logger object
+    """
+    if LOGGER is not None:
+        return LOGGER
+    logger = logging.getLogger(name)
+    logger.setLevel(logging.INFO)
+
+    for handler in logger.handlers:
+        logger.removeHandler(handler)
+    if logfile is True:
+        logger.addHandler(FILE_HANDLER)
+    elif isinstance(logfile, str):
+        logger.addHandler(logging.FileHandler(logfile))
+
+    if verbose:
+        logger.addHandler(STREAM_HANDLER)
+
+    return logger

pyemu/utils/os_utils.py

@@ -11,6 +11,7 @@
 import time
 from datetime import datetime
 from ..pyemu_warnings import PyemuWarning
+from . import log_utils
 
 ext = ""
 bin_path = os.path.join("..", "bin")
@@ -173,8 +174,10 @@ def run_sp(cmd_str, cwd=".", verbose=True, logfile=False, **kwargs):
 
     # print warning if shell is True
     if shell:
-        warnings.warn("shell=True is not recommended and may cause issues, but hey! YOLO", PyemuWarning)
-
+        warnings.warn(
+            "shell=True is not recommended and may cause issues, but hey! YOLO",
+            PyemuWarning,
+        )
 
     bwd = os.getcwd()
     os.chdir(cwd)
@@ -184,26 +187,19 @@ def run_sp(cmd_str, cwd=".", verbose=True, logfile=False, **kwargs):
 
     try:
         cmd_ins = [i for i in cmd_str.split()]
-        log_stream = open(os.path.join('pyemu.log'), 'w+', newline='') if logfile else None
-        with sp.Popen(cmd_ins, stdout=sp.PIPE, 
-                      stderr=sp.STDOUT, text=True,
-                      shell=shell, bufsize=1) as process:
+        logger = log_utils.get_logger(verbose=verbose, logfile=logfile)
+        with sp.Popen(
+            cmd_ins, stdout=sp.PIPE, stderr=sp.STDOUT, text=True, shell=shell, bufsize=1
+        ) as process:
             for line in process.stdout:
-                if verbose:
-                    print(line, flush=True, end='')
-                if logfile:
-                    log_stream.write(line.strip('\n'))
-                    log_stream.flush()
-            process.wait() # wait for the process to finish
+                logger.info(line.rstrip("\n"))
+            process.wait()  # wait for the process to finish
             retval = process.returncode
 
     except Exception as e:
         os.chdir(bwd)
         raise Exception("run() raised :{0}".format(str(e)))
 
-    finally:
-        if logfile:
-            log_stream.close()
     os.chdir(bwd)
 
     if "window" in platform.platform().lower():