partial merge from #337 for testing

CONTRIBUTING.rst

@@ -0,0 +1,14 @@
+Contributing to Aurora
+----------------------
+
+
+If you'd like to contribute, start by searching through the `issues <https://github.com/simpeg/aurora/issues>`_ to see whether someone else has raised a similar idea or question.  If you don't see your idea listed, open an issue, and if there are code changes, also a pull request.
+
+
+There are many ways to contribute to the aurora, such as:
+
+* Report/fix bugs or issues encountered when using the software
+* Suggest additional features or functionalities
+* Fix editorial inconsistencies or inaccuracies
+
+Aurora is hosted by simpeg, please refer to their  `contributing guidelines page <https://docs.simpeg.xyz/latest/content/getting_started/contributing/index.html>`_. for more details.

aurora/general_helper_functions.py

@@ -1,5 +1,9 @@
+"""
+This module contains from miscellaneous functions and some global paths.
+"""
 import inspect
-import os
+
+# import os
 import pathlib
 import scipy.io as sio
 import subprocess
@@ -20,19 +24,15 @@
 BAND_SETUP_PATH = CONFIG_PATH.joinpath("emtf_band_setup")
 
 
-def get_mth5_ascii_data_path():
+def get_test_path() -> pathlib.Path:
     """
-    Get the path to the
+    Gets the path to where the test are.
+
     Returns
     -------
-    mth5_data_path: pathlib.Path
-        This is the place where the legacy test files (ascii MT data from EMTF) are archived
+    test_path: pathlib.Path
+        Object that points to where aurora's tests are.
     """
-    mth5_data_path = pathlib.Path(mth5.__file__).parent.joinpath("data")
-    return mth5_data_path
-
-
-def get_test_path():
     test_path = AURORA_PATH.joinpath("tests")
     if not test_path.exists():
         msg = (
@@ -44,6 +44,18 @@ def get_test_path():
     return test_path
 
 
+def get_mth5_ascii_data_path():
+    """
+    Get the path to the
+    Returns
+    -------
+    mth5_data_path: pathlib.Path
+        This is the place where the legacy test files (ascii MT data from EMTF) are archived
+    """
+    mth5_data_path = pathlib.Path(mth5.__file__).parent.joinpath("data")
+    return mth5_data_path
+
+
 try:
     FIGURES_PATH = DATA_PATH.joinpath("figures")
     FIGURES_PATH.mkdir(exist_ok=True, parents=True)
@@ -79,58 +91,58 @@ def count_lines(file_name):
 
 def execute_subprocess(cmd, **kwargs):
     """
+    A wrapper for subprocess.call
 
     Parameters
     ----------
     cmd : string
         command as it would be typed in a terminal
-    kwargs
-
-    Returns
-    -------
+    kwargs: denotes keyword arguments that would be passed to subprocess
 
-    """
-    """
-    A wrapper for subprocess.call
     """
     exit_status = subprocess.call([cmd], shell=True, **kwargs)
     if exit_status != 0:
         raise Exception("Failed to execute \n {}".format(cmd))
     return
 
 
-def execute_command(cmd, **kwargs):
-    """
-    Executes command in terminal from script.
-
-    Parameters:
-        cmd (str): command to exectute from a terminal
-        kwargs: exec_dir (str): the directory from which to execute
-        kwargs: no_exception: suppress output if exception
-
-    Other Parameters:
-        exit_status: :code:`0` is good, otherwise there is some problem
-
-    .. note:: When executing :code:`rm *` this crashes if the directory we are removing
-        from is empty
-
-    .. note:: if you can you should probably use execute_subprocess() instead
-    """
-    exec_dir = kwargs.get("exec_dir", os.path.expanduser("~/"))
-    allow_exception = kwargs.get("allow_exception", True)
-    logger.info("executing from {}".format(exec_dir))
-    cwd = os.getcwd()
-    os.chdir(exec_dir)
-    exit_status = os.system(cmd)
-    if exit_status != 0:
-        logger.info(f"exit_status of {cmd} = {exit_status}")
-        if allow_exception:
-            raise Exception(f"Failed to successfully execute \n {cmd}")
-    os.chdir(cwd)
+# TODO: Add test for execute_command or delete.
+# def execute_command(cmd, **kwargs):
+#     """
+#     Executes command in terminal from script.
+#
+#     Parameters:
+#     ----------
+#     cmd : str
+#         command to execute from a terminal
+#     kwargs: exec_dir (str): the directory from which to execute
+#     kwargs: no_exception: suppress output if exception
+#
+#     Other Parameters:
+#         exit_status: :code:`0` is good, otherwise there is some problem
+#
+#     .. note:: When executing :code:`rm *` this crashes if the directory we are removing
+#         from is empty
+#
+#     .. note:: if you can you should probably use execute_subprocess() instead
+#     """
+#     exec_dir = kwargs.get("exec_dir", os.path.expanduser("~/"))
+#     allow_exception = kwargs.get("allow_exception", True)
+#     logger.info("executing from {}".format(exec_dir))
+#     cwd = os.getcwd()
+#     os.chdir(exec_dir)
+#     exit_status = os.system(cmd)
+#     if exit_status != 0:
+#         logger.info(f"exit_status of {cmd} = {exit_status}")
+#         if allow_exception:
+#             raise Exception(f"Failed to successfully execute \n {cmd}")
+#     os.chdir(cwd)
 
 
 def save_to_mat(data, variable_name, filename):
     """
+    Saves numpy array in matlab format.
+
     Example Usage:
     x = X.to_array(dim="channel")
     save_to_mat(x.data, "x", "x.mat")
@@ -148,9 +160,6 @@ def save_to_mat(data, variable_name, filename):
     filename : string
         The filepath to output
 
-    Returns
-    -------
-
     """
     sio.savemat(filename, {variable_name: data})
     return