Merge pull request #50 from AdamTheisen/master

Updates to documentation and more

CONTRIBUTING.rst

@@ -13,7 +13,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/AdamTheisen/arm-community-toolkit/issues.
+Report bugs at https://github.com/ANL-DIGR/ACT/issues
 
 If you are reporting a bug, please include:
 
@@ -35,14 +35,14 @@ is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-ARM Community Toolkit could always use more documentation, whether
-as part of the official ARM Community Toolkit docs, in docstrings,
+Atmospheric data Community Toolkit could always use more documentation, whether
+as part of the official Atmospheric data Community Toolkit docs, in docstrings,
 or even on the web in blog posts, articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/AdamTheisen/arm-community-toolkit/issues.
+The best way to send feedback is to file an issue at https://github.com/ANL-DIGR/ACT/issues
 
 If you are proposing a feature:
 
@@ -200,7 +200,7 @@ An example:
 
             """
             Returns `xarray.Dataset` with stored data and metadata from a
-            user-defined query of ARM-standard netCDF files from a single
+            user-defined query of standard netCDF files from a single
             datastream.
 
             Parameters
@@ -299,7 +299,7 @@ An example:
 
 
         def test_correct_ceil():
-            # Make a fake ARM dataset to test with, just an array with 1e-7
+            # Make a fake dataset to test with, just an array with 1e-7
             # for half of it.
             fake_data = 10 * np.ones((300, 20))
             fake_data[:, 10:] = -1
@@ -410,7 +410,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 2.7, 3.6, 3.7 for PyPy. Check
-   https://travis-ci.org/AdamTheisen/arm-community-toolkit/pull_requests
+   https://travis-ci.org/ANL-DIGR/ACT
    and make sure that the tests pass for all supported Python versions.
 
 After creating a pull request through GitHub, and outside checker TravisCI

LICENSE.txt

@@ -0,0 +1,11 @@
+Copyright 2019 UChicago Argonne LLC
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,6 +1,5 @@
 include AUTHORS.rst
 include CONTRIBUTING.rst
-include LICENSE
 include README.rst
 
 recursive-exclude * __pycache__

README.rst

@@ -5,13 +5,9 @@ Atmospheric Community Toolkit (ACT)
 .. image:: https://img.shields.io/travis/ANL-DIGR/ACT.svg
         :target: https://travis-ci.org/ANL-DIGR/ACT
 
-Package for connecting Atmospheric Radation Measurement (ARM) users to the
+Package for connecting Atmospheric data users to the
 data. Has the ability to download, read, and visualize multi-file datasets from
-ARM datastreams. Currently, multi-panel timeseries plots are supported. For
-more on ARM and ARM datastreams:
-
-* ARM: https://www.arm.gov/
-* ARM Data Discovery: https://www.archive.arm.gov/discovery/
+multiple data sources. Currently, multi-panel timeseries plots are supported. 
 
 * Free software: 3-clause BSD license
 

act/corrections/ceil.py

@@ -1,30 +1,30 @@
 import numpy as np
 
 
-def correct_ceil(arm_obj, fill_value=1e-7):
+def correct_ceil(obj, fill_value=1e-7):
     """
     This procedure corrects celiometer data by filling all zero and
     negative values of backscatter with fill_value and then converting
     the backscatter data into logarithmic space.
 
     Parameters
     ----------
-    arm_obj: ARM Dataset object
+    obj: Dataset object
         The ceiliometer dataset to correct. The backscatter data should be
         in linear space.
     fill_value: float
         The fill_value to use. The fill_value is entered in linear space.
 
     Returns
     -------
-    arm_obj: ARM Dataset object
+    obj: Dataset object
         The celiometer dataset containing the corrected values.
     """
 
-    backscat = arm_obj['backscatter'].data
+    backscat = obj['backscatter'].data
     backscat[backscat <= 0] = fill_value
     backscat = np.log10(backscat)
 
-    arm_obj['backscatter'].data = backscat
+    obj['backscatter'].data = backscat
 
-    return arm_obj
+    return obj

act/discovery/__init__.py

@@ -13,4 +13,4 @@
 
     download_data
 """
-from .get_files import download_data
+from .get_armfiles import download_data

act/plotting/plot.py

@@ -70,7 +70,7 @@ class with this set to None will create a new figure handle. See the
 
     Parameters
     ----------
-    arm_obj: ACT Dataset, dict, or tuple
+    obj: ACT Dataset, dict, or tuple
         The ACT Dataset to display in the object. If more than one dataset
         is to be specified, then a tuple can be used if all of the datasets
         conform to ARM standards. Otherwise, a dict with a key corresponding
@@ -90,29 +90,29 @@ class with this set to None will create a new figure handle. See the
         Keyword arguments passed to :func:`plt.figure`.
 
     """
-    def __init__(self, arm_obj, subplot_shape=(1,), ds_name=None,
+    def __init__(self, obj, subplot_shape=(1,), ds_name=None,
                  subplot_kw=None, **kwargs):
-        if isinstance(arm_obj, xr.Dataset):
-            if arm_obj.act.datastream is not None:
-                self._arm = {arm_obj.act.datastream: arm_obj}
+        if isinstance(obj, xr.Dataset):
+            if obj.act.datastream is not None:
+                self._arm = {obj.act.datastream: obj}
             elif ds_name is not None:
-                self._arm = {ds_name: arm_obj}
+                self._arm = {ds_name: obj}
             else:
                 warnings.warn(("Could not discern datastream" +
                                "name and dict or tuple were " +
                                "not provided. Using default" +
                                "name of act_datastream!"), UserWarning)
 
-                self._arm = {'act_datastream': arm_obj}
+                self._arm = {'act_datastream': obj}
 
         # Automatically name by datastream if a tuple of object is supplied
-        if isinstance(arm_obj, tuple):
+        if isinstance(obj, tuple):
             self._arm = {}
-            for arm_objs in arm_obj:
-                self._arm[arm_objs.act.datastream] = arm_objs
+            for objs in obj:
+                self._arm[objs.act.datastream] = objs
 
-        if isinstance(arm_obj, dict):
-            self._arm = arm_obj
+        if isinstance(obj, dict):
+            self._arm = obj
 
         self.fields = {}
         self.ds = {}
@@ -307,8 +307,8 @@ class TimeSeriesDisplay(Display):
     until add_subplots or plots is called.
 
     """
-    def __init__(self, arm_obj, subplot_shape=(1,), ds_name=None, **kwargs):
-        super().__init__(arm_obj, subplot_shape, ds_name, **kwargs)
+    def __init__(self, obj, subplot_shape=(1,), ds_name=None, **kwargs):
+        super().__init__(obj, subplot_shape, ds_name, **kwargs)
 
     def day_night_background(self, dsname=None, subplot_index=(0, )):
         """
@@ -969,8 +969,8 @@ class and has therefore has the same attributes as that class.
         WindDisplay = act.plotting.WindRoseDisplay(sonde_ds, figsize=(8,10))
 
     """
-    def __init__(self, arm_obj, subplot_shape=(1,), ds_name=None, **kwargs):
-        super().__init__(arm_obj, subplot_shape, ds_name,
+    def __init__(self, obj, subplot_shape=(1,), ds_name=None, **kwargs):
+        super().__init__(obj, subplot_shape, ds_name,
                          subplot_kw=dict(projection='polar'), **kwargs)
 
     def set_thetarng(self, trng=(0., 360.), subplot_index=(0,)):
@@ -1155,14 +1155,14 @@ class and has therefore has the same attributes as that class.
         plt.show()
 
     """
-    def __init__(self, arm_obj, subplot_shape=(1,), ds_name=None, **kwargs):
+    def __init__(self, obj, subplot_shape=(1,), ds_name=None, **kwargs):
         # We want to use our routine to handle subplot adding, not the main
         # one
         if not METPY_AVAILABLE:
             raise ImportError("MetPy need to be installed on your system to " +
                               "make Skew-T plots.")
         new_kwargs = kwargs.copy()
-        super().__init__(arm_obj, None, ds_name,
+        super().__init__(obj, None, ds_name,
                          subplot_kw=dict(projection='skewx'), **new_kwargs)
 
         # Make a SkewT object for each subplot

act/tests/test_plotting.py

@@ -1,7 +1,7 @@
 import matplotlib
 matplotlib.use('Agg')
 import act.io.armfiles as arm
-import act.discovery.get_files as get_data
+import act.discovery.get_armfiles as get_data
 import act.tests.sample_files as sample_files
 import act.corrections.ceil as ceil
 import pytest

docs/source/API/index.rst

@@ -5,7 +5,7 @@ API Reference
 :Release: |version|
 :Date: |today|
 
-This shows the details of the API of the ARM Community Toolkit. Documentation 
+This shows the details of the API of the Atmospheric data Community Toolkit. Documentation 
 of each procedure in each module is provided as a reference.
 
 .. toctree::

docs/source/CONTRIBUTING.rst

@@ -13,7 +13,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/AdamTheisen/arm-community-toolkit/issues.
+Report bugs at https://github.com/ANL-DIGR/ACT/issues
 
 If you are reporting a bug, please include:
 
@@ -35,14 +35,14 @@ is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-ARM Community Toolkit could always use more documentation, whether
-as part of the official ARM Community Toolkit docs, in docstrings,
+Atmospheric data Community Toolkit could always use more documentation, whether
+as part of the official Atmospheric data Community Toolkit docs, in docstrings,
 or even on the web in blog posts, articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/AdamTheisen/arm-community-toolkit/issues.
+The best way to send feedback is to file an issue at https://github.com/ANL-DIGR/ACT/issues
 
 If you are proposing a feature:
 
@@ -57,7 +57,7 @@ Get Started!
 Ready to contribute? Here's are a few steps we will go over for contributing
 to `act`.
 
-1. Fork the `arm-community-toolkit` repo on GitHub and clone your fork locally.
+1. Fork the `ACT` repo on GitHub and clone your fork locally.
 
 2. Install your local copy into an Anaconda environment. Assuming you have
    anaconda installed.
@@ -75,7 +75,7 @@ to `act`.
 
 Fork and Cloning the ACT Repository
 -----------------------------------
-To start, you will first fork the `arm-community-toolkit` repo on GitHub by
+To start, you will first fork the `ACT` repo on GitHub by
 clicking the fork icon button found on the main page here:
 
 - https://github.com/ANL-DIGR/ACT
@@ -200,7 +200,7 @@ An example:
 
             """
             Returns `xarray.Dataset` with stored data and metadata from a
-            user-defined query of ARM-standard netCDF files from a single
+            user-defined query of standard netCDF files from a single
             datastream.
 
             Parameters
@@ -299,7 +299,7 @@ An example:
 
 
         def test_correct_ceil():
-            # Make a fake ARM dataset to test with, just an array with 1e-7
+            # Make a fake dataset to test with, just an array with 1e-7
             # for half of it.
             fake_data = 10 * np.ones((300, 20))
             fake_data[:, 10:] = -1
@@ -410,7 +410,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 2.7, 3.6, 3.7 for PyPy. Check
-   https://travis-ci.org/AdamTheisen/arm-community-toolkit/pull_requests
+   https://travis-ci.org/ANL-DIGR/ACT
    and make sure that the tests pass for all supported Python versions.
 
 After creating a pull request through GitHub, and outside checker TravisCI

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# ARM Community Toolkit documentation build configuration file, created by
+# Atmospheric data Community Toolkit documentation build configuration file, created by
 # sphinx-quickstart on Thu Jun 28 12:35:56 2018.
 #
 # This file is execfile()d with the current directory set to its
@@ -192,7 +192,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (master_doc, 'act', 'Atmospheric Community Toolkit Documentation',
-     author, 'act', 'Package for connecting ARM users to the data',
+     author, 'act', 'Package for connecting users to the data',
      'Miscellaneous'),
 ]
 

docs/source/usage.rst

@@ -8,7 +8,7 @@ Start by importing Atmospheric Community Toolkit.
 
     import act
 
-The Atmospheric Community Toolkit comes with modules for loading ARM datasets.
+The Atmospheric data Community Toolkit comes with modules for loading ARM datasets.
 The main dataset object that is used in ACT is based off of an extension of 
 the `xarray.Dataset<http://xarray.pydata.org/en/stable/generated/xarray.Dataset.html>`
 object. In particular ACT adds a DatasetAccessor that stores the additional