1.0.0 (#28)

* Adds package_settings module (multi-site support)

* Fixes bug when updating models without primary receiver data

* Raises pressure cut lower bound for P014 to 870 mbar

* Adds get_all_receiver_data function

* Fixes order of columns returned by measured_pwv

* Adds requirements.txt

MANIFEST.in

@@ -2,6 +2,6 @@ include README.md
 include LICENSE.txt
 include pwv_kpno/CONFIG.txt
 graft pwv_kpno/site_data
-graft pwv_kpno/sims_phosim
+graft pwv_kpno/default_atmosphere
 graft pwv_kpno/suomi_data
 graft tests

README.md

@@ -3,82 +3,15 @@
   <br>
 </h1>
 
-<h4 align="center">
-Providing models of the atmospheric transmission function at
-Kitt Peak National Observatory
-</h4>
-
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-[![release](https://img.shields.io/badge/version-0.12.1-blue.svg)]()
+[![release](https://img.shields.io/badge/version-1.0.0-blue.svg)]()
 [![python](https://img.shields.io/badge/python-2.7,%203.5,%203.6,%203.7-blue.svg)]()
 [![license](https://img.shields.io/badge/license-GPL%20v3.0-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
 [![Build Status](https://travis-ci.org/mwvgroup/pwv_kpno.svg?branch=master)](https://travis-ci.org/mwvgroup/pwv_kpno)
 [![Coverage Status](https://coveralls.io/repos/github/mwvgroup/pwv_kpno/badge.svg?branch=master)](https://coveralls.io/github/mwvgroup/pwv_kpno?branch=master)
 [![arxiv](https://img.shields.io/badge/astro--ph.IM-arXiv%3A1806.09701-B31B1B.svg)](https://arxiv.org/abs/1806.09701)
 
-For package documentation and installation instructions, please see
-[https://mwvgroup.github.io/pwv_kpno/](https://mwvgroup.github.io/pwv_kpno/)
-
-## Overview
-
 **pwv_kpno** is a Python package for modeling the atmospheric absorption due
-to H<sub>2</sub>O at Kitt Peak National Observatory. It provides atmospheric
-models from 3,000 to 12,000 Angstroms for years 2010 onward. Understanding atmospheric
-effects is important when calibrating ground based astronomical observations.
-Traditionally, determining the detailed atmospheric transmission function at a
-given date and time required performing dedicated spectrographic observations.
-**pwv_kpno** provides an alternative that can be performed at the user's
-convenience.
-
-Atmospheric absorption in the near-infrared is highly dependent on the column
-density of precipitable water vapor (PWV). By measuring the delay of GPS
-signals through the atmosphere, the [SuomiNet](http://www.suominet.ucar.edu)
-project provides accurate PWV measurements for multiple, international
-locations. The **pwv_kpno** package uses published SuomiNet data in conjunction
-with MODTRAN models to determine the modeled atmospheric transmission function
-at Kitt Peak in close to real time. The package also provides automated
-retrieval and processing of SuomiNet data, allowing photometry to typically be
-corrected within an hour of observation.
-
-**pwv_kpno** is open source software released under the GNU General Public
-License. Issues, pull requests, and feedback are welcome.
-
-## How to Cite
-
-If you use **pwv_kpno** as part of any published work or research, we ask that
-you please use the following standard acknowledgement:
-
-&nbsp;&nbsp;&nbsp;&nbsp;*This research made use of the pwv_kpno python package,*<br>
-&nbsp;&nbsp;&nbsp;&nbsp;*an open source project that provides models for the*<br>
-&nbsp;&nbsp;&nbsp;&nbsp;*atmospheric absorption due to precipitable water vapor*<br>
-&nbsp;&nbsp;&nbsp;&nbsp;*in the near-infrared (Perrefort, Wood-Vasey et al. 2018)*<br>
-
-If the publisher allows, you can also include a footnote with a link pointing
-to the documentation page:
-[https://mwvgroup.github.io/pwv_kpno/](https://mwvgroup.github.io/pwv_kpno/)
-
-# Acknowledgements
-
-This work is based in part on observations taken at Kitt Peak National
-Observatory, National Optical Astronomy Observatory (NOAO Prop. IDs: 2011B-0482
-and 2012B-0500; PI: Wood-Vasey), which is operated by the Association of
-Universities for Research in Astronomy (AURA) under a cooperative agreement
-with the National Science Foundation.
-
-This work was supported in part by the US Department of Energy Office of Science 
-under DE-SC0007914.
-
-# Additional Resources
-
-- An up time monitor for the SuomiNet website can be found
-  [here](https://stats.uptimerobot.com/gn1xqsJvj)
-
-- For more information on the Kitt Peak National Observatory, see
-  [www.noao.edu/kpno/](https://www.noao.edu/kpno/)
-
-- To learn more about the SuomiNet project, see
-  [www.suominet.ucar.edu/overview.html](http://www.suominet.ucar.edu/overview.html)
-
-- For an additional example on the correlation between GPS signals and
-  atmospheric modeling, see
-  [Blake and Shaw, 2011](https://arxiv.org/abs/1109.6703)
+to H<sub>2</sub>O. For a full description of this package, including
+documentation and usage examples, please see
+[https://mwvgroup.github.io/pwv_kpno/](https://mwvgroup.github.io/pwv_kpno/)

pwv_kpno/__init__.py

@@ -16,11 +16,37 @@
 #    You should have received a copy of the GNU General Public License
 #    along with pwv_kpno.  If not, see <http://www.gnu.org/licenses/>.
 
-"""pwv_kpno provides models for the atmospheric transmission function at Kitt
-Peak National Observatory due to precipitable water vapor. Models cover
-wavelengths from 7,000 to 11,000 Angstroms for years 2010 onward. Documentation
-is available online at https://mwvgroup.github.io/pwv_kpno/ or through the
-standard python help function.
+"""pwv_kpno provides models for the atmospheric transmission function due to
+precipitable water vapor (PWV). Using PWV measurements published
+by the SuomiNet project (https://www.suominet.ucar.edu), this package is
+capable of returning the modeled PWV transmission for a given date, time, and
+airmass at customizable geographic locations. By default, this functionality
+is set to model Kitt Peak National Observatory. Default models cover
+wavelengths from 3,000 to 12,000 Angstroms at a resolution of 0.05 Angstroms.
+
+For more information on using this package, documentation is available online
+at https://mwvgroup.github.io/pwv_kpno/ or through the standard python help
+function.
+
+An incomplete guide to getting started:
+
+    To model the effects of PWV absorption on a black body, see the
+    documentation for the `blackbody_with_atm` module:
+
+      >>> from pwv_kpno import blackbody_with_atm as bb_atm
+
+
+    To model the atmospheric transmission function, either for a known PWV
+    concentration or for a datetime at a particular location, see the `pw_atm`
+    module:
+
+      >>> from pwv_kpno import pwv_atm
+
+
+    To configure this package to model a custom geographical site, and to
+    modify other package settings, see the `package_settings` module:
+
+      >>> from pwv_kpno import package_settings
 """
 
 from . import blackbody_with_atm
@@ -29,13 +55,20 @@
 
 __authors__ = ['Daniel Perrefort']
 __copyright__ = 'Copyright 2017, Daniel Perrefort'
-__credits__ = ['Michael Wood-Vasey', 'Azalee Bostroem',
-               'Jessica Kroboth', 'Alexander Afanasyev']
+__credits__ = [
+    'W. M. Wood-Vasey',
+    'K.Azalee Bostroem',
+    'Jessica Kroboth',
+    'Tom Matheson',
+    'Alexander Afanasyev',
+]
 
 __license__ = 'GPL V3'
-__version__ = '0.12.1'
+__version__ = '1.0.0'
 __email__ = 'djperrefort@pitt.edu'
-__status__ = 'Development'
+__status__ = 'Release'
+
+from .package_settings import settings as _settings
 
 from .package_settings import settings as _settings
 

pwv_kpno/_atm_model.py

@@ -21,6 +21,8 @@
 work done by Azalee Bostroem.
 """
 
+from typing import Union
+
 import numpy as np
 import scipy.interpolate as interpolate
 from astropy.table import Table
@@ -31,14 +33,14 @@
 
 __license__ = 'GPL V3'
 __email__ = 'djperrefort@pitt.com'
-__status__ = 'Development'
+__status__ = 'Release'
 
 
 def _calc_num_density_conversion():
-    """Calculate conversion factor from PWV to integrated number density
+    """Calculate conversion factor from PWV * cross section to optical depth
 
     Returns:
-        The conversion factor from PWV to number density in 1 / (mm * cm^2)
+        The conversion factor in units of 1 / (mm * cm^2)
     """
 
     n_a = 6.02214129E23       # 1 / mol (Avogadro's constant)
@@ -53,8 +55,8 @@ def _calc_num_density_conversion():
 
 
 def create_pwv_atm_model(mod_lambda, mod_cs, out_lambda):
-    # type: (np.ndarray, np.ndarray, np.ndarray) -> Table
-    """Creates a table of conversion factors from PWV to number density
+    # type: (Union[list, np.ndarray], Union[list, np.ndarray], Union[list, np.ndarray]) -> Table
+    """Creates a table of conversion factors from PWV to optical depth
 
     Expects input and output wavelengths to be in same units. Expects modeled
     cross sections to be in cm^2.
@@ -65,18 +67,24 @@ def create_pwv_atm_model(mod_lambda, mod_cs, out_lambda):
         out_lambda (ndarray): Array of desired output wavelengths
 
     Returns:
-        A table with columns 'wavelength' and '1/mm_cm_2'
+        A table with columns 'wavelength' and '1/mm'
     """
 
+    mod_cs = np.array(mod_cs)
+    if (mod_cs < 0).any():
+        raise ValueError('Cross sections cannot be negative.')
+
     if np.array_equal(mod_lambda, out_lambda):
-        out_cs = mod_cs
+        out_cs = mod_cs  # This function requires ndarray behavior
 
     else:
         interp_cs = interpolate.interp1d(mod_lambda, mod_cs)
         out_cs = interp_cs(out_lambda)
 
     pwv_num_density = out_cs * _calc_num_density_conversion()
-    out_table = Table([out_lambda, pwv_num_density],
-                      names=['wavelength', '1/mm_cm_2'])
+    out_table = Table(
+        data=[out_lambda, pwv_num_density],
+        names=['wavelength', '1/mm']
+    )
 
     return out_table