Merge pull request #79 from spacetelescope/0.9.9.x

0.9.9 release

CODE_OF_CONDUCT.md

@@ -0,0 +1,24 @@
+# Spacetelescope Open Source Code of Conduct
+
+We expect all "spacetelescope" organization projects to adopt a code of conduct that ensures a productive, respectful environment for all open source contributors and participants. We are committed to providing a strong and enforced code of conduct and expect everyone in our community to follow these guidelines when interacting with others in all forums. Our goal is to keep ours a positive, inclusive, successful, and growing community. The community of participants in open source Astronomy projects is made up of members from around the globe with a diverse set of skills, personalities, and experiences. It is through these differences that our community experiences success and continued growth. 
+
+
+As members of the community,
+
+- We pledge to treat all people with respect and provide a harassment- and bullying-free environment, regardless of sex, sexual orientation and/or gender identity, disability, physical appearance, body size, race, nationality, ethnicity, and religion. In particular, sexual language and imagery, sexist, racist, or otherwise exclusionary jokes are not appropriate.
+
+- We pledge to respect the work of others by recognizing acknowledgment/citation requests of original authors. As authors, we pledge to be explicit about how we want our own work to be cited or acknowledged.
+
+- We pledge to welcome those interested in joining the community, and realize that including people with a variety of opinions and backgrounds will only serve to enrich our community. In particular, discussions relating to pros/cons of various technologies, programming languages, and so on are welcome, but these should be done with respect, taking proactive measure to ensure that all participants are heard and feel confident that they can freely express their opinions.
+
+- We pledge to welcome questions and answer them respectfully, paying particular attention to those new to the community. We pledge to provide respectful criticisms and feedback in forums, especially in discussion threads resulting from code contributions.
+
+- We pledge to be conscientious of the perceptions of the wider community and to respond to criticism respectfully. We will strive to model behaviors that encourage productive debate and disagreement, both within our community and where we are criticized. We will treat those outside our community with the same respect as people within our community.
+
+- We pledge to help the entire community follow the code of conduct, and to not remain silent when we see violations of the code of conduct. We will take action when members of our community violate this code such as such as contacting conduct@stsci.edu (all emails sent to this address will be treated with the strictest confidence) or talking privately with the person.
+
+This code of conduct applies to all community situations online and offline, including mailing lists, forums, social media, conferences, meetings, associated social events, and one-to-one interactions.
+
+Parts of this code of conduct have been adapted from the Astropy and Numfocus codes of conduct.
+http://www.astropy.org/code_of_conduct.html
+https://www.numfocus.org/about/code-of-conduct/

doc/rtd-pip-requirements

@@ -3,4 +3,4 @@ numpy
 matplotlib
 astropy-helpers
 astropy
-scipy
+scipy>=0.18

doc/source/appendixa.rst

@@ -24,6 +24,8 @@ Stellar models:
 |:ref:`pysynphot-appendixa-ck04`      |$PYSYN_CDBS/grid/ck04models    |Yes           |
 +-------------------------------------+-------------------------------+              |
 |:ref:`pysynphot-appendixa-kurucz1993`|$PYSYN_CDBS/grid/k93models     |              |
++-------------------------------------+-------------------------------+              |
+|:ref:`pysynphot-appendixa-phoenix`   |$PYSYN_CDBS/grid/phoenix       |              |
 +-------------------------------------+-------------------------------+--------------+
 |:ref:`pysynphot-appendixa-calspec`   |$PYSYN_CDBS/calspec            |No            |
 +-------------------------------------+-------------------------------+              |
@@ -45,8 +47,6 @@ Non-stellar models:
 +-------------------------------------+-------------------------------+--------------+
 |Atlas/Catalog                        |Installation Path              |Interpolatable|
 +=====================================+===============================+==============+
-|:ref:`pysynphot-appendixa-phoenix`   |$PYSYN_CDBS/grid/phoenix       |Yes           |
-+-------------------------------------+-------------------------------+--------------+
 |:ref:`pysynphot-appendixa-bc95`      |$PYSYN_CDBS/grid/bc95/templates|No            |
 +-------------------------------------+-------------------------------+              |
 |:ref:`pysynphot-appendixa-kc96`      |$PYSYN_CDBS/grid/kc96          |              |
@@ -77,7 +77,7 @@ The atlas data files are organized in a similar naming convention as
 :ref:`pysynphot-appendixa-kurucz1993`, and are easily accessible using
 `~pysynphot.catalog.Icat` (also see :ref:`pysynphot-spec-atlas`).
 
-The example below generates a spectrum with metallicity :math:`\log Z = +0.1`,
+The example below generates a spectrum with metallicity ``[M/H] = +0.1``,
 temperature :math:`T_{\textnormal{eff}} = 10000 \textnormal{K}`, and gravity
 :math:`\log g = 3.0`:
 
@@ -112,7 +112,7 @@ absolute flux is needed, the model spectrum must be
 
 The following example shows the header from one of the atlas data files.
 This file contains all the models for a star of metallicity
-:math:`\log Z = 0.0` (``p00``) and effective temperature
+``[M/H] = 0.0`` (``p00``) and effective temperature
 :math:`T_{\textnormal{eff}} = 8000 \textnormal{K}` (``8000``), which cover a
 range of gravities from :math:`\log g = +1.0` (``g10``) to
 :math:`\log g = +5.0` (``g50``).
@@ -157,7 +157,7 @@ HISTORY   and effective temperature but different gravity.
 
 The example below shows you how to manually select the flux for a specific
 model characterized by a given metallicity, effective temperature, and gravity.
-The filename ``kp01_10000`` means :math:`\log Z = +0.1` (``p01``) and
+The filename ``kp01_10000`` means ``[M/H] = +0.1`` (``p01``) and
 :math:`T_{\textnormal{eff}} = 10000 \textnormal{K}` (``10000``). The column
 name ``g30`` means :math:`\log g = 3.0`:
 
@@ -173,6 +173,36 @@ The easier way to to use `~pysynphot.catalog.Icat` (also see
 >>> sp = S.Icat('k93models', 10000, 0.1, 3.0)
 
 
+.. _pysynphot-appendixa-phoenix:
+
+Phoenix Models
+==============
+
+The ``$PYSYN_CDBS/grid/phoenix`` directory contains models provided by
+`F. Allard et al. <http://perso.ens-lyon.fr/france.allard/>`_
+and can be found in the
+`Star, Brown Dwarf, and Planet Simulator <http://phoenix.ens-lyon.fr/simulator/index.faces>`_. They use static, spherical symmetric, 1D simulations to completely
+describe the atmospheric emission spectrum. The models account for the
+formation of molecular bands, such as those of water vapor, methane, or
+titanium dioxide, solving for the transfer equation over more than 20,000
+wavelength points on average, producing synthetic spectra with 2 Angstroms
+resolution. The line selection is repeated at each iteration of the model
+until it has converged and the thermal structure obtained. The models here
+are calculated with a cloud model, valid across the entire parameter range.
+See
+`Phoenix models README file <http://www.stsci.edu/hst/observatory/crds/SIfileInfo/pysynphottables/index_phoenix_models_html>`_
+for more details.
+The atlas data files are organized in a similar naming convention as
+:ref:`pysynphot-appendixa-kurucz1993`, and are easily accessible using
+`~pysynphot.catalog.Icat` (also see :ref:`pysynphot-spec-atlas`).
+
+The example below generates a spectrum with metallicity ``[M/H] = +0.1``,
+temperature :math:`T_{\textnormal{eff}} = 10000 \textnormal{K}`, and gravity
+:math:`\log g = 3.0`:
+
+>>> sp = S.Icat('phoenix', 10000, 0.1, 3.0)
+
+
 .. _pysynphot-appendixa-calspec:
 
 HST Calibration Spectra
@@ -398,36 +428,6 @@ The example below loads a source spectrum of spectral type G0V from the atlas:
 >>> sp = S.FileSpectrum(filename)
 
 
-.. _pysynphot-appendixa-phoenix:
-
-Phoenix Models
-==============
-
-The ``$PYSYN_CDBS/grid/phoenix`` directory contains models provided by
-`F. Allard et al. <http://perso.ens-lyon.fr/france.allard/>`_
-and can be found in the
-`Star, Brown Dwarf, and Planet Simulator <http://phoenix.ens-lyon.fr/simulator/index.faces>`_. They use static, spherical symmetric, 1D simulations to completely
-describe the atmospheric emission spectrum. The models account for the
-formation of molecular bands, such as those of water vapor, methane, or
-titanium dioxide, solving for the transfer equation over more than 20,000
-wavelength points on average, producing synthetic spectra with 2 Angstroms
-resolution. The line selection is repeated at each iteration of the model
-until it has converged and the thermal structure obtained. The models here
-are calculated with a cloud model, valid across the entire parameter range.
-See
-`Phoenix models README file <http://www.stsci.edu/hst/observatory/crds/SIfileInfo/pysynphottables/index_phoenix_models_html>`_
-for more details.
-The atlas data files are organized in a similar naming convention as
-:ref:`pysynphot-appendixa-kurucz1993`, and are easily accessible using
-`~pysynphot.catalog.Icat` (also see :ref:`pysynphot-spec-atlas`).
-
-The example below generates a spectrum with metallicity :math:`\log Z = +0.1`,
-temperature :math:`T_{\textnormal{eff}} = 10000 \textnormal{K}`, and gravity
-:math:`\log g = 3.0`:
-
->>> sp = S.Icat('phoenix', 10000, 0.1, 3.0)
-
-
 .. _pysynphot-appendixa-bc95:
 
 Bruzual-Charlot Atlas

doc/source/index.rst

@@ -261,7 +261,7 @@ References
 
 .. _synphot-ref-greenfield2007:
 
-* `Greenfield, P. & Jedrzejewski, R. 2007, Using Python for Interactive Data Analysis (Baltimore, MD: STScI) <http://stsdas.stsci.edu/perry/pydatatut.pdf>`_
+* `Greenfield, P. & Jedrzejewski, R. 2007, Using Python for Interactive Data Analysis (Baltimore, MD: STScI) <http://ssb.stsci.edu/perry/pydatatut.pdf>`_
 
 .. _synphot-ref-gunn2001:
 
@@ -301,7 +301,7 @@ References
 
 .. _synphot-ref-laidler2009:
 
-* `Laidler, V. 2009, TSR 2009-01: Pysynphot Commissioning Report (Baltimore, MD: STScI) <http://stsdas.stsci.edu/tsr/2009_01/>`_
+* `Laidler, V. 2009, TSR 2009-01: Pysynphot Commissioning Report (Baltimore, MD: STScI) <http://ssb.stsci.edu/tsr/2009_01/>`_
 
 .. _synphot-ref-laidler2008:
 

doc/source/spectrum.rst

@@ -266,8 +266,8 @@ you want, as shown in the example above.
 However, three of the atlases (:ref:`pysynphot-appendixa-ck04`,
 :ref:`pysynphot-appendixa-kurucz1993`, and :ref:`pysynphot-appendixa-phoenix`)
 have a grid of basis spectra which are indexed for various combinations of
-effective temperature (:math:`T_{\textnormal{eff}}`) in Kelvin, log metallicity
-(:math:`\log Z`), and log surface gravity (:math:`\log g`). They are best
+effective temperature (:math:`T_{\textnormal{eff}}`) in Kelvin, metallicity
+(``[M/H]``), and log surface gravity (:math:`\log g`). They are best
 accessed with a special `~pysynphot.catalog.Icat` class.
 You may specify any combination of the properties, so long as each is
 within the allowed range, which differs from atlas to atlas. For example,
@@ -277,7 +277,7 @@ which means that no spectrum can be constructed for effective temperatures
 below 3499 K or above 50001 K (i.e., an exception will be raised).
 The example below obtains the spectrum for a
 :ref:`pysynphot-appendixa-kurucz1993` model with
-:math:`T_{\textnormal{eff}} = 6000 \; \textnormal{K}`, :math:`\log Z = 0`, and
+:math:`T_{\textnormal{eff}} = 6000 \; \textnormal{K}`, ``[M/H] = 0``, and
 :math:`\log g = 4.3`:
 
 >>> sp = S.Icat('k93models', 6440, 0, 4.3)

pysynphot/catalog.py

@@ -4,9 +4,9 @@
 
 Spectra are constructed from basis spectra which are indexed for various
 combinations of effective temperature (:math:`T_{\\textnormal{eff}}`),
-metallicity (:math:`Z`), and log surface gravity (:math:`\\log g`).
+metallicity (``[M/H]``), and log surface gravity (:math:`\\log g`).
 The user may specify any combination of :math:`T_{\\textnormal{eff}}`,
-:math:`Z`, and :math:`\\log g` so long as each parameter is within the range
+``[M/H]``, and :math:`\\log g` so long as each parameter is within the range
 for that parameter defined by the catalog.
 
 For example, the :ref:`pysynphot-appendixa-ck04` catalog contains spectra for
@@ -96,7 +96,7 @@ def __init__(self,catdir,Teff,metallicity,log_g):
         self.parameter_names = ['Teff','metallicity','log G']
 
         filename = locations.CAT_TEMPLATE.replace('*',catdir)
-        self.name="%s(Teff=%g,z=%g,logG=%g)"%(catdir,Teff,metallicity,log_g)
+        self.name="%s(Teff=%g,metallicity=%g,logG=%g)"%(catdir,Teff,metallicity,log_g)
 
         if filename in CATALOG_CACHE:
             indices = CATALOG_CACHE[filename]
@@ -204,6 +204,11 @@ def _getSpectrum(self, parlist, basename):
                                                   os.path.join(basename,filename))
         sp = spectrum.TabularSourceSpectrum(filename, fluxname=column)
 
+        totflux = sp.integrate()
+        if not N.isfinite(totflux) or totflux <= 0:
+            raise exceptions.ParameterOutOfBounds(
+                "Parameter '{0}' has no valid data.".format(parlist))
+
         result = []
         for member in parlist:
             result.append(member)