Merge pull request #238 from spacetelescope/loaders

This PR addresses documentation and packaging for specviz. Imports for various modules have been enable with init, automodapi sphinx extension from astropy is used for API building, requirements have been updated, and imports have been updated to reference relative paths in project instead of absolutes.

docs/rtd-pip-requirements

@@ -1 +1,2 @@
 astropy >= 1.1
+automodapi

docs/source/api.rst

@@ -0,0 +1,25 @@
+SpecViz API
+===========
+
+Analysis Functions
+------------------
+.. automodapi:: specviz.analysis
+  :no-heading:
+
+
+SpecViz core
+------------
+.. automodapi:: specviz.core
+  :no-heading:
+
+
+Interfaces
+----------
+.. automodapi:: specviz.interfaces
+  :no-heading:
+
+
+I/O module
+----------
+.. automodapi:: specviz.io
+  :no-heading:

docs/source/conf.py

@@ -39,7 +39,8 @@
     'sphinx.ext.pngmath',
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
-]
+    'sphinx_automodapi.automodapi'
+    ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/source/index.rst

@@ -65,7 +65,7 @@ References/API
 .. toctree::
    :maxdepth: 1
 
-   api/index
+   api
 
 
 Indices and tables

requirements.txt

@@ -5,6 +5,7 @@ cython
 numpy
 scipy
 astropy
+sphinx_automodapi
 git+https://github.com/nmearl/specutils.git
 git+https://github.com/nmearl/pyqtgraph.git
 -e .

setup.py

@@ -122,6 +122,7 @@
       scripts=scripts,
       install_requires=[
           'astropy',
+          'numpy',
           'cython',
           'specutils',
           'numpy>=1.10',

specviz/__init__.py

@@ -4,6 +4,8 @@
 This is an Astropy affiliated package.
 """
 
+from __future__ import absolute_import
+
 # Affiliated packages may add whatever they like to this file, but
 # should keep this content at the top.
 # ----------------------------------------------------------------------------
@@ -12,4 +14,10 @@
 
 # For egg_info test builds to pass, put package imports here.
 if not _ASTROPY_SETUP_:
-    from specviz import * 
+    from . import analysis
+    from . import core
+    from . import data
+    ### interfaces causes a fault upon import
+    from . import interfaces
+    from . import io
+    from . import ui

specviz/analysis/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import absolute_import
+
+from .statistics import *
+from .utils import *
+from .models import *

specviz/analysis/models/__init__.py

@@ -1 +1,4 @@
+from __future__ import absolute_import
 
+from .blackbody import *
+from .spline import *

specviz/analysis/models/blackbody.py

@@ -10,7 +10,6 @@
 
 
 class BlackBody(Fittable1DModel):
-
     temp = Parameter(default=5000, min=10.)
     norm = Parameter(default=1.)
 
@@ -42,4 +41,3 @@ def initialize(self, instance, wave, flux):
         sum_model = np.sum(instance.evaluate(wave.value, instance.temp.value, 1.))
 
         instance.norm = sum_data / sum_model
-

specviz/analysis/models/spline.py

@@ -19,7 +19,7 @@ def evaluate(self, x, degree, smooth):
 
 
 class Spline1DInitializer(object):
-
+    
     def initialize(self, instance, wave, flux):
         instance.wave = wave
         instance.flux = flux

specviz/interfaces/__init__.py

@@ -0,0 +1,3 @@
+from .decorators import *
+### Don't import registires - causes an error
+#from .registries import *

specviz/interfaces/decorators.py

@@ -8,6 +8,7 @@
 
 from ..core.data import Spectrum1DRef
 
+__all__ = ['data_loader']
 
 def data_loader(label, identifier, priority=-1, **kwargs):
     """

specviz/interfaces/registries.py

@@ -8,9 +8,15 @@
 import logging
 
 import astropy.io.registry as io_registry
+
+#-- local
 from ..core.data import Spectrum1DRef
 from ..io.yaml_loader import FitsYamlRegister, AsciiYamlRegister
+from ..io.loaders import *
 
+__all__ = ['Registry',
+           'PluginRegistry',
+           'LoaderRegistry']
 
 class Registry(object):
     """
@@ -79,21 +85,23 @@ def __init__(self):
     def _load_py(self):
         """ Loads built-in and custom python loaders
 
+        Loaders from the io.loaders module will be included from the
+        import statement.
         Python modules (.py ending) found in the following locations will be
         auto-loaded into the registry for data loading.
 
         1.  .specviz folder in the user's HOME directory
-        2.  io/loaders distributed with this package
 
         """
 
-        cur_path = os.path.abspath(os.path.join(__file__, '..', '..', 'io',
-                                                'loaders'))
         usr_path = os.path.join(os.path.expanduser('~'), '.specviz')
 
         # This order determines priority in case of duplicates; paths higher
         # in this list take precedence
-        check_paths = [usr_path, cur_path]
+        #
+        # Leaving in list format incase other locations want to be added
+        # in the future
+        check_paths = [usr_path]
 
         if not os.path.exists(usr_path):
             os.mkdir(usr_path)
@@ -103,7 +111,6 @@ def _load_py(self):
                 mod = mod.split('.')[0]
                 sys.path.insert(0, path)
                 mod = importlib.import_module(mod)
-                members = inspect.getmembers(mod, predicate=inspect.isfunction)
 
                 # for _, func in members:
                 #     if hasattr(func, 'loader_wrapper') and func.loader_wrapper:

specviz/io/__init__.py

@@ -0,0 +1 @@
+from .loaders import *

specviz/io/loaders/__init__.py

@@ -0,0 +1,3 @@
+from .generic_loader import *
+from .hstcos_loader import *
+from .hststis_loader import *

specviz/io/loaders/generic_loader.py

@@ -1,6 +1,3 @@
-from specviz.interfaces.decorators import data_loader
-from specviz.core.data import Spectrum1DRef
-
 import os
 
 from astropy.io import fits
@@ -9,6 +6,10 @@
 from astropy.units import Unit
 from astropy.nddata import StdDevUncertainty
 
+from ...interfaces import data_loader
+from ...core.data import Spectrum1DRef
+
+__all__ = ['fits_identify', 'simple_generic_loader']
 
 def fits_identify(*args, **kwargs):
     """
@@ -38,4 +39,3 @@ def simple_generic_loader(file_name, **kwargs):
 
     return Spectrum1DRef(data=data, name=name, wcs=wcs,
                          uncertainty=uncertainty, unit=unit, meta=meta)
-

specviz/io/loaders/hstcos_loader.py

@@ -1,16 +1,17 @@
-from specviz.interfaces.decorators import data_loader
-from specviz.core.data import Spectrum1DRef
-
 import os
 
 from astropy.io import fits
 from astropy.units import Unit
 from astropy.nddata import StdDevUncertainty
 
+from ...interfaces import data_loader
+from ...core.data import Spectrum1DRef
+
+__all__ = ['cos_identify', 'cos_spectrum_loader']
 
 def cos_identify(*args, **kwargs):
-    """
-    Check whether given file contains HST/COS spectral data.
+    """ Check whether given file contains HST/COS spectral data.
+
     """
 
     with fits.open(args[0]) as hdu:

specviz/io/loaders/hststis_loader.py

@@ -1,12 +1,13 @@
-from specviz.interfaces.decorators import data_loader
-from specviz.core.data import Spectrum1DRef
-
 import os
 
 from astropy.io import fits
 from astropy.units import Unit
 from astropy.nddata import StdDevUncertainty
 
+from ...interfaces import data_loader
+from ...core.data import Spectrum1DRef
+
+__all__ = ['stis_identify', 'stis_spectrum_loader']
 
 def stis_identify(*args, **kwargs):
     """