addressing comments, second iteration

Author: burnout87

astroquery/desi/__init__.py

@@ -20,14 +20,15 @@ class Conf(_config.ConfigNamespace):
     """
     Configuration parameters for `astroquery.desi`.
     """
-    server = _config.ConfigItem(
-        ['https://portal.nersc.gov/cfs/cosmo/data/legacysurvey/',
+    legacysurvey_service_url = _config.ConfigItem(
+        ['https://www.legacysurvey.org/viewer/fits-cutout',
          ],
-        'base url')
+        'url for the LegacySurvey service')
 
-    timeout = _config.ConfigItem(
-        30,
-        'Time limit for connecting to template_module server.')
+    tap_service_url = _config.ConfigItem(
+        ['https://datalab.noirlab.edu/tap',
+         ],
+        'url for the TAP service')
 
 
 conf = Conf()

astroquery/desi/core.py

@@ -1,46 +1,48 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 import urllib.error
 import requests
+import warnings
 
 import pyvo as vo
 import numpy as np
+import astropy.coordinates as coord
 
 from astroquery.exceptions import NoResultsWarning
 from astroquery.query import BaseQuery
 from astroquery.utils import commons, async_to_sync
-
-from . import conf
-
+from astroquery.desi import conf
 
 __all__ = ['DESILegacySurvey', 'DESILegacySurveyClass']
 
 
-@async_to_sync
 class DESILegacySurveyClass(BaseQuery):
-    URL = conf.server
-    TIMEOUT = conf.timeout
 
-    def query_region(self, coordinates, radius, data_release=9):
+    def query_region(self, coordinates, radius, *, data_release=9):
         """
         Queries a region around the specified coordinates.
 
         Parameters
         ----------
-        coordinates : str or `astropy.coordinates`.
-            coordinates around which to query
-        radius : str or `astropy.units.Quantity`.
-            the radius of the cone search
+        coordinates : `astropy.coordinates`
+            coordinates around which to query.
+        radius : `astropy.units.Quantity`
+            the radius of the cone search.
+        data_release: int
+            the data release of the LegacySurvey to use.
 
         Returns
         -------
         response : `astropy.table.Table`
         """
 
-        url = 'https://datalab.noirlab.edu/tap'
-        tap_service = vo.dal.TAPService(url)
-        qstr = "SELECT all * FROM ls_dr" + str(data_release) + ".tractor WHERE dec>" + str(coordinates.dec.deg - radius.deg) + " and dec<" + str(
-            coordinates.dec.deg + radius.deg) + " and ra>" + str(coordinates.ra.deg - radius.deg / np.cos(coordinates.dec.deg * np.pi / 180.)) + " and ra<" + str(
-            coordinates.ra.deg + radius.deg / np.cos(coordinates.dec.deg * np.pi / 180))
+        tap_service = vo.dal.TAPService(conf.tap_service_url)
+        coordinates_transformed = coordinates.transform_to(coord.ICRS)
+
+        qstr = (f"SELECT all * FROM ls_dr{data_release}.tractor WHERE "
+               f"dec>{coordinates_transformed.dec.deg - radius.deg} and "
+               f"dec<{coordinates_transformed.dec.deg + radius.deg} and "
+               f"ra>{coordinates_transformed.ra.deg - radius.deg / np.cos(coordinates_transformed.dec.deg * np.pi / 180.)} and "
+               f"ra<{coordinates_transformed.ra.deg + radius.deg / np.cos(coordinates_transformed.dec.deg * np.pi / 180)}")
 
         tap_result = tap_service.run_sync(qstr)
         tap_result = tap_result.to_table()
@@ -50,26 +52,44 @@ def query_region(self, coordinates, radius, data_release=9):
 
         return filtered_table
 
-    def get_images(self, position, data_release=9, pixels=None, radius=None, show_progress=True, image_band='g'):
+    def get_images(self, position, pixels, radius, *, data_release=9, show_progress=True, image_band='g'):
         """
+        Downloads the images for a certain region of interest.
+
+        Parameters
+        -------
+        position: `astropy.coordinates`.
+            coordinates around which we define our region of interest.
+        radius: `astropy.units.Quantity`.
+            the radius of the cone search.
+        data_release: int
+            the data release of the LegacySurvey to use.
+
         Returns
         -------
-        A list of `astropy.io.fits.HDUList` objects.
+        list: A list of `astropy.io.fits.HDUList` objects.
         """
 
+        position_transformed = position.transform_to(coord.ICRS)
+
         image_size_arcsec = radius.arcsec
         pixsize = 2 * image_size_arcsec / pixels
 
-        image_url = 'https://www.legacysurvey.org/viewer/fits-cutout?ra=' + str(position.ra.deg) + '&dec=' + str(position.dec.deg) + '&size=' + str(
-            pixels) + '&layer=ls-dr' + str(data_release) + '&pixscale=' + str(pixsize) + '&bands=' + image_band
+        image_url = (f"{conf.legacysurvey_service_url}?"
+                    f"ra={position_transformed.ra.deg}&"
+                    f"dec={position_transformed.dec.deg}&"
+                    f"size={pixels}&"
+                    f"layer=ls-dr{data_release}&"
+                    f"pixscale={pixsize}&"
+                    f"bands={image_band}")
 
         file_container = commons.FileContainer(image_url, encoding='binary', show_progress=show_progress)
 
         try:
             fits_file = file_container.get_fits()
         except (requests.exceptions.HTTPError, urllib.error.HTTPError) as e:
-            # TODO not sure this is the most suitable exception
-            raise NoResultsWarning(f"{str(e)} - Problem retrieving the file at the url: {str(image_url)}")
+            fits_file = None
+            warnings.warn(f"{str(e)} - Problem retrieving the file at the url: {image_url}", NoResultsWarning)
 
         return [fits_file]
 

astroquery/desi/tests/setup_package.py

@@ -5,6 +5,5 @@
 def get_package_data():
     paths = [os.path.join('data', '*.txt'),
              os.path.join('data', '*.fits'),
-             os.path.join('data', '*.fits.gz'),
              ]
     return {'astroquery.desi.tests': paths}

astroquery/desi/tests/test_module.py renamed to astroquery/desi/tests/test_desi.py

@@ -6,13 +6,13 @@
 
 from astropy.table import Table
 from astropy.io import fits
-from pyvo.dal import TAPResults
+from astropy import coordinates as coord
+from astroquery.utils.mocks import MockResponse
+from astroquery.utils import commons
+from astroquery import desi
 from urllib import parse
 from contextlib import contextmanager
 
-from ... import desi
-from ...utils.mocks import MockResponse
-from ...utils import commons
 
 DATA_FILES = {
     'dummy_tap_table': 'dummy_table.txt',
@@ -21,18 +21,15 @@
 }
 
 coords = commons.ICRSCoord('11h04m27s +38d12m32s')
-radius = commons.ArcminRadiusGenerator(0.5)
+radius = coord.Angle(0.5, unit='arcmin')
 pixels = 60
 data_release = 9
 emispheres_list = ['north', 'south']
 
 
 @pytest.fixture
 def patch_get(request):
-    try:
-        mp = request.getfixturevalue("monkeypatch")
-    except AttributeError:  # pytest < 3
-        mp = request.getfuncargvalue("monkeypatch")
+    mp = request.getfixturevalue("monkeypatch")
 
     mp.setattr(desi.DESILegacySurvey, '_request', get_mockreturn)
     return mp
@@ -68,10 +65,7 @@ def get_readable_fileobj_mockreturn(filename, **kwargs):
 
 @pytest.fixture
 def patch_tap(request):
-    try:
-        mp = request.getfixturevalue("monkeypatch")
-    except AttributeError:  # pytest < 3
-        mp = request.getfuncargvalue("monkeypatch")
+    mp = request.getfixturevalue("monkeypatch")
 
     mp.setattr(vo.dal.TAPService, 'run_sync', tap_mockreturn)
     return mp
@@ -95,7 +89,7 @@ def tap_mockreturn(url, params=None, timeout=10, **kwargs):
     content_table = Table.read(data_path(DATA_FILES['dummy_tap_table']),
                                format='ascii.csv', comment='#')
     votable_table = astropy.io.votable.from_table(content_table)
-    return TAPResults(votable_table)
+    return vo.dal.TAPResults(votable_table)
 
 
 def data_path(filename):

astroquery/desi/tests/test_module_remote.py renamed to astroquery/desi/tests/test_desi_remote.py

@@ -1,18 +1,17 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
-
 import pytest
+import astroquery.desi
+
 from astropy.io.fits import HDUList
+from astropy.coordinates import SkyCoord
+from astropy.coordinates import Angle
+from astropy.table import Table
 from astroquery.exceptions import NoResultsWarning
 
 
 @pytest.mark.remote_data
 class TestLegacySurveyClass:
 
     def test_query_region(self):
-        import astroquery.desi
-        from astropy.coordinates import SkyCoord
-        from astropy.coordinates import Angle
-        from astropy.table import Table
 
         ra = Angle('11h04m27s', unit='hourangle').degree
         dec = Angle('+38d12m32s', unit='hourangle').degree
@@ -26,9 +25,6 @@ def test_query_region(self):
 
     @pytest.mark.parametrize("valid_inputs", [True, False])
     def test_get_images(self, valid_inputs):
-        import astroquery.desi
-        from astropy.coordinates import SkyCoord
-        from astropy.coordinates import Angle
 
         if valid_inputs:
             ra = Angle('11h04m27s', unit='hourangle').degree
@@ -45,9 +41,9 @@ def test_get_images(self, valid_inputs):
         radius = Angle(radius_input, unit='arcmin')
 
         if valid_inputs:
-            query1 = astroquery.desi.DESILegacySurvey.get_images(pos, data_release=9, radius=radius, pixels=pixels)
+            query1 = astroquery.desi.DESILegacySurvey.get_images(pos, pixels, radius, data_release=9)
             assert isinstance(query1, list)
             assert isinstance(query1[0], HDUList)
         else:
             with pytest.raises(NoResultsWarning):
-                astroquery.desi.DESILegacySurvey.get_images(pos, data_release=9, radius=radius, pixels=pixels)
+                astroquery.desi.DESILegacySurvey.get_images(pos, pixels, radius, data_release=9)

astroquery/utils/commons.py

@@ -42,10 +42,6 @@ def FK4CoordGenerator(*args, **kwargs):
     return coord.SkyCoord(*args, frame='fk4', **kwargs)
 
 
-def ArcminRadiusGenerator(*args, **kwargs):
-    return coord.Angle(*args, unit='arcmin', **kwargs)
-
-
 ICRSCoord = coord.SkyCoord
 CoordClasses = (coord.SkyCoord, BaseCoordinateFrame)
 

docs/desi/desi.rst

@@ -1,8 +1,8 @@
 .. _astroquery.desi:
 
-************************************
+*********************************************
 DESI LegacySurvey Queries (`astroquery.desi`)
-************************************
+*********************************************
 
 Getting started
 ===============
@@ -12,13 +12,13 @@ Presented below are examples that illustrate the different types of queries
 that can be formulated.
 
 Query a region
-===============
+==============
 
 This example shows how to query a certain region with DesiLegacySurvey.
 We'll use a set of coordinates that define the region of interest,
 and search within a 5 arcmin radius.
 
-.. code-block:: python
+.. doctest-remote-data::
 
     >>> from astroquery.desi import DESILegacySurvey
     >>> from astropy.coordinates import Angle, SkyCoord
@@ -28,41 +28,43 @@ and search within a 5 arcmin radius.
     >>> radius = Angle(5, unit='arcmin')
     >>> table_out = DESILegacySurvey.query_region(coordinates, radius, data_release=9)
     >>> print(table_out[:5])
-
-         ls_id              dec                 ra         ... type wise_coadd_id
-    ---------------- ------------------ ------------------ ... ---- -------------
+         ls_id              dec                ra         ... type wise_coadd_id
+                                                          ...
+    ---------------- ----------------- ------------------ ... ---- -------------
     9907734382838387 38.12628495570797  166.0838654387131 ...  PSF      1667p378
     9907734382838488 38.12798336424771  166.0922968862182 ...  PSF      1667p378
     9907734382838554 38.12858283671958  166.0980673954384 ...  REX      1667p378
-    9907734382838564 38.12840803351445 166.09921863682337 ...  EXP      1667p378
-    9907734382838584 38.12836885301038 166.10070750146636 ...  REX      1667p378
+    9907734382838564 38.12840803351445  166.09921863682337 ...  EXP      1667p378
+    9907734382838584 38.12836885301038  166.10070750146636 ...  REX      1667p378
 
 The result is an astropy.Table.
 
 Get images
-===============
+==========
 
 To download images for a certain region of interest,
 we can define our region in the same way used in the example above.
 
-.. code-block:: python
+.. doctest-remote-data::
 
     >>> from astroquery.desi import DESILegacySurvey
     >>> from astropy.coordinates import Angle, SkyCoord
+    >>>
     >>> ra = Angle('11h04m27s', unit='hourangle').degree
     >>> dec = Angle('+38d12m32s', unit='hourangle').degree
-    >>> pos = SkyCoord(ra, dec, unit='degree')
-    >>> radius = Angle(0.5, unit='arcmin')
+    >>> radius_input = 0.5
     >>> pixels = 60
-    >>> im = DESILegacySurvey.get_images(pos, data_release=9, radius=radius, pixels=pixels)
+    >>>
+    >>> pos = SkyCoord(ra, dec, unit='degree')
+    >>> radius = Angle(radius_input, unit='arcmin')
+    >>> im = DESILegacySurvey.get_images(pos, pixels, radius, data_release=9)
 
 All the information we need can be found within the object "im".
 
-.. code-block:: python
+.. doctest-remote-data::
 
     >>> hdul = im[0]
     >>> hdul[0].header
-
     SIMPLE  =                    T / file does conform to FITS standard
     BITPIX  =                  -32 / number of bits per data pixel
     NAXIS   =                    2 / number of data axes
@@ -88,24 +90,3 @@ All the information we need can be found within the object "im".
 
 The variable "im" is a list of `~astropy.io.fits.HDUList` objects, one entry for
 each corresponding object.
-
-In case a set of not valid coordinates is provided, then a `astroquery.exceptions.NoResultsWarning`
-exception is raised, as shown in the example below.
-
-.. code-block:: python
-
-    >>> from astroquery.desi import DESILegacySurvey
-    >>> from astropy.coordinates import Angle, SkyCoord
-    >>> ra = Angle('86.633212', unit='degree').degree
-    >>> dec = Angle('22.01446', unit='degree').degree
-    >>> radius_input = 3
-    >>> pixels = 1296000
-
-    >>> pos = SkyCoord(ra, dec, unit='degree')
-    >>> radius = Angle(radius_input, unit='arcmin')
-    >>> pixels = 60
-    >>> im = DESILegacySurvey.get_images(pos, data_release=9, radius=radius, pixels=pixels)
-
-.. code-block:: python
-
-    astroquery.exceptions.NoResultsWarning: HTTP Error 500: Internal Server Error - Problem retrieving the file at the url: https://www.legacysurvey.org/viewer/fits-cutout?ra=86.633212&dec=22.01446&size=1296000&layer=ls-dr9&pixscale=0.0002777777777777778&bands=g

docs/index.rst

@@ -195,6 +195,7 @@ The following modules have been completed using a common API:
   cds/cds.rst
   linelists/cdms/cdms.rst
   dace/dace.rst
+  desi/desi.rst
   esa/hsa/hsa.rst
   esa/hubble/hubble.rst
   esa/iso/iso.rst