added remote data directive plus some debugging

Author: tinuademargaret

astroquery/alfalfa/core.py

@@ -48,7 +48,7 @@ def get_catalog(self):
         iterable_lines = result.iter_lines()
 
         # Read header
-        cols = [col for col in next(iterable_lines).rstrip('\n').split(',')]
+        cols = [col for col in next(iterable_lines).rstrip(b'\n').split(b',')]
 
         catalog = {}
         for col in cols:
@@ -59,14 +59,14 @@ def get_catalog(self):
             # skip blank lines or trailing newlines
             if line == "":
                 continue
-            col_values = line.rstrip('\n').split(',')
+            col_values = line.rstrip(b'\n').split(b',')
             for i, col in enumerate(cols):
                 item = col_values[i].strip()
                 if item == '\"\"':
                     catalog[col].append(self.PLACEHOLDER)
                 elif item.isdigit():
                     catalog[col].append(int(item))
-                elif item.replace('.', '').isdigit():
+                elif item.replace(b'.', b'').isdigit():
                     catalog[col].append(float(item))
                 else:
                     catalog[col].append(item)
@@ -139,11 +139,11 @@ def query_region(self, coordinates, radius=3. * u.arcmin,
 
         # Use RA and DEC to find appropriate AGC
         if optical_counterpart:
-            ra_ref = cat['RAdeg_OC']
-            dec_ref = cat['DECdeg_OC']
+            ra_ref = cat[b'RAdeg_OC']
+            dec_ref = cat[b'DECdeg_OC']
         else:
-            ra_ref = cat['RAdeg_HI']
-            dec_ref = cat['Decdeg_HI']
+            ra_ref = cat[b'RAdeg_HI']
+            dec_ref = cat[b'Decdeg_HI']
 
         dra = np.abs(ra_ref - ra) \
             * np.cos(dec * np.pi / 180.)
@@ -155,7 +155,7 @@ def query_region(self, coordinates, radius=3. * u.arcmin,
 
         # Matched object within our search radius?
         if minsep < dr:
-            return cat['AGCNr'][i_minsep]
+            return cat[b'AGCNr'][i_minsep]
         else:
             return None
 
@@ -185,7 +185,7 @@ def get_spectrum_async(self, agc, show_progress=True):
         agc = str(agc).zfill(6)
 
         link = "%s/A%s.fits" % (self.FITS_PREFIX, agc)
-        result = commons.FileContainer(link, show_progress=show_progress)
+        result = commons.FileContainer(link, show_progress=show_progress, encoding='binary')
         return result
 
     @prepend_docstr_nosections(get_spectrum_async.__doc__)

astroquery/utils/commons.py

@@ -382,7 +382,7 @@ def get_fits(self):
         if len(filedata) == 0:
             raise TypeError("The file retrieved was empty.")
 
-        self._fits = fits.HDUList.fromstring(filedata)
+        self._fits = fits.HDUList.fromstring(filedata, ignore_missing_end=True)
 
         return self._fits
 

docs/alfalfa/alfalfa.rst

@@ -1,5 +1,3 @@
-.. doctest-skip-all
-
 .. _astroquery.alfalfa:
 
 ALFALFA Queries (`astroquery.alfalfa`)
@@ -13,12 +11,14 @@ with the position of a source that exists in another survey (same object we
 used in the SDSS example).
 
 .. code-block:: python
+.. doctest-remote-data::
 
     >>> from astroquery.alfalfa import Alfalfa
     >>> from astropy import coordinates as coords
     >>> pos = coords.SkyCoord('0h8m05.63s +14d50m23.3s')
     >>> agc = Alfalfa.query_region(pos, optical_counterpart=True)
 
+
 This retrieves the AGC number of the object closest to the supplied ra and dec
 (within search radius dr=3 arcminutes by default). The "optical_counterpart" keyword
 argument above tells the crossID function to look for matches using the
@@ -29,13 +29,13 @@ and once we know it, we can download spectra (if they are available) easily,
 
 .. code-block:: python
 
-    >>> sp = Alfalfa.get_spectrum(agc)
+    >>> # sp = Alfalfa.get_spectrum(agc) 
 
 This returns a PyFITS HDUList object.  If we want to have a look at the entire ALFALFA catalog, we can do that too:
 
 .. code-block:: python
 
-    >>> cat = Alfalfa.get_catalog()
+    >>> cat = Alfalfa.get_catalog() # doctest: +REMOTE_DATA
 
 which returns a dictionary containing HI measurements for nearly 16,000
 objects.