Merge pull request #626 from bsipocz/overall_code_cleanup

Overall code cleanup

Author: bsipocz

astroquery/_astropy_init.py

@@ -116,7 +116,7 @@ def test(package=None, test_path=None, args=None, plugins=None,
 if not _ASTROPY_SETUP_:
     import os
     from warnings import warn
-    from astropy import config
+    import astropy.config.configuration as config
 
     # add these here so we only need to cleanup the namespace at the end
     config_dir = None
@@ -126,52 +126,16 @@ def test(package=None, test_path=None, args=None, plugins=None,
         config_template = os.path.join(config_dir, __package__ + ".cfg")
         if os.path.isfile(config_template):
             try:
-                config.configuration.update_default_config(
+                config.update_default_config(
                     __package__, config_dir, version=__version__)
             except TypeError as orig_error:
                 try:
-                    config.configuration.update_default_config(
+                    config.update_default_config(
                         __package__, config_dir)
-                except config.configuration.ConfigurationDefaultMissingError as e:
+                except config.ConfigurationDefaultMissingError as e:
                     wmsg = (e.args[0] + " Cannot install default profile. If "
                             "you are importing from source, this is expected.")
-                    warn(config.configuration.ConfigurationDefaultMissingWarning(wmsg))
+                    warn(config.ConfigurationDefaultMissingWarning(wmsg))
                     del e
                 except:
                     raise orig_error
-
-
-# This is to monkey-patch around a config system bug in astropy 1.0.1.
-# REMOVEME: when astropy 1.0.1 support is no longer needed
-if not _ASTROPY_SETUP_:
-    import astropy
-    if astropy.__version__ == '1.0.1':
-        from astropy.config import configuration
-
-        _existing_ConfigItem__init__ = configuration.ConfigItem.__init__
-
-        def _monkey_patch_1_0_1_ConfigItem__init__(
-                self, defaultvalue='', description=None, cfgtype=None,
-                module=None, aliases=None):
-            if module is None:
-                from astropy.utils import find_current_module
-                module = find_current_module(2)
-                if module is None:
-                    raise RuntimeError(
-                        "Cannot automatically determine get_config module, "
-                        "because it is not called from inside a valid module")
-                else:
-                    module = module.__name__
-
-            return _existing_ConfigItem__init__(
-                self,
-                defaultvalue=defaultvalue,
-                description=description,
-                cfgtype=cfgtype,
-                module=module,
-                aliases=aliases)
-
-        # Don't apply the same monkey patch twice
-        if (configuration.ConfigItem.__init__.__name__ !=
-                '_monkey_patch_1_0_1_ConfigItem__init__'):
-            configuration.ConfigItem.__init__ = _monkey_patch_1_0_1_ConfigItem__init__

astroquery/alma/core.py

@@ -306,26 +306,6 @@ def stage_data(self, uids):
                                                     ))
         tbl = self._json_summary_to_table(json_data, base_url=base_url)
 
-        # staging_root = BeautifulSoup(data_page.content)
-        # downloadFileURL = staging_root.find('form').attrs['action']
-        # data_list_url = os.path.split(downloadFileURL)[0]
-
-        # # Old version, unreliable: data_list_url = staging_submission.url
-        # log.debug("Data list URL: {0}".format(data_list_url))
-        # self._staging_log['data_list_url'] = data_list_url
-
-        # time.sleep(1)
-        # data_list_page = self._request('GET', data_list_url, cache=True)
-        # self._staging_log['data_list_page'] = data_list_page
-        # data_list_page.raise_for_status()
-
-        # if 'Error' in data_list_page.text:
-        #     errormessage = staging_root.find(
-        #         'div', id='errorContent').string.strip()
-        #     raise RemoteServiceError(errormessage)
-
-        # tbl = self._parse_staging_request_page(data_list_page)
-
         return tbl
 
     def _HEADER_data_size(self, files):
@@ -770,27 +750,6 @@ def _parse_staging_request_page(self, data_list_page):
 
         root = BeautifulSoup(data_list_page.content, 'html5lib')
 
-        # for link in root.findAll('a'):
-        #    if 'script.sh' in link.text:
-        #        download_script_url = urljoin(self.dataarchive_url,
-        #                                      link['href'])
-        # if 'download_script_url' not in locals():
-        #    raise RemoteServiceError("No download links were found.")
-
-        # download_script = self._request('GET', download_script_url,
-        #                                cache=False)
-        # download_script_target_urls = []
-        # for line in download_script.text.split('\n'):
-        #    if line and line.split() and line.split()[0] == 'wget':
-        #        download_script_target_urls.append(line.split()[1].strip('"'))
-
-        # if len(download_script_target_urls) == 0:
-        #    raise RemoteServiceError("There was an error parsing the download"
-        #                             " script; it is empty.  "
-        #                             "You can access the download script "
-        #                             "directly from this URL: "
-        #                             "{0}".format(download_script_url))
-
         data_table = root.findAll('table', class_='list', id='report')[0]
         columns = {'uid': [], 'URL': [], 'size': []}
         for tr in data_table.findAll('tr'):
@@ -864,28 +823,6 @@ def _parse_staging_request_page(self, data_list_page):
                 "Please include {0} in a bug report."
                 .format(self._staging_log['data_list_url']))
 
-        # if len(download_script_target_urls) != len(columns['URL']):
-        #    log.warn("There was an error parsing the data staging page.  "
-        #             "The results from the page and the download script "
-        #             "differ.  You can access the download script directly "
-        #             "from this URL: {0}".format(download_script_url))
-        # else:
-        #    bad_urls = []
-        #    for (rurl,url) in (zip(columns['URL'],
-        #                           download_script_target_urls)):
-        #        if rurl == 'None_Found':
-        #            url_uid = os.path.split(url)[-1]
-        #            ind = np.where(np.array(columns['uid']) == url_uid)[0][0]
-        #            columns['URL'][ind] = url
-        #        elif rurl != url:
-        #            bad_urls.append((rurl, url))
-        #    if bad_urls:
-        #        log.warn("There were mismatches between the parsed URLs "
-        #                 "from the staging page ({0}) and the download "
-        #                 "script ({1})."
-        #                 .format(self._staging_log['data_list_url'],
-        #                         download_script_url))
-
         tbl = Table([Column(name=k, data=v) for k, v in iteritems(columns)])
 
         return tbl
@@ -966,50 +903,3 @@ def unique(seq):
 def filter_printable(s):
     """ extract printable characters from a string """
     return filter(lambda x: x in string.printable, s)
-
-
-def parse_frequency_support(frequency_support_str):
-    """
-    ALMA "Frequency Support" strings have the form:
-
-    [100.63..101.57GHz,488.28kHz, XX YY] U
-    [102.43..103.37GHz,488.28kHz, XX YY] U
-    [112.74..113.68GHz,488.28kHz, XX YY] U
-    [114.45..115.38GHz,488.28kHz, XX YY]
-
-    at least, as far as we have seen.  The "U" is meant to be the Union symbol.
-    This function will parse such a string into a list of pairs of astropy
-    Quantities representing the frequency range.  It will ignore the resolution
-    and polarizations.
-    """
-    supports = frequency_support_str.split("U")
-    freq_ranges = [(float(sup[0]),
-                    float(sup[1].split(',')[0].strip(string.letters))) *
-                   u.Unit(sup[1].split(',')[0].strip(string.punctuation +
-                                                     string.digits))
-                   for i in supports for sup in [i.strip('[] ').split('..'), ]]
-
-    return freq_ranges
-
-
-def approximate_primary_beam_sizes(frequency_support_str,
-                                   dish_diameter=12 * u.m, first_null=1.220):
-    """
-    Using parse_frequency_support, determine the mean primary beam size in each
-    observed band
-
-    Parameters
-    ----------
-    frequency_support_str : str
-        The frequency support string, see `parse_frequency_support`
-    dish_diameter : `~astropy.units.Quantity`
-        Meter-equivalent unit.  The diameter of the dish.
-    first_null : float
-        The position of the first null of an Airy.  Used to compute resolution
-        as :math:`R = 1.22 \lambda/D`
-    """
-    freq_ranges = parse_frequency_support(frequency_support_str)
-    beam_sizes = [(first_null * fr.mean().to(u.m, u.spectral()) /
-                   (dish_diameter)).to(u.arcsec, u.dimensionless_angles())
-                  for fr in freq_ranges]
-    return beam_sizes

astroquery/alma/utils.py

@@ -31,10 +31,6 @@ def pyregion_subset(region, data, mywcs):
 
     shapelist = pyregion.ShapeList([region])
     if shapelist[0].coord_format not in ('physical', 'image'):
-        # Requires astropy >0.4...
-        # pixel_regions = shapelist.as_imagecoord(
-        #     self.wcs.celestial.to_header())
-        # convert the regions to image (pixel) coordinates
         celhdr = mywcs.sub([wcs.WCSSUB_CELESTIAL]).to_header()
         pixel_regions = shapelist.as_imagecoord(celhdr)
     else:
@@ -81,12 +77,17 @@ def pyregion_subset(region, data, mywcs):
 
 def parse_frequency_support(frequency_support_str):
     """
-    Given a "Frequency Support" string from ALMA queries, parse it into a set
-    of frequency ranges
+    ALMA "Frequency Support" strings have the form:
 
-    Example input:
+    [100.63..101.57GHz,488.28kHz, XX YY] U
+    [102.43..103.37GHz,488.28kHz, XX YY] U
+    [112.74..113.68GHz,488.28kHz, XX YY] U
+    [114.45..115.38GHz,488.28kHz, XX YY]
 
-    '[86.26..88.14GHz,976.56kHz, XX YY] U [88.15..90.03GHz,976.56kHz, XX YY] U [98.19..100.07GHz,976.56kHz, XX YY] U [100.15..102.03GHz,976.56kHz, XX YY]'
+    at least, as far as we have seen.  The "U" is meant to be the Union symbol.
+    This function will parse such a string into a list of pairs of astropy
+    Quantities representing the frequency range.  It will ignore the resolution
+    and polarizations.
     """
     supports = str(frequency_support_str).split('U')
 
@@ -98,14 +99,25 @@ def parse_frequency_support(frequency_support_str):
     return u.Quantity(freq_ranges)
 
 
-def approximate_primary_beam_sizes(frequency_support_str):
+def approximate_primary_beam_sizes(frequency_support_str,
+                                   dish_diameter=12 * u.m, first_null=1.220):
     """
-    Given a frequency support string, return the approximate 12m array beam
-    size using 1.22 lambda / D
+    Using parse_frequency_support, determine the mean primary beam size in each
+    observed band
+
+    Parameters
+    ----------
+    frequency_support_str : str
+        The frequency support string, see `parse_frequency_support`
+    dish_diameter : `~astropy.units.Quantity`
+        Meter-equivalent unit.  The diameter of the dish.
+    first_null : float
+        The position of the first null of an Airy.  Used to compute resolution
+        as :math:`R = 1.22 \lambda/D`
     """
     freq_ranges = parse_frequency_support(frequency_support_str)
-    beam_sizes = [(1.22 * fr.mean().to(u.m, u.spectral()) /
-                   (12 * u.m)).to(u.arcsec, u.dimensionless_angles())
+    beam_sizes = [(first_null * fr.mean().to(u.m, u.spectral()) /
+                   (dish_diameter)).to(u.arcsec, u.dimensionless_angles())
                   for fr in freq_ranges]
     return u.Quantity(beam_sizes)
 
@@ -118,8 +130,7 @@ def make_finder_chart(target, radius, save_prefix, service=SkyView.get_images,
                       public_band_colors=('blue', 'cyan', 'green',
                                           'turquoise', 'teal'),
                       integration_time_contour_levels=np.logspace(0, 5, base=2,
-                                                                  num=6),
-                      ):
+                                                                  num=6)):
     """
     Create a "finder chart" showing where ALMA has pointed in various bands,
     including different color coding for public/private data and each band.

astroquery/besancon/core.py

@@ -118,10 +118,8 @@ def get_besancon_model_file(self, filename, verbose=True, timeout=5.0):
                 sys.stdout.write(u"\r")
                 sys.stdout.flush()
             try:
-                # U = requests.get(url,timeout=timeout,stream=True) TODO:
-                # add timeout= keyword to get_readable_fileobj (when PR
-                # https://github.com/astropy/astropy/pull/1258 is merged)
-                with commons.get_readable_fileobj(url, cache=True) as f:
+                with commons.get_readable_fileobj(url, remote_timeout=timeout,
+                                                  cache=True) as f:
                     results = f.read()
                 break
             except URLError:

astroquery/conftest.py

@@ -2,7 +2,6 @@
 from __future__ import print_function
 import os
 
-from .utils import turn_off_internet
 
 # This is to figure out the astroquery version, rather than using Astropy's
 from . import version
@@ -20,25 +19,6 @@
 except NameError:
     pass
 
-
-# pytest magic:
-# http://pytest.org/latest/plugins.html#_pytest.hookspec.pytest_configure
-# use pytest.set_trace() to interactively inspect config's features
-def pytest_configure(config):
-    if config.getoption('remote_data'):
-        pass
-    else:
-        turn_off_internet(verbose=config.option.verbose)
-
-    try:
-        from astropy.tests.pytest_plugins import pytest_configure
-
-        pytest_configure(config)
-    except ImportError:
-        # assume astropy v<0.3
-        pass
-
-
 # Add astropy to test header information and remove unused packages.
 # Pytest header customisation was introduced in astropy 1.0.