Fixing more warnings and removing them from the config

astroquery/alfalfa/tests/test_alfalfa.py

@@ -38,7 +38,9 @@ def patch_get_readable_fileobj(request):
     @contextmanager
     def get_readable_fileobj_mockreturn(filename, **kwargs):
         file_obj = data_path(DATA_FILES['spectrum'])  # TODO: add images option
-        yield open(file_obj, 'rb')  # read as bytes, assuming FITS
+        # read as bytes, assuming FITS
+        with open(file_obj, 'rb') as inputfile:
+            yield inputfile
 
     mp = request.getfixturevalue("monkeypatch")
 

astroquery/besancon/tests/test_besancon.py

@@ -65,11 +65,11 @@ def get_readable_fileobj_mockreturn(filename, **kwargs):
         if isinstance(filename, str):
             if '1376235131.430670' in filename:
                 is_binary = kwargs.get('encoding', None) == 'binary'
-                file_obj = open(data_path('1376235131.430670.resu'),
-                                "r" + ('b' if is_binary else ''))
+                with open(data_path('1376235131.430670.resu'), "r" + ('b' if is_binary else '')) as file_obj:
+                    yield file_obj
         else:
             file_obj = filename
-        yield file_obj
+            yield file_obj
 
     mp = request.getfixturevalue("monkeypatch")
 

astroquery/cadc/tests/test_cadctap.py

@@ -177,7 +177,9 @@ def raise_for_status(self):
         class CapabilitiesResponse:
             def __init__(self):
                 caps_file = data_path('tap_caps.xml')
-                self.text = open(caps_file, 'r').read()
+                with open(caps_file, 'r') as infile:
+                    text = infile.read()
+                self.text = text
 
             def raise_for_status(self):
                 pass

astroquery/casda/tests/test_casda.py

@@ -11,6 +11,7 @@
 import astropy.units as u
 from astropy.table import Table, Column
 from astropy.io.votable import parse
+from astropy.io.votable.exceptions import W03, W50
 from astroquery import log
 import numpy as np
 
@@ -269,7 +270,8 @@ def test_query_region_async_box(patch_get):
 
 
 def test_filter_out_unreleased():
-    all_records = parse(data_path('partial_unreleased.xml'), verify='warn').get_first_table().to_table()
+    with pytest.warns(W03):
+        all_records = parse(data_path('partial_unreleased.xml'), verify='warn').get_first_table().to_table()
     assert all_records[0]['obs_release_date'] == '2017-08-02T03:51:19.728Z'
     assert all_records[1]['obs_release_date'] == '2218-01-02T16:51:00.728Z'
     assert all_records[2]['obs_release_date'] == ''
@@ -331,7 +333,8 @@ def test_stage_data(patch_get):
     casda = Casda()
     fake_login(casda, USERNAME, PASSWORD)
     casda.POLL_INTERVAL = 1
-    urls = casda.stage_data(table, verbose=True)
+    with pytest.warns(W50, match="Invalid unit string 'pixels'"):
+        urls = casda.stage_data(table, verbose=True)
     assert urls == ['http://casda.csiro.au/download/web/111-000-111-000/askap_img.fits.checksum',
                     'http://casda.csiro.au/download/web/111-000-111-000/askap_img.fits']
 
@@ -348,7 +351,8 @@ def test_cutout(patch_get):
     casda = Casda()
     fake_login(casda, USERNAME, PASSWORD)
     casda.POLL_INTERVAL = 1
-    urls = casda.cutout(table, coordinates=centre, radius=radius, verbose=True)
+    with pytest.warns(W50, match="Invalid unit string 'pixels'"):
+        urls = casda.cutout(table, coordinates=centre, radius=radius, verbose=True)
     assert urls == ['http://casda.csiro.au/download/web/111-000-111-000/cutout.fits.checksum',
                     'http://casda.csiro.au/download/web/111-000-111-000/cutout.fits']
 
@@ -367,7 +371,8 @@ def test_cutout_no_args(patch_get):
     casda.POLL_INTERVAL = 1
     with pytest.raises(ValueError,
             match=r"Please provide cutout parameters such as coordinates, band or channel\.") as excinfo:
-        casda.cutout(table)
+        with pytest.warns(W50, match="Invalid unit string 'pixels'"):
+            casda.cutout(table)
 
 
 def test_cutout_unauthorised(patch_get):

astroquery/exoplanet_orbit_database/exoplanet_orbit_database.py

@@ -1,6 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 import json
 import os
+import warnings
 
 from astropy.utils.data import download_file
 from astropy.io import ascii
@@ -30,9 +31,9 @@ def __init__(self):
     def param_units(self):
         if self._param_units is None:
             module_dir = os.path.dirname(os.path.abspath(__file__))
-            units_file = open(os.path.join(module_dir, 'data',
-                                           'exoplanet_orbit_database_units.json'))
-            self._param_units = json.load(units_file)
+            filename = os.path.join(module_dir, 'data', 'exoplanet_orbit_database_units.json')
+            with open(filename) as units_file:
+                self._param_units = json.load(units_file)
 
         return self._param_units
 
@@ -82,7 +83,11 @@ def get_table(self, cache=True, show_progress=True, table_path=None):
                     except ValueError:
                         print(f"WARNING: Unit {self.param_units[col]} not recognised")
 
-            self._table = QTable(exoplanets_table)
+            # Masked quantities are not supported in older astropy, warnings are raised for <v5.0
+            with warnings.catch_warnings():
+                warnings.filterwarnings('ignore', message='dropping mask in Quantity column',
+                                        category=UserWarning)
+                self._table = QTable(exoplanets_table)
 
         return self._table
 

astroquery/heasarc/tests/test_heasarc_remote_isdc.py

@@ -3,6 +3,9 @@
 import pytest
 import requests
 
+from astropy.time import Time, TimeDelta
+import astropy.units as u
+
 from ...heasarc import Heasarc, Conf
 from ...utils import commons
 
@@ -78,13 +81,11 @@ def test_compare_time(self, patch_get):
         patch_get.assume_fileid_for_request(
             lambda url, params: f"last-month-{params['tablehead'].split()[-1]}")
 
-        from astropy.time import Time, TimeDelta
-
         object_name = 'Crab'
 
         heasarc = Heasarc()
 
-        month_ago = (Time.now() - TimeDelta(30)).isot[:10]
+        month_ago = (Time.now() - TimeDelta(30 * u.day)).isot[:10]
         today = Time.now().isot[:10]
         T = month_ago + " .. " +  today
 

astroquery/ipac/irsa/ibe/core.py

@@ -8,7 +8,6 @@
  https://irsa.ipac.caltech.edu/ibe/
 """
 
-
 import os
 import webbrowser
 from bs4 import BeautifulSoup
@@ -270,7 +269,7 @@ def list_missions(self, cache=True):
             response = self._request('GET', url, timeout=self.TIMEOUT,
                                      cache=cache)
 
-            root = BeautifulSoup(response.text)
+            root = BeautifulSoup(response.text, 'html5lib')
             links = root.findAll('a')
 
             missions = [os.path.basename(a.attrs['href'].rstrip('/'))
@@ -308,7 +307,7 @@ def list_datasets(self, mission=None, cache=True):
         response = self._request('GET', url, timeout=self.TIMEOUT,
                                  cache=cache)
 
-        root = BeautifulSoup(response.text)
+        root = BeautifulSoup(response.text, 'html5lib')
         links = root.findAll('a')
         datasets = [a.text for a in links
                     if a.attrs['href'].count('/') >= 4  # shown as '..'; ignore
@@ -362,7 +361,7 @@ def list_tables(self, mission=None, dataset=None, cache=True):
         response = self._request('GET', url, timeout=self.TIMEOUT,
                                  cache=cache)
 
-        root = BeautifulSoup(response.text)
+        root = BeautifulSoup(response.text, 'html5lib')
         return [tr.find('td').string for tr in root.findAll('tr')[1:]]
 
     # Unfortunately, the URL construction for each data set is different, and

astroquery/ipac/irsa/sha/tests/test_sha.py

@@ -22,8 +22,8 @@ def data_path(filename):
 def get_mockreturn(url, params=None, stream=False, timeout=10, **kwargs):
     if stream:
         filename = data_path(DATA_FILES['img'])
-        return MockResponse(open(filename, 'rb').read(),
-                            content_type='image/fits', **kwargs)
+        with open(filename, 'rb') as infile:
+            return MockResponse(infile.read(), content_type='image/fits', **kwargs)
     elif params['RA'] == 163.6136:
         filename = data_path(DATA_FILES['pos_t'])
     elif params['NAIFID'] == 2003226:

astroquery/ipac/ned/tests/test_ned.py

@@ -1,6 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
 import os
+from contextlib import contextmanager
 
 from numpy import testing as npt
 import pytest
@@ -47,12 +48,14 @@ def patch_get(request):
 
 @pytest.fixture
 def patch_get_readable_fileobj(request):
+    @contextmanager
     def get_readable_fileobj_mockreturn(filename, cache=True, encoding=None,
                                         show_progress=True):
         # Need to read FITS files with binary encoding: should raise error
         # otherwise
         assert encoding == 'binary'
-        return open(data_path(DATA_FILES['image']), 'rb')
+        with open(data_path(DATA_FILES['image']), 'rb') as infile:
+            yield infile
 
     mp = request.getfixturevalue("monkeypatch")
 
@@ -138,7 +141,8 @@ def test_photometry(patch_get):
 
 
 def test_extract_image_urls():
-    html_in = open(data_path(DATA_FILES['extract_urls']), 'r').read()
+    with open(data_path(DATA_FILES['extract_urls']), 'r') as infile:
+        html_in = infile.read()
     url_list = ned.core.Ned._extract_image_urls(html_in)
     assert len(url_list) == 5
     for url in url_list:

astroquery/mast/tests/test_mast.py

@@ -614,7 +614,7 @@ def test_catalogs_query_criteria(patch_post):
     assert isinstance(result, Table)
 
     with pytest.raises(InvalidQueryError) as invalid_query:
-        mast.Catalogs.query_criteria(catalog="Tic", objectName="M10")
+        mast.Catalogs.query_criteria(catalog="Tic", objectname="M10")
     assert "non-positional" in str(invalid_query.value)
 
 

astroquery/nvas/tests/test_nvas.py

@@ -60,11 +60,11 @@ def patch_get_readable_fileobj(request):
     def get_readable_fileobj_mockreturn(filename, **kwargs):
         encoding = kwargs.get('encoding', None)
         if encoding == 'binary':
-            file_obj = open(data_path(DATA_FILES["image"]), 'rb')
+            with open(data_path(DATA_FILES["image"]), 'rb') as file_obj:
+                yield file_obj
         else:
-            file_obj = open(data_path(DATA_FILES["image"]),
-                            "r", encoding=encoding)
-        yield file_obj
+            with open(data_path(DATA_FILES["image"]), "r", encoding=encoding) as file_obj:
+                yield file_obj
 
     mp = request.getfixturevalue("monkeypatch")
 
@@ -95,7 +95,8 @@ def test_parse_coordinates(coordinates):
 
 
 def test_extract_image_urls():
-    html_in = open(data_path(DATA_FILES['image_search']), 'r').read()
+    with open(data_path(DATA_FILES['image_search']), 'r') as infile:
+        html_in = infile.read()
     image_list = nvas.core.Nvas.extract_image_urls(html_in)
     assert len(image_list) == 2
 

astroquery/ogle/tests/test_ogle.py

@@ -5,8 +5,11 @@
 import pytest
 from astropy.coordinates import SkyCoord
 from astropy import units as u
+from astropy.utils.exceptions import AstropyDeprecationWarning
+
 from astroquery.utils.mocks import MockResponse
 
+
 DATA_FILES = {'gal_0_3': 'gal_0_3.txt'}
 
 
@@ -56,4 +59,5 @@ def test_ogle_list_values(patch_post):
     coordinates
     """
     co_list = [[0, 0, 0], [3, 3, 3]]
-    ogle.core.Ogle.query_region(coord=co_list)
+    with pytest.warns(AstropyDeprecationWarning):
+        ogle.core.Ogle.query_region(coord=co_list)

astroquery/sdss/core.py

@@ -1002,7 +1002,7 @@ def _args_to_payload(self, coordinates=None,
             else:
                 if field_help is not True:
                     warnings.warn(f"{field_help} isn't a valid 'photobj_field' or "
-                                  "'specobj_field' field, valid fields are"
+                                  "'specobj_field' field, valid fields are "
                                   "returned.")
                 return {'photoobj_all': photoobj_all,
                         'specobj_all': specobj_all}

astroquery/sdss/tests/test_sdss.py

@@ -504,8 +504,8 @@ def test_field_help_region(patch_request):
     existing_s_field = sdss.SDSS.query_region(coords,
                                               field_help='spectroSynFlux_r')
 
-    non_existing_field = sdss.SDSS.query_region(coords,
-                                                field_help='nonexist')
+    with pytest.warns(UserWarning, match="nonexist isn't a valid 'photobj_field' or 'specobj_field'"):
+        non_existing_field = sdss.SDSS.query_region(coords, field_help='nonexist')
 
     assert existing_p_field is None
     assert existing_s_field is None

astroquery/simbad/tests/test_simbad.py

@@ -125,15 +125,12 @@ def test_parse_result():
     result1 = sb._parse_result(
         MockResponseSimbad('query id '), simbad.core.SimbadVOTableResult)
     assert isinstance(result1, Table)
-    with pytest.raises(TableParseError) as ex:
+    expected_exception = 'Failed to parse SIMBAD result! The raw response can be found in self.last_response, '
+
+    with pytest.raises(TableParseError, match=expected_exception):
         sb._parse_result(MockResponseSimbad('query error '),
                 simbad.core.SimbadVOTableResult)
-    assert str(ex.value) == ('Failed to parse SIMBAD result! The raw response '
-                             'can be found in self.last_response, and the '
-                             'error in self.last_table_parse_error. '
-                             'The attempted parsed result is in '
-                             'self.last_parsed_result.\n Exception: 7:115: '
-                             'no element found')
+
     assert isinstance(sb.last_response.text, str)
     assert isinstance(sb.last_response.content, bytes)
 
@@ -361,15 +358,18 @@ def test_votable_fields():
             set(['main_id', 'coordinates', 'rot', 'z_value', 'velocity']))
     sb.remove_votable_fields('rot', 'main_id', 'coordinates')
     assert set(sb.get_votable_fields()) == set(['z_value', 'velocity'])
-    sb.remove_votable_fields('rot', 'main_id', 'coordinates')
+    # Warning is expected as we removed the 'coordinates' field above:
+    with pytest.warns(UserWarning, match="coordinates: this field is not set"):
+        sb.remove_votable_fields('rot', 'main_id', 'coordinates')
     assert set(sb.get_votable_fields()) == set(['z_value', 'velocity'])
-    sb.remove_votable_fields('z_value', 'velocity')
-    assert (set(sb.get_votable_fields()) ==
-            set(['main_id', 'coordinates']))
+    with pytest.warns(UserWarning, match="All fields have been removed. Resetting"):
+        sb.remove_votable_fields('z_value', 'velocity')
+    assert set(sb.get_votable_fields()) == set(['main_id', 'coordinates'])
     sb.add_votable_fields('rot', 'z_value', 'velocity')
-    sb.reset_votable_fields()
     assert (set(sb.get_votable_fields()) ==
-            set(['main_id', 'coordinates']))
+            set(['main_id', 'coordinates', 'rot', 'z_value', 'velocity']))
+    sb.reset_votable_fields()
+    assert set(sb.get_votable_fields()) == set(['main_id', 'coordinates'])
 
 
 def test_query_criteria1(patch_post):
@@ -394,9 +394,9 @@ def test_simbad_settings1():
     sb = simbad.core.Simbad()
     assert sb.get_votable_fields() == ['main_id', 'coordinates']
     sb.add_votable_fields('ra', 'dec(5)')
-    sb.remove_votable_fields('ra', 'dec')
-    assert (sb.get_votable_fields() ==
-            ['main_id', 'coordinates', 'dec(5)'])
+    with pytest.warns(UserWarning, match="dec: this field is not set"):
+        sb.remove_votable_fields('ra', 'dec')
+    assert sb.get_votable_fields() == ['main_id', 'coordinates', 'dec(5)']
     sb.reset_votable_fields()
 
 

astroquery/ukidss/tests/test_ukidss.py

@@ -41,10 +41,11 @@ def get_readable_fileobj_mockreturn(filename, **kwargs):
         is_binary = kwargs.get('encoding', None) == 'binary'
         mode = 'rb' if is_binary else 'r'
         if "fits" in filename:
-            file_obj = open(data_path(DATA_FILES["image"]), mode)
+            with open(data_path(DATA_FILES["image"]), mode) as file_obj:
+                yield file_obj
         else:
-            file_obj = open(data_path(DATA_FILES["votable"]), mode)
-        yield file_obj
+            with open(data_path(DATA_FILES["votable"]), mode) as file_obj:
+                yield file_obj
 
     mp = request.getfixturevalue("monkeypatch")
 
@@ -135,7 +136,8 @@ def test_get_image_list(patch_get, patch_get_readable_fileobj):
 
 
 def test_extract_urls():
-    html_in = open(data_path(DATA_FILES["image_results"]), 'r').read()
+    with open(data_path(DATA_FILES["image_results"]), 'r') as infile:
+        html_in = infile.read()
     urls = ukidss.core.Ukidss.extract_urls(html_in)
     assert len(urls) == 1
 

astroquery/vamdc/core.py

@@ -13,7 +13,7 @@
 __doctest_skip__ = ['VamdcClass.*']
 
 
-@deprecated('0.4.2', 'the module relies on an unmaintained library and is'
+@deprecated('0.4.2', 'the vamdc astroquery module relies on an unmaintained library and is'
             'considered deprecated until completely refactored or upstream'
             'is stablised.')
 @async_to_sync

astroquery/vizier/tests/test_vizier.py

@@ -229,7 +229,8 @@ def test_keywords(self):
         v = vizier.core.Vizier(keywords=['optical', 'chandra', 'ans'])
         assert str(v.keywords) == ('-kw.Mission=ANS\n-kw.Mission='
                                    'Chandra\n-kw.Wavelength=optical')
-        v = vizier.core.Vizier(keywords=['xy', 'optical'])
+        with pytest.warns(UserWarning, match="xy : No such keyword"):
+            v = vizier.core.Vizier(keywords=['xy', 'optical'])
         assert str(v.keywords) == '-kw.Wavelength=optical'
         v.keywords = ['optical', 'cobe']
         assert str(v.keywords) == '-kw.Mission=COBE\n-kw.Wavelength=optical'