Merge pull request #2520 from bsipocz/TST_fix_warnings

TST: fix warnings and stop ignoring them

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 +65,10 @@ 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 filename
 
     mp = request.getfixturevalue("monkeypatch")
 

astroquery/cadc/tests/test_cadctap.py

@@ -7,6 +7,7 @@
 """
 from io import BytesIO
 from urllib.parse import urlsplit, parse_qs
+from pathlib import Path
 import os
 import sys
 
@@ -177,7 +178,7 @@ def raise_for_status(self):
         class CapabilitiesResponse:
             def __init__(self):
                 caps_file = data_path('tap_caps.xml')
-                self.text = open(caps_file, 'r').read()
+                self.text = Path(caps_file).read_text()
 
             def raise_for_status(self):
                 pass
@@ -406,7 +407,7 @@ def test_get_images():
        Mock(side_effect=lambda x, y, z: ['https://some.url']))
 def test_get_images_async():
     with patch('astroquery.utils.commons.get_readable_fileobj', autospec=True) as readable_fobj_mock:
-        readable_fobj_mock.return_value = open(data_path('query_images.fits'), 'rb')
+        readable_fobj_mock.return_value = Path(data_path('query_images.fits'))
 
     cadc = Cadc()
     readable_objs = cadc.get_images_async('08h45m07.5s +54d18m00s',

astroquery/cadc/tests/test_cadctap_remote.py

@@ -8,6 +8,7 @@
 import pytest
 import os
 import requests
+from pathlib import Path
 from datetime import datetime
 from astropy.coordinates import SkyCoord
 from astropy.io import fits
@@ -66,7 +67,8 @@ def test_query_region(self):
         assert len(result) == len(result2[result2['collection'] == 'CFHT'])
 
         # search for a target
-        results = cadc.query_region(SkyCoord.from_name('M31'), radius=0.016)
+        with pytest.warns(UserWarning, match='Radius should be of '):
+            results = cadc.query_region(SkyCoord.from_name('M31'), radius=0.016)
         assert len(results) > 20
 
     def test_query_name(self):
@@ -179,7 +181,6 @@ def test_authsession(self):
         result = cadc.exec_sync(query)
         assert len(result) == 0
 
-    @pytest.mark.xfail(reason='#2325')
     def test_get_images(self):
         cadc = Cadc()
         coords = '08h45m07.5s +54d18m00s'
@@ -223,7 +224,6 @@ def test_get_images_against_AS(self):
 
         assert len(filtered_resp_urls) == len(image_urls)
 
-    @pytest.mark.xfail(reason='#2325')
     def test_get_images_async(self):
         cadc = Cadc()
         coords = '01h45m07.5s +23d18m00s'
@@ -293,3 +293,20 @@ def test_list_jobs(self):
         if len(jobs) > 5:
             jobs_subset = cadc.list_async_jobs(last=5)
             assert len(jobs_subset) == 5
+
+    @pytest.mark.xfail(reason='https://github.com/astropy/astroquery/issues/2538')
+    def test_uploads(self, tmp_path):
+        cadc = Cadc()
+        # save a few observations on a local file
+        output_file = Path(tmp_path, 'my_observations.xml')
+        cadc.exec_sync("SELECT TOP 3 observationID FROM caom2.Observation",
+                       output_file=output_file)
+        assert output_file.exists()
+
+        # now use them to join with the remote table
+        results = cadc.exec_sync(
+            "SELECT o.observationID, intent FROM caom2.Observation o JOIN "
+            "tap_upload.test_upload tu ON o.observationID=tu.observationID",
+            uploads={'test_upload': output_file})
+
+        assert len(results) == 3

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']
 
@@ -363,7 +367,8 @@ 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\."):
-        casda.cutout(table)
+        with pytest.warns(W50, match="Invalid unit string 'pixels'"):
+            casda.cutout(table)
 
 
 def test_cutout_unauthorised(patch_get):

astroquery/eso/tests/test_eso_remote.py

@@ -1,6 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 import numpy as np
 import pytest
+import warnings
 
 from astroquery.exceptions import LoginError, NoResultsWarning
 from astroquery.eso import Eso
@@ -15,6 +16,9 @@
 # TODO: make this a configuration item
 SKIP_SLOW = True
 
+SGRA_SURVEYS = ['195.B-0283', 'GIRAFFE', 'HARPS', 'HAWKI', 'KMOS',
+                'MW-BULGE-PSFPHOT', 'VPHASplus', 'VVV', 'VVVX', 'XSHOOTER']
+
 
 @pytest.mark.remote_data
 class TestEso:
@@ -81,6 +85,7 @@ def test_empty_return(self):
         eso = Eso()
         surveys = eso.list_surveys(cache=False)
         assert len(surveys) > 0
+
         # Avoid SESAME
         with pytest.warns(NoResultsWarning):
             result_s = eso.query_surveys(surveys[0], coord1=202.469575,
@@ -142,6 +147,8 @@ def test_retrieve_data_and_calib(self):
         # list.
         assert len(result) == 1
 
+    # TODO: remove filter when https://github.com/astropy/astroquery/issues/2539 is fixed
+    @pytest.mark.filterwarnings("ignore::pytest.PytestUnraisableExceptionWarning")
     @pytest.mark.parametrize('instrument', instrument_list)
     def test_help(self, instrument):
         eso = Eso()
@@ -166,7 +173,7 @@ def test_each_instrument_SgrAstar(self, tmp_path):
         instruments = eso.list_instruments(cache=False)
 
         for instrument in instruments:
-            with pytest.warns(None) as record:
+            with warnings.catch_warnings(record=True) as record:
                 result_i = eso.query_instrument(instrument, coord1=266.41681662,
                                                 coord2=-29.00782497, cache=False)
                 # Sometimes there are ResourceWarnings, we ignore those for this test
@@ -175,36 +182,30 @@ def test_each_instrument_SgrAstar(self, tmp_path):
                 else:
                     assert len(result_i) > 0
 
-    @pytest.mark.filterwarnings("ignore::ResourceWarning")
-    def test_each_survey_SgrAstar(self, tmp_path):
+    def test_each_survey_and_SgrAstar(self, tmp_path):
         eso = Eso()
         eso.cache_location = tmp_path
+        eso.ROW_LIMIT = 5
+
 
         surveys = eso.list_surveys(cache=False)
         for survey in surveys:
-            with pytest.warns(None) as record:
+            if survey in SGRA_SURVEYS:
                 result_s = eso.query_surveys(survey, coord1=266.41681662,
                                              coord2=-29.00782497,
                                              box='01 00 00',
                                              cache=False)
-                # Sometimes there are ResourceWarnings, we ignore those for this test
-                if len(record) > 0 and NoResultsWarning in {record[i].category for i in range(len(record))}:
+                assert len(result_s) > 0
+            else:
+                with pytest.warns(NoResultsWarning):
+                    result_s = eso.query_surveys(survey, coord1=266.41681662,
+                                                 coord2=-29.00782497,
+                                                 box='01 00 00',
+                                                 cache=False)
                     assert result_s is None
-                else:
-                    print([record[i].message for i in range(len(record))])
-                    assert len(result_s) > 0
-
-    @pytest.mark.skipif("SKIP_SLOW")
-    @pytest.mark.parametrize('cache', (False, True))
-    def test_each_survey_nosource(self, tmp_path, cache):
-        eso = Eso()
-        eso.cache_location = tmp_path
-        eso.ROW_LIMIT = 5
 
-        surveys = eso.list_surveys(cache=cache)
-        for survey in surveys:
-            # just test that it doesn't crash
-            eso.query_surveys(survey, cache=cache)
+                    generic_result = eso.query_surveys(survey)
+                    assert len(generic_result) > 0
 
     def test_mixed_case_instrument(self, tmp_path):
         eso = Eso()

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 +3,7 @@
 import pytest
 import requests
 from astropy.time import Time, TimeDelta
+import astropy.units as u
 
 from ...heasarc import Heasarc, Conf
 from ...utils import commons
@@ -83,7 +84,7 @@ def test_compare_time(self, patch_get):
 
         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/irsa/tests/test_irsa_remote.py

@@ -49,8 +49,9 @@ def test_query_region_async_polygon(self):
 
     def test_query_region_polygon(self):
         polygon = [(10.1, 10.1), (10.0, 10.1), (10.0, 10.0)]
-        result = Irsa.query_region(
-            "m31", catalog="fp_psc", spatial="Polygon", polygon=polygon, cache=False)
+        with pytest.warns(UserWarning, match='Polygon endpoints are being interpreted'):
+            result = Irsa.query_region("m31", catalog="fp_psc", spatial="Polygon",
+                                       polygon=polygon, cache=False)
 
         assert isinstance(result, Table)
 

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: