MAINT: fixing warning handling for remaining non-remote tests, and some remote cases

Author: bsipocz

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
 
@@ -177,9 +178,7 @@ def raise_for_status(self):
         class CapabilitiesResponse:
             def __init__(self):
                 caps_file = data_path('tap_caps.xml')
-                with open(caps_file, 'r') as infile:
-                    text = infile.read()
-                self.text = text
+                self.text = Path(caps_file).read_text()
 
             def raise_for_status(self):
                 pass
@@ -408,7 +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
@@ -180,7 +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'
@@ -224,7 +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'
@@ -294,3 +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)#'my_observations.xml')
+#        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})#'my_observations.xml'})
+
+        assert len(results) == 3

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/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)
 

docs/cadc/cadc.rst

@@ -444,6 +444,7 @@ Multiple temporary tables to be used at once can be specified as such.
 
 More details about temporary table upload can be found in the IVOA TAP specification.
 
+.. TODO: remove the IGNORE_WARNINGS once https://github.com/astropy/astroquery/issues/2538 is fixed
 .. doctest-remote-data::
 
     >>> from astroquery.cadc import Cadc
@@ -460,14 +461,15 @@ More details about temporary table upload can be found in the IVOA TAP specifica
     >>> # 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': 'my_observations.xml'})
+    ...                          uploads={'test_upload': 'my_observations.xml'})  # doctest: +IGNORE_WARNINGS
     >>> print(results)  # doctest: +IGNORE_OUTPUT
               observationID             intent
     ---------------------------------- -------
                 c13a_060826_044314_ori science
     tess2021167190903-s0039-1-3-0210-s science
                              tu1657207 science
 
+
 The feature allows a user to save the results of a query to use them later or
 correlate them with data in other TAP services.
 

docs/ipac/irsa/irsa.rst

@@ -175,7 +175,7 @@ is an ra, dec pair expressed in degrees:
 
     >>> from astroquery.ipac.irsa import Irsa
     >>> table = Irsa.query_region("m31", catalog="fp_psc", spatial="Polygon",
-    ... polygon = [(10.1, 10.1), (10.0, 10.1), (10.0, 10.0)])
+    ... polygon = [(10.1, 10.1), (10.0, 10.1), (10.0, 10.0)])  # doctest: +IGNORE_WARNINGS
     >>> print(table)
         ra        dec         clon         clat     ... ext_key  j_h   h_k   j_k
        deg        deg                               ...

setup.cfg

@@ -47,6 +47,10 @@ filterwarnings =
 # utils.commons.parse_coordinates, we should remove its usage:
     ignore:Coordinate string is being interpreted as an ICRS coordinate:astroquery.exceptions.InputWarning
     ignore:Coordinate string is being interpreted as an ICRS coordinate:UserWarning
+# To be removed with a fix for https://github.com/astropy/astroquery/issues/2523
+    ignore::bs4.builder.XMLParsedAsHTMLWarning
+# To be removed with a fix for https://github.com/astropy/astroquery/issues/2242
+     ignore::astropy.io.votable.exceptions.E02
 # Warnings from yet to be refactored or to be removed modules
     ignore:Experimental. ALFALFA:UserWarning
     ignore:Experimental. Fermi-LAT:UserWarning