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/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/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/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'}
 
 
@@ -49,11 +52,11 @@ def test_ogle_list(patch_post):
     co_list = [co, co, co]
     ogle.core.Ogle.query_region(coord=co_list)
 
-
 def test_ogle_list_values(patch_post):
     """
     Test multiple pointings using a nested-list of decimal degree Galactic
     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/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

setup.cfg

@@ -38,26 +38,25 @@ filterwarnings =
     ignore: Experimental:UserWarning:
 # This is a temporary measure, all of these should be fixed:
     ignore:distutils Version classes are deprecated:DeprecationWarning
-    ignore::pytest.PytestUnraisableExceptionWarning
     ignore::numpy.VisibleDeprecationWarning
     ignore:unclosed <ssl.SSLSocket:ResourceWarning
     ignore::UserWarning
-    ignore::astroquery.exceptions.InputWarning
-    ignore::astropy.utils.exceptions.AstropyDeprecationWarning
-    ignore::astropy.io.votable.exceptions.W03
-    ignore::astropy.io.votable.exceptions.W06
-    ignore::astropy.io.votable.exceptions.W15
+# Various VO warnings from vo_conesearch
     ignore::astropy.io.votable.exceptions.W21
-    ignore::astropy.io.votable.exceptions.W22
     ignore::astropy.io.votable.exceptions.W42
-    ignore::astropy.io.votable.exceptions.W49
-    ignore::astropy.io.votable.exceptions.W50
-    ignore:leap-second auto-update failed:astropy.utils.exceptions.AstropyWarning
     ignore:numpy.ndarray size changed:RuntimeWarning
     ignore:OverflowError converting::astropy
-# Upstream, remove when fixed, PRs have been opened
-    ignore::DeprecationWarning:pyvo
-    ignore::DeprecationWarning:regions
+# utils.commons.FileContainer needs a refactor
+    ignore:FITS files must be read as binaries:astroquery.exceptions.InputWarning
+# 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
+# Warnings from deprecated or known-to-be-broken modules
+    ignore:The legacy NRAO archive this module uses has been retired:UserWarning
+    ignore:vamdclib could not be imported; the vamdc astroquery module will not work:UserWarning
+    ignore:the vamdc astroquery module:astropy.utils.exceptions.AstropyDeprecationWarning
+# Leap second update related warning
+    ignore:leap-second auto-update failed:astropy.utils.exceptions.AstropyWarning
 # Should ignore these for astropy<5.0
     ignore:getName|currentThread:DeprecationWarning:astropy
 # This should be cleared once we requre astropy>=4.1