Merge branch 'main' into gaia-astroquery-1.1

Author: mhsarmiento

.github/workflows/ci_crontests.yml

@@ -24,9 +24,9 @@ jobs:
           - name: Python 3.9 with all dependencies with remote data
             os: ubuntu-latest
             python: '3.9'
-            toxenv: py39-test-alldeps-devdeps
+            toxenv: py39-test-alldeps-devdeps-online
             toxargs: -v
-            toxposargs: --remote-data -v --durations=50
+            toxposargs: -v --durations=50
 
           - name: pre-repease dependencies with all dependencies
             os: ubuntu-latest

CHANGES.rst

@@ -34,6 +34,11 @@ casda
 - Use the standard ``login`` method for authenticating, which supports the system
   keyring [#2386]
 
+ipac.nexsci.nasa_exoplanet_archive
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- The deprecated methods ``query_planet()`` and ``query_star()`` have been removed.
+
 jplsbdb
 ^^^^^^^
 
@@ -53,6 +58,12 @@ gaia
 With this change the epoch photometry service returns all data associated to
 a given source. [#2376]
 
+oac
+^^^
+
+- Fix bug in parsing events that contain html tags (e.g. in their alias
+  field). [#2423]
+
 Infrastructure, Utility and Other Changes and Additions
 -------------------------------------------------------
 

astroquery/esa/iso/tests/setup_package.py

@@ -9,8 +9,6 @@
 
 """
 
-from __future__ import absolute_import
-
 import os
 
 

astroquery/exoplanet_orbit_database/__init__.py

@@ -5,8 +5,6 @@
 
 :Author: Brett M. Morris ([email protected])
 """
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
 from .exoplanet_orbit_database import (ExoplanetOrbitDatabase,
                                        ExoplanetOrbitDatabaseClass)
 from astropy import config as _config

astroquery/exoplanet_orbit_database/exoplanet_orbit_database.py

@@ -1,6 +1,4 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
 import json
 import os
 

astroquery/exoplanet_orbit_database/tests/test_exoplanet_orbit_database.py

@@ -1,5 +1,3 @@
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
 import os
 
 import pytest

astroquery/ipac/nexsci/nasa_exoplanet_archive/core.py

@@ -17,7 +17,6 @@
 from astropy.io import ascii
 from astropy.io.votable import parse_single_table
 from astropy.table import QTable
-from astropy.utils import deprecated, deprecated_renamed_argument
 from astropy.utils.exceptions import AstropyWarning
 
 # Import astroquery utilities
@@ -629,25 +628,6 @@ def _parse_result(self, response, verbose=False):
 
         return data
 
-    def _handle_all_columns_argument(self, **kwargs):
-        """
-        Deal with the ``all_columns`` argument that was exposed by earlier versions
-
-        This method will warn users about this deprecated argument and update the query syntax
-        to use ``select='*'``.
-        """
-        # We also have to manually pop these arguments from the dict because
-        # `deprecated_renamed_argument` doesn't do that for some reason for all supported astropy
-        # versions (v3.1 was beheaving as expected)
-        kwargs.pop("show_progress", None)
-        kwargs.pop("table_path", None)
-
-        # Deal with `all_columns` properly
-        if kwargs.pop("all_columns", None):
-            kwargs["select"] = kwargs.get("select", "*")
-
-        return kwargs
-
     @class_or_instance
     def _request_to_sql(self, request_payload):
         """Convert request_payload dict to SQL query string to be parsed by TAP."""
@@ -677,51 +657,5 @@ def _request_to_sql(self, request_payload):
 
         return tap_query
 
-    @deprecated(since="v0.4.1", alternative="query_object")
-    @deprecated_renamed_argument(["show_progress", "table_path"],
-                                 [None, None], "v0.4.1", arg_in_kwargs=True)
-    def query_planet(self, planet_name, cache=None, **criteria):
-        """
-        Search the ``exoplanets`` table for a confirmed planet
-
-        Parameters
-        ----------
-        planet_name : str
-            The name of a confirmed planet. If ``regularize`` is ``True``, an attempt will be made
-            to regularize this name using the ``aliastable`` table.
-        cache : bool, optional
-            Should the request result be cached? This can be useful for large repeated queries,
-            but since the data in the archive is updated regularly, this defaults to ``False``.
-        **criteria
-            Any other filtering criteria to apply. Values provided using the ``where`` keyword will
-            be ignored.
-        """
-        criteria = self._handle_all_columns_argument(**criteria)
-        criteria["where"] = "pl_name='{0}'".format(planet_name.strip())
-        return self.query_criteria("exoplanets", cache=cache, **criteria)
-
-    @deprecated(since="v0.4.1", alternative="query_object")
-    @deprecated_renamed_argument(["show_progress", "table_path"],
-                                 [None, None], "v0.4.1", arg_in_kwargs=True)
-    def query_star(self, host_name, cache=None, **criteria):
-        """
-        Search the ``exoplanets`` table for a confirmed planet host
-
-        Parameters
-        ----------
-        host_name : str
-            The name of a confirmed planet host. If ``regularize`` is ``True``, an attempt will be
-            made to regularize this name using the ``aliastable`` table.
-        cache : bool, optional
-            Should the request result be cached? This can be useful for large repeated queries,
-            but since the data in the archive is updated regularly, this defaults to ``False``.
-        **criteria
-            Any other filtering criteria to apply. Values provided using the ``where`` keyword will
-            be ignored.
-        """
-        criteria = self._handle_all_columns_argument(**criteria)
-        criteria["where"] = "pl_hostname='{0}'".format(host_name.strip())
-        return self.query_criteria("exoplanets", cache=cache, **criteria)
-
 
 NasaExoplanetArchive = NasaExoplanetArchiveClass()

astroquery/ipac/nexsci/nasa_exoplanet_archive/tests/test_nasa_exoplanet_archive.py

@@ -168,46 +168,6 @@ def test_get_access_url():
     assert get_access_url('aliaslookup') == conf.url_aliaslookup
 
 
-def test_backwards_compat(patch_get):
-    """
-    These are the tests from the previous version of this interface.
-    They query old tables by default and should return InvalidTableError.
-    """
-    NasaExoplanetArchiveMock = NasaExoplanetArchiveClass()
-
-    NasaExoplanetArchiveMock._tap_tables = ['list']
-
-    # test_hd209458b_exoplanets_archive
-    with pytest.warns(AstropyDeprecationWarning):
-        with pytest.raises(InvalidTableError) as error:
-            NasaExoplanetArchiveMock.query_planet("HD 209458 b ")
-        assert "replaced" in str(error)
-
-    # test_hd209458b_exoplanet_archive_coords
-    with pytest.warns(AstropyDeprecationWarning):
-        with pytest.raises(InvalidTableError) as error:
-            NasaExoplanetArchiveMock.query_planet("HD 209458 b ")
-        assert "replaced" in str(error)
-
-    # test_hd209458_stellar_exoplanet
-    with pytest.warns(AstropyDeprecationWarning):
-        with pytest.raises(InvalidTableError) as error:
-            NasaExoplanetArchiveMock.query_star("HD 209458")
-        assert "replaced" in str(error)
-
-    # test_hd136352_stellar_exoplanet_archive
-    with pytest.warns(AstropyDeprecationWarning):
-        with pytest.raises(InvalidTableError) as error:
-            NasaExoplanetArchiveMock.query_star("HD 136352")
-        assert "replaced" in str(error)
-
-    # test_exoplanet_archive_query_all_columns
-    with pytest.warns(AstropyDeprecationWarning):
-        with pytest.raises(InvalidTableError) as error:
-            NasaExoplanetArchiveMock.query_planet("HD 209458 b ", all_columns=True)
-        assert "replaced" in str(error)
-
-
 @pytest.mark.parametrize("table,query", API_TABLES)
 def test_api_tables(patch_get, table, query):
     NasaExoplanetArchiveMock = NasaExoplanetArchiveClass()

astroquery/oac/core.py

@@ -12,6 +12,7 @@
 
 import json
 import csv
+import re
 
 import astropy.units as u
 from astropy.table import Column, Table
@@ -435,7 +436,12 @@ def _args_to_payload(self, event, quantity,
 
     def _format_output(self, raw_output):
         if self.FORMAT == 'csv':
-            split_output = raw_output.splitlines()
+
+            fixed_raw_output = re.sub('<[^<]+?>', '', raw_output)
+            split_output = fixed_raw_output.splitlines()
+
+            # Remove any HTML tags
+
             columns = list(csv.reader([split_output[0]], delimiter=',',
                            quotechar='"'))[0]
             rows = split_output[1:]

astroquery/oac/tests/test_oac_remote.py

@@ -59,25 +59,27 @@ def test_query_region_box_json(self):
                                 data_format='json')
         assert isinstance(phot, dict)
 
-    @pytest.mark.xfail(reason="Upstream API issue.  See #1130")
     def test_get_photometry(self):
         phot = OAC.get_photometry(event="SN2014J")
         assert isinstance(phot, Table)
+        assert len(phot) > 0
 
     def test_get_photometry_b(self):
         phot = OAC.get_photometry(event="SN2014J")
         assert isinstance(phot, Table)
+        assert len(phot) > 0
 
-    @pytest.mark.xfail(reason="Upstream API issue.  See #1130")
     def test_get_single_spectrum(self):
         spec = OAC.get_single_spectrum(event="SN2014J",
                                        time=self.test_time)
         assert isinstance(spec, Table)
+        assert len(spec) > 0
 
     def test_get_single_spectrum_b(self):
         test_time = 56680
         spec = OAC.get_single_spectrum(event="SN2014J", time=test_time)
         assert isinstance(spec, Table)
+        assert len(spec) > 0
 
     def test_get_spectra(self):
         spec = OAC.get_spectra(event="SN2014J")