Merge branch 'main' into gaia-astroquery-1.1

.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")

astroquery/query.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 abc
 import inspect
 import pickle

astroquery/sdss/core.py

@@ -2,8 +2,6 @@
 """
 Access Sloan Digital Sky Survey database online.
 """
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
 import io
 import warnings
 import numpy as np

astroquery/sdss/field_names.py

@@ -1,7 +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 warnings
 

docs/casda/casda.rst

@@ -80,10 +80,16 @@ from the keyring, or if in an interactive environment then it will be requested.
     >>> casda = Casda()
     >>> casda.login(username='[email protected]')
 
+.. Note::
+
+   Prior to Astroquery v0.4.7, authentication required creating an instance of the ``Casda`` class
+   with a username and password. e.g.: ``casda = Casda(username, password)``
 
 Data Access
 ===========
 
+.. versionadded:: 0.4.4
+
 In order to access data in CASDA you must first stage the data using the :meth:`~astroquery.casda.CasdaClass.stage_data` 
 method.
 This is because only some of the data in CASDA is held on disc at any particular time.
@@ -111,10 +117,15 @@ taken in scheduling block 2338 is shown below:
     >>> url_list = casda.stage_data(subset)
     >>> filelist = casda.download_files(url_list, savedir='/tmp')
 
+.. Note::
+
+   Due to server side changes, downloads now require Astroquery v0.4.6 or later.
 
 Cutouts
 =======
 
+.. versionadded:: 0.4.7
+
 As well as accessing full data products, the CASDA service can produce cutout images and cubes from larger data products.
 The cutout support in AstroQuery allows both spatial and spectral cutouts.
 To produce a spatial cutout, pass in a coordinate and either a radius or a height and a width to the 

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{37,38,39,310}-test{,-alldeps,-oldestdeps,-devdeps,-predeps}{,-cov}
+    py{37,38,39,310}-test{,-alldeps,-oldestdeps,-devdeps,-predeps}{,-online}{,-cov}
     codestyle
     build_docs
 requires =
@@ -26,6 +26,10 @@ changedir = .tmp/{envname}
 
 description = run tests
 
+setenv =
+    PYTEST_ARGS = ''
+    online: PYTEST_ARGS = --remote-data=any --reruns=1 --reruns-delay 10
+
 deps =
     devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
     devdeps: git+https://github.com/astropy/pyvo.git#egg=pyvo
@@ -38,6 +42,7 @@ deps =
     oldestdeps: matplotlib==3.3.*
     oldestdeps: pyvo==1.1
     cov: codecov
+    online: pytest-rerunfailures
 
 extras =
     test
@@ -47,8 +52,8 @@ extras =
 commands =
     pip freeze
     # FIXME: there are too many failures in the docs example gallery, ignore it for now
-    !cov: pytest --pyargs astroquery {toxinidir}/docs --ignore={toxinidir}/docs/gallery* {posargs}
-    cov:  pytest --pyargs astroquery {toxinidir}/docs --ignore={toxinidir}/docs/gallery* --cov astroquery --cov-config={toxinidir}/setup.cfg {posargs}
+    !cov: pytest --pyargs astroquery {toxinidir}/docs --ignore={toxinidir}/docs/gallery* {env:PYTEST_ARGS} {posargs}
+    cov:  pytest --pyargs astroquery {toxinidir}/docs --ignore={toxinidir}/docs/gallery* --cov astroquery --cov-config={toxinidir}/setup.cfg {env:PYTEST_ARGS} {posargs}
     cov: coverage xml -o {toxinidir}/coverage.xml
 
 pip_pre =