Merge pull request #2309 from bsipocz/alma_deprecation_cleanup

Alma deprecation cleanup

Author: bsipocz

CHANGES.rst

@@ -20,6 +20,12 @@ esa.hubble
 
 - Changed query_target method to use TAP instead of AIO [#2268]
 
+alma
+^^^^
+
+- Deprecated keywords and ``stage_data`` method has been removed. Optional
+  keyword arguments are now keyword only. [#2309]
+
 casda
 ^^^^^
 

astroquery/alma/core.py

@@ -8,16 +8,15 @@
 import string
 import requests
 import warnings
+
 from pkg_resources import resource_filename
 from bs4 import BeautifulSoup
 import pyvo
-
 from urllib.parse import urljoin
+
 from astropy.table import Table, Column, vstack
 from astroquery import log
-from astropy.utils import deprecated
 from astropy.utils.console import ProgressBar
-from astropy.utils.exceptions import AstropyDeprecationWarning
 from astropy import units as u
 from astropy.time import Time
 from pyvo.dal.sia2 import SIA_PARAMETERS_DESC
@@ -236,7 +235,7 @@ def tap(self):
             self._tap = pyvo.dal.tap.TAPService(baseurl=self.tap_url)
         return self._tap
 
-    def query_object_async(self, object_name, cache=None, public=True,
+    def query_object_async(self, object_name, *, public=True,
                            science=True, payload=None, **kwargs):
         """
         Query the archive for a source name.
@@ -245,7 +244,6 @@ def query_object_async(self, object_name, cache=None, public=True,
         ----------
         object_name : str
             The object name.  Will be resolved by astropy.coord.SkyCoord
-        cache : deprecated
         public : bool
             True to return only public datasets, False to return private only,
             None to return both
@@ -262,7 +260,7 @@ def query_object_async(self, object_name, cache=None, public=True,
         return self.query_async(public=public, science=science,
                                 payload=payload, **kwargs)
 
-    def query_region_async(self, coordinate, radius, cache=None, public=True,
+    def query_region_async(self, coordinate, radius, *, public=True,
                            science=True, payload=None, **kwargs):
         """
         Query the ALMA archive with a source name and radius
@@ -273,8 +271,6 @@ def query_region_async(self, coordinate, radius, cache=None, public=True,
             the identifier or coordinates around which to query.
         radius : str / `~astropy.units.Quantity`, optional
             the radius of the region
-        cache : Deprecated
-            Cache the query?
         public : bool
             True to return only public datasets, False to return private only,
             None to return both
@@ -299,18 +295,15 @@ def query_region_async(self, coordinate, radius, cache=None, public=True,
         return self.query_async(public=public, science=science,
                                 payload=payload, **kwargs)
 
-    def query_async(self, payload, cache=None, public=True, science=True,
-                    legacy_columns=False, max_retries=None,
-                    get_html_version=None,
-                    get_query_payload=None, **kwargs):
+    def query_async(self, payload, *, public=True, science=True,
+                    legacy_columns=False, get_query_payload=None, **kwargs):
         """
         Perform a generic query with user-specified payload
 
         Parameters
         ----------
         payload : dictionary
             Please consult the `help` method
-        cache : deprecated
         public : bool
             True to return only public datasets, False to return private only,
             None to return both
@@ -327,17 +320,6 @@ def query_async(self, payload, cache=None, public=True, science=True,
         Table with results. Columns are those in the ALMA ObsCore model
         (see ``help_tap``) unless ``legacy_columns`` argument is set to True.
         """
-        local_args = dict(locals().items())
-
-        for arg in local_args:
-            # check if the deprecated attributes have been used
-            for dep in ['cache', 'max_retries', 'get_html_version']:
-                if arg[0] == dep and arg[1] is not None:
-                    warnings.warn(
-                        ("Argument '{}' has been deprecated "
-                         "since version 4.0.1 and will be ignored".format(arg[0])),
-                        AstropyDeprecationWarning)
-                    del kwargs[arg[0]]
 
         if payload is None:
             payload = {}
@@ -385,7 +367,7 @@ def query_async(self, payload, cache=None, public=True, science=True,
             return legacy_result
         return result
 
-    def query_sia(self, pos=None, band=None, time=None, pol=None,
+    def query_sia(self, *, pos=None, band=None, time=None, pol=None,
                   field_of_view=None, spatial_resolution=None,
                   spectral_resolving_power=None, exptime=None,
                   timeres=None, publisher_did=None,
@@ -500,54 +482,7 @@ def _get_dataarchive_url(self):
                              "on github.")
         return self.dataarchive_url
 
-    @deprecated(since="v0.4.1", alternative="get_data_info")
-    def stage_data(self, uids, expand_tarfiles=False, return_json=False):
-        """
-        Obtain table of ALMA files
-
-        DEPRECATED: Data is no longer staged. This method is deprecated and
-        kept here for backwards compatibility reasons but it's not fully
-        compatible with the original implementation.
-
-        Parameters
-        ----------
-        uids : list or str
-            A list of valid UIDs or a single UID.
-            UIDs should have the form: 'uid://A002/X391d0b/X7b'
-        expand_tarfiles : DEPRECATED
-        return_json : DEPRECATED
-            Note: The returned astropy table can be easily converted to json
-            through pandas:
-            output = StringIO()
-            stage_data(...).to_pandas().to_json(output)
-            table_json = output.getvalue()
-
-        Returns
-        -------
-        data_file_table : Table
-            A table containing 3 columns: the UID, the file URL (for future
-            downloading), and the file size
-        """
-
-        if return_json:
-            raise AttributeError(
-                'return_json is deprecated. See method docs for a workaround')
-        table = Table()
-        res = self.get_data_info(uids, expand_tarfiles=expand_tarfiles)
-        p = re.compile(r'.*(uid__.*)\.asdm.*')
-        if res:
-            table['name'] = [u.split('/')[-1] for u in res['access_url']]
-            table['id'] = [p.search(x).group(1) if 'asdm' in x else 'None'
-                           for x in table['name']]
-            table['type'] = res['content_type']
-            table['size'] = res['content_length']
-            table['permission'] = ['UNKNOWN'] * len(res)
-            table['mous_uid'] = [uids] * len(res)
-            table['URL'] = res['access_url']
-            table['isProprietary'] = res['readable']
-        return table
-
-    def get_data_info(self, uids, expand_tarfiles=False,
+    def get_data_info(self, uids, *, expand_tarfiles=False,
                       with_auxiliary=True, with_rawdata=True):
 
         """
@@ -685,7 +620,7 @@ def _HEADER_data_size(self, files):
 
         return data_sizes, totalsize.to(u.GB)
 
-    def download_files(self, files, savedir=None, cache=True,
+    def download_files(self, files, *, savedir=None, cache=True,
                        continuation=True, skip_unauthorized=True,
                        verify_only=False):
         """
@@ -821,7 +756,7 @@ def _parse_result(self, response, verbose=False):
 
         return response
 
-    def retrieve_data_from_uid(self, uids, cache=True):
+    def retrieve_data_from_uid(self, uids, *, cache=True):
         """
         Stage & Download ALMA data.  Will print out the expected file size
         before attempting the download.
@@ -854,7 +789,7 @@ def retrieve_data_from_uid(self, uids, cache=True):
         downloaded_files = self.download_files(file_urls)
         return downloaded_files
 
-    def _get_auth_info(self, username, store_password=False,
+    def _get_auth_info(self, username, *, store_password=False,
                        reenter_password=False):
         """
         Get the auth info (user, password) for use in another function
@@ -1032,7 +967,7 @@ def cycle0_table(self):
             self._cycle0_table.rename_column('col2', 'uid')
         return self._cycle0_table
 
-    def get_files_from_tarballs(self, downloaded_files, regex=r'.*\.fits$',
+    def get_files_from_tarballs(self, downloaded_files, *, regex=r'.*\.fits$',
                                 path='cache_path', verbose=True):
         """
         Given a list of successfully downloaded tarballs, extract files
@@ -1082,7 +1017,7 @@ def get_files_from_tarballs(self, downloaded_files, regex=r'.*\.fits$',
 
         return filelist
 
-    def download_and_extract_files(self, urls, delete=True, regex=r'.*\.fits$',
+    def download_and_extract_files(self, urls, *, delete=True, regex=r'.*\.fits$',
                                    include_asdm=False, path='cache_path',
                                    verbose=True):
         """
@@ -1196,53 +1131,7 @@ def help(self, cache=True):
         print("Alma.query(payload=dict(project_code='2017.1.01355.L', "
               "source_name_alma='G008.67'))")
 
-    def _json_summary_to_table(self, data, base_url):
-        """
-        Special tool to convert some JSON metadata to a table Obsolete as of
-        March 2020 - should be removed along with stage_data_prefeb2020
-        """
-        from ..utils import url_helpers
-        columns = {'mous_uid': [], 'URL': [], 'size': []}
-        for entry in data['node_data']:
-            # de_type can be useful (e.g., MOUS), but it is not necessarily
-            # specified
-            # file_name and file_key *must* be specified.
-            is_file = \
-                (entry['file_name'] != 'null' and entry['file_key'] != 'null')
-            if is_file:
-                # "de_name": "ALMA+uid://A001/X122/X35e",
-                columns['mous_uid'].append(entry['de_name'][5:])
-                if entry['file_size'] == 'null':
-                    columns['size'].append(np.nan * u.Gbyte)
-                else:
-                    columns['size'].append(
-                        (int(entry['file_size']) * u.B).to(u.Gbyte))
-                # example template for constructing url:
-                # https://almascience.eso.org/dataPortal/requests/keflavich/940238268/ALMA/
-                # uid___A002_X9d6f4c_X154/2013.1.00546.S_uid___A002_X9d6f4c_X154.asdm.sdm.tar
-                # above is WRONG... except for ASDMs, when it's right
-                # should be:
-                # 2013.1.00546.S_uid___A002_X9d6f4c_X154.asdm.sdm.tar/2013.1.00546.S_uid___A002_X9d6f4c_X154.asdm.sdm.tar
-                #
-                # apparently ASDMs are different from others:
-                # templates:
-                # https://almascience.eso.org/dataPortal/requests/keflavich/946895898/ALMA/
-                # 2013.1.00308.S_uid___A001_X196_X93_001_of_001.tar/2013.1.00308.S_uid___A001_X196_X93_001_of_001.tar
-                # uid___A002_X9ee74a_X26f0/2013.1.00308.S_uid___A002_X9ee74a_X26f0.asdm.sdm.tar
-                url = url_helpers.join(base_url,
-                                       entry['file_key'],
-                                       entry['file_name'])
-                if 'null' in url:
-                    raise ValueError("The URL {0} was created containing "
-                                     "'null', which is invalid.".format(url))
-                columns['URL'].append(url)
-
-        columns['size'] = u.Quantity(columns['size'], u.Gbyte)
-
-        tbl = Table([Column(name=k, data=v) for k, v in columns.items()])
-        return tbl
-
-    def get_project_metadata(self, projectid, cache=True):
+    def get_project_metadata(self, projectid, *, cache=True):
         """
         Get the metadata - specifically, the project abstract - for a given project ID.
         """