Refactor: Made splatalogue kwargs keyword only

Author: nkphysics

astroquery/splatalogue/build_species_table.py

@@ -32,7 +32,7 @@ def data_path(filename: str):
     return os.path.join(data_dir, filename)
 
 
-def get_json_species_ids(outfile='splat-species.json', base_url=conf.base_url):
+def get_json_species_ids(*, outfile='splat-species.json', base_url=conf.base_url):
     """
     Uses BeautifulSoup to scrape the NRAO Splatalogue species
     selector form, and caches the result as JSON. The file

astroquery/splatalogue/core.py

@@ -76,7 +76,7 @@ def set_default_options(self, **kwargs):
         """
         self.data.update(self._parse_kwargs(**kwargs))
 
-    def get_species_ids(self, restr=None, reflags=0, recache=False):
+    def get_species_ids(self, *, restr=None, reflags=0, recache=False):
         """
         Get a dictionary of "species" IDs, where species refers to the molecule
         name, mass, and chemical composition.
@@ -95,7 +95,7 @@ def get_species_ids(self, restr=None, reflags=0, recache=False):
         --------
         >>> import re
         >>> import pprint # unfortunate hack required for documentation testing
-        >>> rslt = Splatalogue.get_species_ids('Formaldehyde')
+        >>> rslt = Splatalogue.get_species_ids(restr='Formaldehyde')
         >>> pprint.pprint(rslt)
         {'03023 H2CO - Formaldehyde': '194',
          '03106 H213CO - Formaldehyde': '324',
@@ -107,7 +107,7 @@ def get_species_ids(self, restr=None, reflags=0, recache=False):
          '03301 D213CO - Formaldehyde': '1220',
          '03315 HDC18O - Formaldehyde': '21141',
          '0348 D2C18O - Formaldehyde': '21140'}
-        >>> rslt = Splatalogue.get_species_ids('H2CO')
+        >>> rslt = Splatalogue.get_species_ids(restr='H2CO')
         >>> pprint.pprint(rslt)
         {'03023 H2CO - Formaldehyde': '194',
          '03109 H2COH+ - Hydroxymethylium ion': '224',
@@ -125,9 +125,9 @@ def get_species_ids(self, restr=None, reflags=0, recache=False):
          '08903 CH3CHNH2COOH - II - α-Alanine': '1322'}
         >>> # note the whitespace, preventing H2CO within other
         >>> # more complex molecules
-        >>> Splatalogue.get_species_ids(' H2CO ')
+        >>> Splatalogue.get_species_ids(restr=' H2CO ')
         {'03023 H2CO - Formaldehyde': '194'}
-        >>> Splatalogue.get_species_ids(' h2co ', re.IGNORECASE)
+        >>> Splatalogue.get_species_ids(restr=' h2co ', reflags=re.IGNORECASE)
         {'03023 H2CO - Formaldehyde': '194'}
 
         """
@@ -137,7 +137,7 @@ def get_species_ids(self, restr=None, reflags=0, recache=False):
             self._species_ids = load_species_table.species_lookuptable(recache=recache)
 
         if restr is not None:
-            return self._species_ids.find(restr, reflags)
+            return self._species_ids.find(restr, flags=reflags)
         else:
             return self._species_ids
 
@@ -160,7 +160,7 @@ def _default_kwargs(self):
                       show_nrao_recommended=False,)
         return self._parse_kwargs(**kwargs)
 
-    def _parse_kwargs(self, min_frequency=None, max_frequency=None,
+    def _parse_kwargs(self, *, min_frequency=None, max_frequency=None,
                       band='any', top20=None, chemical_name=None,
                       chem_re_flags=0, energy_min=None, energy_max=None,
                       energy_type=None, intensity_lower_limit=None,
@@ -319,7 +319,7 @@ def _parse_kwargs(self, min_frequency=None, max_frequency=None,
             payload['sid[]'] = []
         elif chemical_name is not None:
             if parse_chemistry_locally:
-                species_ids = self.get_species_ids(chemical_name, chem_re_flags)
+                species_ids = self.get_species_ids(restr=chemical_name, reflags=chem_re_flags)
                 if len(species_ids) == 0:
                     raise ValueError("No matching chemical species found.")
                 payload['sid[]'] = list(species_ids.values())
@@ -408,7 +408,7 @@ def _parse_kwargs(self, min_frequency=None, max_frequency=None,
 
         return payload
 
-    def _validate_kwargs(self, min_frequency=None, max_frequency=None,
+    def _validate_kwargs(self, *, min_frequency=None, max_frequency=None,
                          band='any', **kwargs):
         """
         Check that either min_frequency + max_frequency or band are specified
@@ -419,7 +419,7 @@ def _validate_kwargs(self, min_frequency=None, max_frequency=None,
                                  "a valid Band.")
 
     @prepend_docstr_nosections("\n" + _parse_kwargs.__doc__)
-    def query_lines_async(self, min_frequency=None, max_frequency=None,
+    def query_lines_async(self, *, min_frequency=None, max_frequency=None,
                           cache=True, **kwargs):
         """
 
@@ -462,7 +462,7 @@ def query_lines_async(self, min_frequency=None, max_frequency=None,
 
         return response
 
-    def _parse_result(self, response, verbose=False):
+    def _parse_result(self, response, *, verbose=False):
         """
         Parse a response into an `~astropy.table.Table`
 
@@ -478,7 +478,7 @@ def _parse_result(self, response, verbose=False):
 
         return result
 
-    def get_fixed_table(self, columns=None):
+    def get_fixed_table(self, *, columns=None):
         """
         Convenience function to get the table with html column names made human
         readable.  It returns only the columns identified with the ``columns``

astroquery/splatalogue/load_species_table.py

@@ -8,7 +8,7 @@
 
 class SpeciesLookuptable(dict):
 
-    def find(self, s, flags=0, return_dict=True,):
+    def find(self, s, *, flags=0, return_dict=True,):
         """
         Search dictionary keys for a regex match to string s
 
@@ -38,7 +38,7 @@ def find(self, s, flags=0, return_dict=True,):
             return out.values()
 
 
-def species_lookuptable(filename='splat-species.json', recache=False):
+def species_lookuptable(*, filename='splat-species.json', recache=False):
     """
     Function to format the species ID results from scraping Splatalogue
     into a ``SpeciesLookuptable`` object.

astroquery/splatalogue/slap.py

@@ -7,7 +7,7 @@
 """
 
 
-def slap_default_payload(request='queryData', version='2.0', wavelength='',
+def slap_default_payload(*, request='queryData', version='2.0', wavelength='',
                          chemical_element='', initial_level_energy='',
                          final_level_energy='', temperature='', einstein_a=''):
     """

astroquery/splatalogue/tests/test_splatalogue.py

@@ -17,16 +17,18 @@ def data_path(filename):
 
 
 def test_simple(patch_post):
-    splatalogue.Splatalogue.query_lines(114 * u.GHz, 116 * u.GHz,
+    splatalogue.Splatalogue.query_lines(min_frequency=114 * u.GHz,
+                                        max_frequency=116 * u.GHz,
                                         chemical_name=' CO ')
 
 
 @pytest.mark.remote_data
 def test_init(patch_post):
-    x = splatalogue.Splatalogue.query_lines(114 * u.GHz, 116 * u.GHz,
+    x = splatalogue.Splatalogue.query_lines(min_frequency=114 * u.GHz,
+                                            max_frequency=116 * u.GHz,
                                             chemical_name=' CO ')
     S = splatalogue.Splatalogue(chemical_name=' CO ')
-    y = S.query_lines(114 * u.GHz, 116 * u.GHz)
+    y = S.query_lines(min_frequency=114 * u.GHz, max_frequency=116 * u.GHz)
     # it is not currently possible to test equality between tables:
     # masked arrays fail
     # assert y == x
@@ -43,14 +45,16 @@ def test_load_species_table():
 
 # regression test: get_query_payload should work (#308)
 def test_get_payload():
-    q = splatalogue.core.Splatalogue.query_lines_async(1 * u.GHz, 10 * u.GHz,
+    q = splatalogue.core.Splatalogue.query_lines_async(min_frequency=1 * u.GHz,
+                                                       max_frequency=10 * u.GHz,
                                                        get_query_payload=True)
     assert '__utma' in q
 
 
 # regression test: line lists should ask for only one line list, not all
 def test_line_lists():
-    q = splatalogue.core.Splatalogue.query_lines_async(1 * u.GHz, 10 * u.GHz,
+    q = splatalogue.core.Splatalogue.query_lines_async(min_frequency=1 * u.GHz,
+                                                       max_frequency=10 * u.GHz,
                                                        line_lists=['JPL'],
                                                        get_query_payload=True)
     assert q['displayJPL'] == 'displayJPL'
@@ -61,20 +65,23 @@ def test_line_lists():
 # uses get_query_payload to avoid having to monkeypatch
 def test_linelist_type():
     with pytest.raises(TypeError) as exc:
-        splatalogue.core.Splatalogue.query_lines_async(1 * u.GHz, 10 * u.GHz,
+        splatalogue.core.Splatalogue.query_lines_async(min_frequency=1 * u.GHz,
+                                                       max_frequency=10 * u.GHz,
                                                        line_lists='JPL',
                                                        get_query_payload=True)
     assert exc.value.args[0] == ("Line lists should be a list of linelist "
                                  "names.  See Splatalogue.ALL_LINE_LISTS")
 
 
 def test_top20_crashorno():
-    splatalogue.core.Splatalogue.query_lines_async(114 * u.GHz, 116 * u.GHz,
+    splatalogue.core.Splatalogue.query_lines_async(min_frequency=114 * u.GHz,
+                                                   max_frequency=116 * u.GHz,
                                                    top20='top20',
                                                    get_query_payload=True)
     with pytest.raises(ValueError) as exc:
         splatalogue.core.Splatalogue.query_lines_async(
-            114 * u.GHz, 116 * u.GHz, top20='invalid', get_query_payload=True)
+            min_frequency=114 * u.GHz, max_frequency=116 * u.GHz,
+            top20='invalid', get_query_payload=True)
     assert exc.value.args[0] == "Top20 is not one of the allowed values"
 
 
@@ -103,7 +110,8 @@ def test_band_crashorno():
 
 def test_exclude(patch_post):
     # regression test for issue 616
-    d = splatalogue.Splatalogue.query_lines_async(114 * u.GHz, 116 * u.GHz,
+    d = splatalogue.Splatalogue.query_lines_async(min_frequency=114 * u.GHz,
+                                                  max_frequency=116 * u.GHz,
                                                   chemical_name=' CO ',
                                                   exclude=None,
                                                   get_query_payload=True)
@@ -115,7 +123,8 @@ def test_exclude(patch_post):
     for k, v in exclusions.items():
         assert d[k] == v
 
-    d = splatalogue.Splatalogue.query_lines_async(114 * u.GHz, 116 * u.GHz,
+    d = splatalogue.Splatalogue.query_lines_async(min_frequency=114 * u.GHz,
+                                                  max_frequency=116 * u.GHz,
                                                   chemical_name=' CO ',
                                                   exclude='none',
                                                   get_query_payload=True)

astroquery/splatalogue/tests/test_utils.py

@@ -8,23 +8,26 @@
 
 
 def test_clean(patch_post):
-    x = splatalogue.Splatalogue.query_lines(114 * u.GHz, 116 * u.GHz,
+    x = splatalogue.Splatalogue.query_lines(min_frequency=114 * u.GHz,
+                                            max_frequency=116 * u.GHz,
                                             chemical_name=' CO ')
     c = utils.clean_column_headings(x)
     assert 'Resolved QNs' not in c.colnames
     assert 'QNs' in c.colnames
 
 
 def test_merge(patch_post):
-    x = splatalogue.Splatalogue.query_lines(114 * u.GHz, 116 * u.GHz,
+    x = splatalogue.Splatalogue.query_lines(min_frequency=114 * u.GHz,
+                                            max_frequency=116 * u.GHz,
                                             chemical_name=' CO ')
     c = utils.merge_frequencies(x)
     assert 'Freq' in c.colnames
     assert np.all(c['Freq'] > 0)
 
 
 def test_minimize(patch_post):
-    x = splatalogue.Splatalogue.query_lines(114 * u.GHz, 116 * u.GHz,
+    x = splatalogue.Splatalogue.query_lines(min_frequency=114 * u.GHz,
+                                            max_frequency=116 * u.GHz,
                                             chemical_name=' CO ')
     c = utils.minimize_table(x)
 
@@ -36,7 +39,8 @@ def test_minimize(patch_post):
 
 @pytest.mark.remote_data
 def test_minimize_issue2135():
-    rslt = splatalogue.Splatalogue.query_lines(100*u.GHz, 200*u.GHz,
+    rslt = splatalogue.Splatalogue.query_lines(min_frequency=100*u.GHz,
+                                               max_frequency=200*u.GHz,
                                                chemical_name=' SiO ',
                                                energy_max=1840,
                                                energy_type='eu_k',

astroquery/splatalogue/utils.py

@@ -27,7 +27,7 @@
                        }
 
 
-def clean_column_headings(table, renaming_dict=column_headings_map):
+def clean_column_headings(table, *, renaming_dict=column_headings_map):
     """
     Rename column headings to shorter version that are easier for display
     on-screen / at the terminal
@@ -40,7 +40,7 @@ def clean_column_headings(table, renaming_dict=column_headings_map):
     return table
 
 
-def merge_frequencies(table, prefer='measured',
+def merge_frequencies(table, *, prefer='measured',
                       theor_kwd='Freq-GHz(rest frame,redshifted)',
                       meas_kwd='Meas Freq-GHz(rest frame,redshifted)'):
     """
@@ -79,12 +79,12 @@ def merge_frequencies(table, prefer='measured',
     return table
 
 
-def minimize_table(table, columns=['Species', 'Chemical Name',
-                                   'Resolved QNs',
-                                   'Freq-GHz(rest frame,redshifted)',
-                                   'Meas Freq-GHz(rest frame,redshifted)',
-                                   'Log<sub>10</sub> (A<sub>ij</sub>)',
-                                   'E_U (K)'],
+def minimize_table(table, *, columns=['Species', 'Chemical Name',
+                                      'Resolved QNs',
+                                      'Freq-GHz(rest frame,redshifted)',
+                                      'Meas Freq-GHz(rest frame,redshifted)',
+                                      'Log<sub>10</sub> (A<sub>ij</sub>)',
+                                      'E_U (K)'],
                    merge=True,
                    clean=True):
     """