v0.14.1 (#80)

v0.14.1

README.md

@@ -73,7 +73,7 @@ base_paper1 = saga.object_catalog.load(hosts='paper1', return_as='list')
 
 # count number of satellites
 for base in base_paper1:
-    print(base['HOST_ID'][0], '# of satellites =', saga.is_sat.count(base))
+    print(base['HOSTID'][0], '# of satellites =', saga.is_sat.count(base))
 ```
 
 You can find more examples at https://github.com/sagasurvey/examples/tree/master/notebooks

SAGA/database/core.py

@@ -93,11 +93,13 @@ def isfile(self):
 
 
 class CsvTable(FileObject):
-    _read_default_kwargs = _write_default_kwargs = dict(format="ascii.csv")
+    _read_default_kwargs = dict(format="ascii.csv")
+    _write_default_kwargs = dict(format="ascii.csv", overwrite=True)
 
 
 class FastCsvTable(FileObject):
-    _read_default_kwargs = _write_default_kwargs = dict(format="ascii.fast_csv")
+    _read_default_kwargs = dict(format="ascii.fast_csv")
+    _write_default_kwargs = dict(format="ascii.fast_csv", overwrite=True)
 
 
 class GoogleSheets(FastCsvTable):
@@ -116,13 +118,13 @@ def write(self, table, **kwargs):
 
 class FitsTableGeneric(FileObject):
     _read_default_kwargs = dict(memmap=True)
-    _write_default_kwargs = dict(format="fits")
+    _write_default_kwargs = dict(format="fits", overwrite=True)
 
 
 class FitsTable(FileObject):
     compress_after_write = True
     _read_default_kwargs = dict(cache=False, memmap=True)
-    _write_default_kwargs = dict(format="fits")
+    _write_default_kwargs = dict(format="fits", overwrite=True)
 
     def read(self):
         kwargs_this = dict(self._read_default_kwargs, **self.kwargs)

SAGA/database/saga_database.py

@@ -561,6 +561,8 @@ def resolve_base_version(self, version=None):
     def set_default_base_version(self, version=None):
         _, version_postfix = self.resolve_base_version(version)
         if not version_postfix:
-            version_postfix = '_v2p1'
-        self._file_path_pattern["base"] = self._file_path_pattern["base" + version_postfix]
+            version_postfix = "_v2p1"
+        self._file_path_pattern["base"] = self._file_path_pattern[
+            "base" + version_postfix
+        ]
         self._add_derived_data()

SAGA/hosts/host_catalog.py

@@ -88,7 +88,7 @@ def _master_table(self):
                         "Cannot load master list; attempt to build from scratch..."
                     )
                     self._master_table_ = self.build_master_list()
-                self._master_table_['SAGA_NAME'].fill_value = ""
+                self._master_table_["SAGA_NAME"].fill_value = ""
                 self._master_table_ = self._master_table_.filled()
             self._master_index_ = None
         return self._master_table_
@@ -110,7 +110,7 @@ def _host_table(self):
                         "Cannot load host list; attempt to load master list..."
                     )
                     self._host_table_ = cuts.potential_hosts.filter(self._master_table)
-                self._host_table_['SAGA_NAME'].fill_value = ""
+                self._host_table_["SAGA_NAME"].fill_value = ""
                 self._host_table_ = self._host_table_.filled()
             self._host_index_ = None
         return self._host_table_
@@ -289,7 +289,7 @@ def add_object_stats(self, host_table):
         for col in cols_to_keep:
             if col == "HOSTID":
                 continue
-            if 'need_spec' in col:
+            if "need_spec" in col:
                 d[col].fill_value = 999999
             else:
                 d[col].fill_value = -1
@@ -345,7 +345,9 @@ def load_single(self, host, add_coord=True, use_master=None, include_stats=False
         d = self._annotate_table(d, add_coord=add_coord, include_stats=include_stats)
         return d[0]
 
-    def load_single_near_ra_dec(self, ra, dec, sep=3600, use_master=None, add_coord=True, include_stats=False):
+    def load_single_near_ra_dec(
+        self, ra, dec, sep=3600, use_master=None, add_coord=True, include_stats=False
+    ):
         """
         ra, dec in degrees
         """
@@ -360,7 +362,9 @@ def load_single_near_ra_dec(self, ra, dec, sep=3600, use_master=None, add_coord=
                     ra, dec
                 )
             )
-        cat = self._annotate_table(cat, add_coord=add_coord, include_stats=include_stats)
+        cat = self._annotate_table(
+            cat, add_coord=add_coord, include_stats=include_stats
+        )
         return cat[0]
 
     def build_master_list(self, overwrite=False, overwrite_host_list=False):

SAGA/objects/build.py

@@ -148,11 +148,11 @@ def add_host_info(base, host, overwrite_if_different_host=False):
         return base
 
     if (
-        "HOST_ID" in base.colnames and base["HOST_ID"][0] != host["HOSTID"]
+        "HOSTID" in base.colnames and base["HOSTID"][0] != host["HOSTID"]
     ) and not overwrite_if_different_host:
         raise ValueError("Host info exists and differs from input host info.")
 
-    base["HOST_ID"] = get_empty_str_array(len(base), 48, host["HOSTID"] or "")
+    base["HOSTID"] = get_empty_str_array(len(base), 48, host["HOSTID"] or "")
     base["HOST_PGC"] = np.int32(host["PGC"])
     base["HOST_NSAID"] = np.int32(host["NSAID"])
     base["HOST_NSA1ID"] = np.int32(host["NSA1ID"])

SAGA/objects/object_catalog.py

@@ -86,12 +86,16 @@ def _annotate_catalog(
                 or "{}_mag".format(color[1]) not in table.colnames
             ):
                 continue
-            table[color] = (
-                table["{}_mag".format(color[0])] - table["{}_mag".format(color[1])]
-            )
-            table["{}_err".format(color)] = np.hypot(
-                table["{}_err".format(color[0])], table["{}_err".format(color[1])]
-            )
+            with np.errstate(invalid="ignore"):
+                table[color] = (
+                    table["{}_mag".format(color[0])] - table["{}_mag".format(color[1])]
+                )
+                table["{}_err".format(color)] = np.hypot(
+                    table["{}_err".format(color[0])], table["{}_err".format(color[1])]
+                )
+
+        if "HOST_ID" in table.colnames:
+            table.rename_column("HOST_ID", "HOSTID")
 
         if ensure_all_objid_cols:
             for s in cls._surveys:
@@ -409,6 +413,7 @@ def build_and_write_to_database(
                         manual_lists[key] = val
         print(time.strftime("[%m/%d %H:%M:%S]"), "All other manual lists loaded.")
 
+        failed_count = 0
         catalogs_to_return = list()
         for i, host in enumerate(host_table):
             host_id = host["HOSTID"]
@@ -513,6 +518,7 @@ def get_catalog_or_none(catalog_name):
                 if raise_exception:
                     raise e
                 traceback.print_exc()
+                failed_count += 1
                 continue
             finally:
                 del catalog_dict
@@ -533,8 +539,16 @@ def get_catalog_or_none(catalog_name):
                 if raise_exception:
                     raise e
                 traceback.print_exc()
+                failed_count += 1
                 continue
 
+        print(
+            time.strftime("[%m/%d %H:%M:%S]"),
+            "All done building base catalogs for {}/{} hosts.".format(
+                nhosts - failed_count, nhosts
+            ),
+        )
+
         if return_catalogs:
             return catalogs_to_return
 

SAGA/spectra/read_observed.py

@@ -23,6 +23,8 @@
     "read_palomar",
 ]
 
+# pylint: disable=logging-format-interpolation
+
 
 def heliocentric_correction(
     fits_filepath,
@@ -63,6 +65,13 @@ def read_generic_spectra(
     for f in os.listdir(dir_path):
         if not f.endswith(extension):
             continue
+        if "conflicted copy" in f:
+            logging.warning(
+                "SKIPPING spectra file {}/{} - it's a conflicted copy; check if something went wrong!".format(
+                    dir_path, f
+                )
+            )
+            continue
         try:
             this = Table.read(
                 os.path.join(dir_path, f),

SAGA/version.py

@@ -1,4 +1,4 @@
 """
 SAGA package version
 """
-__version__ = "0.14.0"
+__version__ = "0.14.1"