Format docstrings

spectroscopy/code_src/data_structures_spec.py

@@ -1,50 +1,56 @@
-# setup to store the light curves in a data structure
+# setup to store the spectra in a data structure
 import pandas as pd
 
 
 class MultiIndexDFObject:
     """
-    Pandas MultiIndex data frame to store & manipulate multiband light curves
+    Pandas MultiIndex data frame to store & manipulate spectra.
 
     Examples
     --------
-    # Initialize Pandas MultiIndex data frame for storing the light curve
-    df_lc = MultiIndexDFObject()
+    # Initialize Pandas MultiIndex data frame for storing the spectra
+    df_spec = MultiIndexDFObject()
 
-    #make a single multiindex dataframe
-    dfsingle = pd.DataFrame(dict(flux=[0.1], err=[0.1], time=[time_mjd], objectid=[ccount + 1], /
-        band=[mission], label=lab)).set_index(["objectid", "label", "band", "time"])
+    # Make a single multiindex dataframe
+    df_single = pd.DataFrame(dict(wave=[0.1], flux=[0.1], err=[0.1], instrument=[instrument_name],
+                                  objectid=[ccount + 1], filter=[filter_name],
+                                  mission=[mission_name], label=[lab]))
+    df_single = df_single.set_index(["objectid", "label", "filter", "mission"])
 
-    # Append to existing MultiIndex light curve object
-    df_lc.append(dfsingle)
-
-    #Show the contents
-    df_lc.data
+    # Append to existing MultiIndex object
+    df_spec.append(dfsingle)
 
+    # Show the contents
+    df_spec.data
     """
 
     def __init__(self, data=None):
-        """Create a MultiIndex DataFrame that is empty if data is None, else contains the data.
+        """
+        Create a MultiIndex DataFrame that is empty if data is None, else contains the data.
 
         Parameters
         ----------
         data : pd.DataFrame, optional
             Dataframe to store in the `data` attribute.
         """
+
         index = ["objectid", "label", "filter", "mission"]
         columns = ["wave", "flux", "err", "instrument"]
         self.data = pd.DataFrame(columns=index + columns).set_index(index)
         if data is not None:
             self.append(data)
 
     def append(self, x):
-        """Add a new band of light curve data to the dataframe
+        """
+        Add a new spectra data to the dataframe.
 
         Parameters
         ----------
         x : Pandas dataframe
-            contains columns [flux, fluxerr] and multi-index [objectid, label, band, time]
+            Contains columns ["wave", "flux", "err", "instrument"]
+            and multi-index ["objectid", "label", "filter", "mission"].
         """
+
         if isinstance(x, self.__class__):
             # x is a MultiIndexDFObject. extract the DataFrame
             new_data = x.data
@@ -65,11 +71,13 @@ def append(self, x):
         self.data = pd.concat([self.data, new_data])
 
     def remove(self, x):
-        """ Drop a light curve from the dataframe
+        """
+        Drop a row from the dataframe.
 
         Parameters
         ----------
         x : list of values
-             Index values identifying rows to be dropped.
+            Index values identifying rows to be dropped.
         """
+
         self.data = self.data.drop(x)

spectroscopy/code_src/desi_functions.py

@@ -11,24 +11,23 @@
 
 
 def DESIBOSS_get_spec(sample_table, search_radius_arcsec):
-    '''
-    Retrieves DESI and BOSS spectra for a list of sources.
+    """
+    Retrieve DESI and BOSS spectra for a list of sources.
     Note, that we can also retrieve SDSS-DR16 spectra here, which
     leads to similar results as SDSS_get_spec().
 
     Parameters
     ----------
-    sample_table : `~astropy.table.Table`
-        Table with the coordinates and journal reference labels of the sources
-    search_radius_arcsec : `float`
+    sample_table : astropy.table.Table
+        Table with the coordinates and journal reference labels of the sources.
+    search_radius_arcsec : float
         Search radius in arcseconds. Here its rather half a box size.
 
     Returns
     -------
-    df_lc : MultiIndexDFObject
-        The main data structure to store all spectra
-
-    '''
+    MultiIndexDFObject
+        The spectra returned from the archive.
+    """
 
     # Set up client
     client = SparclClient()
@@ -98,4 +97,4 @@ def DESIBOSS_get_spec(sample_table, search_radius_arcsec):
                                                  )).set_index(["objectid", "label", "filter", "mission"])
                     df_spec.append(dfsingle)
 
-    return (df_spec)
+    return df_spec

spectroscopy/code_src/herschel_functions.py

@@ -16,16 +16,19 @@
 
 def find_max_flux_column(df):
     """
-    Analyzes a DataFrame with flux columns and returns the column with the largest sum.
+    Analyze a DataFrame with flux columns and returns the column with the largest sum.
 
-    Args:
-        df (pandas.DataFrame): The DataFrame containing columns with "flux" in the name.
+    Parameters
+    ----------
+    df : pandas.DataFrame
+        The DataFrame containing columns with "flux" in the name.
 
-    Returns:
-        str: The name of the column with the largest sum of values containing "flux".
+    Returns
+    -------
+    str
+        The name of the column with the largest sum of values containing "flux".
     """
 
-
     # Filter column names containing "flux"
     flux_cols = [col for col in df.columns if "flux" in col.lower()]
 
@@ -44,27 +47,26 @@ def find_max_flux_column(df):
 
 def Herschel_get_spec(sample_table, search_radius_arcsec, datadir,
                       delete_downloaded_data=True):
-    '''
-    Retrieves Herschel spectra from a subset of modes for a list of sources.
+    """
+    Retrieve Herschel spectra from a subset of modes for a list of sources.
 
     Parameters
     ----------
-    sample_table : `~astropy.table.Table`
-        Table with the coordinates and journal reference labels of the sources
-    search_radius_arcsec : `float`
+    sample_table : astropy.table.Table
+        Table with the coordinates and journal reference labels of the sources.
+    search_radius_arcsec : float
         Search radius in arcseconds.
-    datadir : `str`
+    datadir : str
         Data directory where to store the data. Each function will create a
         separate data directory (for example "[datadir]/HST/" for HST data).
-    delete_downloaded_data: `bool`, optional
-        Should the tarfiles be deteled after spectra are extracted?
+    delete_downloaded_data : bool, optional
+        Whether the tar files be deleted after spectra are extracted.
 
     Returns
     -------
-    df_spec : MultiIndexDFObject
-        The main data structure to store all spectra
-
-    '''
+    MultiIndexDFObject
+        The spectra returned from the archive.
+    """
 
     # Initialize multi-index object:
     df_spec = MultiIndexDFObject()

spectroscopy/code_src/keck_functions.py

@@ -9,22 +9,21 @@
 
 
 def KeckDEIMOS_get_spec(sample_table, search_radius_arcsec):
-    '''
-    Retrieves Keck DEIMOS on COSMOS spectra for a list of sources.
+    """
+    Retrieve Keck DEIMOS on COSMOS spectra for a list of sources.
 
     Parameters
     ----------
-    sample_table : `~astropy.table.Table`
-        Table with the coordinates and journal reference labels of the sources
-    search_radius_arcsec : `float`
+    sample_table : astropy.table.Table
+        Table with the coordinates and journal reference labels of the sources.
+    search_radius_arcsec : float
         Search radius in arcseconds.
 
     Returns
     -------
-    df_lc : MultiIndexDFObject
-        The main data structure to store all spectra
-
-    '''
+    MultiIndexDFObject
+        The spectra returned from the archive.
+    """
 
     # Initialize multi-index object:
     df_spec = MultiIndexDFObject()
@@ -84,4 +83,4 @@ def KeckDEIMOS_get_spec(sample_table, search_radius_arcsec):
                                              )).set_index(["objectid", "label", "filter", "mission"])
                 df_spec.append(dfsingle)
 
-    return (df_spec)
+    return df_spec