FIX: Fix many files to remove final warnings in doc build.

act/discovery/nasa.py

@@ -42,13 +42,15 @@ def download_mplnet_data(
         https://mplnet.gsfc.nasa.gov/product-info/
         Level 1 data should never be used for publication.
     product : str
-        MPLNet Product (NRB, CLD, PBL, AER).
-            NRB - Lidar signals; volume depolarization ratos, diagnostics
-            CLD - Cloud Heights, thin cloud extinction and optical depths, cloud
-                    phase
-            AER - Aerosol heights; extinction, backscatter, and aerosol
-                    depolarization ratio profiles; lidar ratio
-            PBL - Surface-Attached Mixed Layer Top and estimated mixed layer AOD
+         MPLNet Product (NRB, CLD, PBL, AER).
+
+        * NRB - Lidar signals; volume depolarization ratios, diagnostics
+        * CLD - Cloud Heights, thin cloud extinction and optical depths, cloud
+          phase
+        * AER - Aerosol heights; extinction, backscatter, and aerosol
+          depolarization ratio profiles; lidar ratio
+        * PBL - Surface-Attached Mixed Layer Top and estimated mixed layer AOD
+
         Information on the MPLNet Products can be found here:
         https://mplnet.gsfc.nasa.gov/product-info/
     year : str
@@ -177,20 +179,21 @@ def get_mplnet_meta(
     Returns a list of meta data from the NASA MPL Network Data
     https://mplnet.gsfc.nasa.gov/mplnet_web_services.cgi?metadata
 
-
     Parameters
     ----------
     sites : str
         How to return MPLNET Site Information
-            all        - produces output on all sites (active and inactive)
-            active     - produces output file containing only active sites
-                       (if year, month, or day are not set then uses today's date)
-            inactive   - produces output file containing only inactive sites
-                       (if year, month, or day are not set then uses today's date)
-            planned    - produces output file containing only planned sites
-            site_name  - produces output file containing only requested site
-            collection - produces output file containing sites in pre-defined
-                         collections (e.g. field campaigns or regions)
+
+        * all        - produces output on all sites (active and inactive)
+        * active     - produces output file containing only active sites
+          (if year, month, or day are not set then uses today's date)
+        * inactive   - produces output file containing only inactive sites
+          (if year, month, or day are not set then uses today's date)
+        * planned    - produces output file containing only planned sites
+        * site_name  - produces output file containing only requested site
+        * collection - produces output file containing sites in pre-defined
+          collections (e.g. field campaigns or regions)
+
     year : str
         Four digit Year for desired product download (YYYY).
         Note Level 1 and 1.5 products are available for
@@ -205,11 +208,13 @@ def get_mplnet_meta(
         in a zip file.
     method : str
         Method for returning JSON list of MPLNET GALION format parameters.
-            station - returns GALION JSON with only station and PI contact info
-            data - return GALION JSON with data elements, station, date and PI
-                contact information
-    print_to_screen : Boolean
-        If true, print MPLNET site identifiers to screen
+
+        * station - returns GALION JSON with only station and PI contact info
+        * data    - returns GALION JSON with data elements, station, date and
+          PI contact information
+
+    print_to_screen : bool
+        If true, print MPLNET site identifiers to screen.
     """
 
     # Add headers

act/io/ameriflux.py

@@ -46,7 +46,6 @@ def read_ameriflux(
         A dictionary containing current variable names and units to be added to that variable.
         Default is None and uses current units from Ameriflux's unit database.
 
-
     Returns
     -------
     ds : xarray.Dataset
@@ -462,40 +461,40 @@ def convert_to_ameriflux(
     **kwargs,
 ):
     """
-
     Returns `xarray.Dataset` with stored data and metadata from a user-defined
     query of ARM-standard netCDF files from a single datastream. Has some procedures
-    to ensure time is correctly fomatted in returned Dataset.
+    to ensure time is correctly formatted in returned Dataset.
 
     Parameters
     ----------
     ds : xarray.Dataset
         Dataset of data to convert to AmeriFlux format
     variable_mapping : dict
-        Dictionary of variables mappings.  The key should be the name of the variable
+        Dictionary of variables mappings. The key should be the name of the variable
         in the Dataset with the values being dictionaries of the AmeriFlux name and units.
-        For example:
+        For example::
+
             var_mapping = {
                 'co2_flux': {'name': 'FC', 'units': 'umol/(m^2 s)'},
             }
+
     soil_mapping : dict
         Dictionary of soil variables mappings following the same formatting as variable_mapping.
-        It is understood that the AmeriFlux name may be the same for some variables.  This
+        It is understood that the AmeriFlux name may be the same for some variables. This
         script attempts to automatically name these measurements. If a variable is not dimensioned
         by a depth nor has a sensor_height attribute, it will automatically assume that it's
         at the first depth in the depth_profile variable.
     depth_profile : list
-        List of depths that the variables will be mapped to.  If a depth is not in this list,
+        List of depths that the variables will be mapped to. If a depth is not in this list,
         the index chosen will be the one closest to the depth value.
-    include_missing_variables : boolean
-        If there variables that are completely missing (-9999) chose whether or not to include
-        them in the DataFrame.
+    include_missing_variables : bool
+        If there are variables that are completely missing (-9999) choose whether or not to
+        include them in the DataFrame.
 
     Returns
     -------
-    df : pandas.DataFrame (or None)
-        Returns a pandas dataframe for easy writing to csv
-
+    df : pandas.DataFrame or None
+        Returns a pandas dataframe for easy writing to csv.
     """
     # Use ARM variable mappings if none provided
     if variable_mapping is None:

act/qc/bsrn_tests.py

@@ -446,30 +446,34 @@ def bsrn_comparison_tests(
             Value used in longwave down less than longwave up test.
         LWdn_gt_LWup_component : int or float
             Value used in longwave down greater than longwave up test.
-        use_dask : boolean
+        use_dask : bool
             Option to use Dask for processing if data is stored in a Dask array
 
         References
         ----------
         Long, Charles N., and Ellsworth G. Dutton. "BSRN Global Network recommended QC tests, V2. x." (2010).
         Long, Charles N., and Y. Shi.  “An Automated Quality Assessment and Control Algorithm for Surface
-            Radiation Measurements.” (2008) https://doi.org/10.2174/1874282300802010023
+        Radiation Measurements.” (2008) https://doi.org/10.2174/1874282300802010023
 
         Examples
         --------
-            .. code-block:: python
 
-                ds = act.io.arm.read_arm_netcdf(act.tests.EXAMPLE_BRS, cleanup_qc=True)
-                ds.qcfilter.bsrn_comparison_tests(
-                    gbl_SW_dn_name='down_short_hemisp',
-                    glb_diffuse_SW_dn_name='down_short_diffuse_hemisp',
-                    direct_normal_SW_dn_name='short_direct_normal',
-                    glb_SW_up_name='up_short_hemisp',
-                    glb_LW_dn_name='down_long_hemisp_shaded',
-                    glb_LW_up_name='up_long_hemisp',
-                    use_dask=True)
-        """
+        An example on how to add BSRN comparison tests:
+
+        .. code-block:: python
 
+            ds = act.io.arm.read_arm_netcdf(act.tests.EXAMPLE_BRS, cleanup_qc=True)
+            ds.qcfilter.bsrn_comparison_tests(
+                gbl_SW_dn_name='down_short_hemisp',
+                glb_diffuse_SW_dn_name='down_short_diffuse_hemisp',
+                direct_normal_SW_dn_name='short_direct_normal',
+                glb_SW_up_name='up_short_hemisp',
+                glb_LW_dn_name='down_long_hemisp_shaded',
+                glb_LW_up_name='up_long_hemisp',
+                use_dask=True
+            )
+
+        """
         if isinstance(test, str):
             test = [test]
 

act/qc/clean.py

@@ -939,16 +939,15 @@ def clean_cf_qc(self, variables=None, sep='__', **kwargs):
     def fix_incorrect_variable_bit_description_attributes(self):
         """
         Method to correct incorrectly defined quality control variable attributes.
-        There are some datastreams with the attribute names incorrectly having 'qc_'
-        prepended to the attribute name. This will fix those attributes so the cleanqc
+        There are some datastreams with the attribute names incorrectly having ``qc_``
+        prepended to the attribute name. This will fix those attributes so the ``cleanqc``
         method can correctly read the attributes.
 
         If the variable long_name starts with the string "Quality check results on"
-        and a variable attribute follows the pattern qc_bit_#_description the 'qc_' part of
-        the variable attribute will be removed.
+        and a variable attribute follows the pattern ``qc_bit_#_description`` the ``qc_``
+        part of the variable attribute will be removed.
 
         """
-
         attr_description_pattern = r'^qc_bit_([0-9]+)_description$'
         attr_assessment_pattern = r'^qc_bit_([0-9]+)_assessment$'
 

act/qc/qctests.py

@@ -1781,42 +1781,42 @@ def add_relative_variability_test(
     ):
         """
         Method to calculate the variability of a variable relative to
-        other variables that are passed in.  The process includes
-        1.) Calculating a rolling standard deviation for all variables passed in
-        2.) For each variable it will subtract the mean standard deviation of all
-            the other variables
-        3.) Variability relative to the mean greater than the threshold passed in
-            will be flagged.
+        other variables that are passed in. The process includes:
+
+        1. Calculating a rolling standard deviation for all variables passed in.
+        2. For each variable it will subtract the mean standard deviation of all
+           the other variables.
+        3. Variability relative to the mean greater than the threshold passed in
+           will be flagged.
 
         Parameters
         ----------
         var_names : list
-            List of data variable names.  At least 2 are required.
+            List of data variable names. At least 2 are required.
         threshold : int or float
             Threshold value to use in test.
         test_assessment : str
             Optional single word describing the assessment of the test.
             Will set a default if not set.
         test_number : int
-            Optional test number to use. If not set will ues next
+            Optional test number to use. If not set will use next
             available test number.
-        flag_value : boolean
+        flag_value : bool
             Indicates that the tests are stored as integers
             not bit packed values in quality control variable.
         prepend_text : str
             Optional text to prepend to the test meaning.
-            Example is indicate what institution added the test.
+            Example is to indicate what institution added the test.
         window : int or float
-            Window to calculate rolling standard deviation
+            Window to calculate rolling standard deviation.
         min_periods : int
-            Minimum number of samples to use for rolling standard deviation
-
+            Minimum number of samples to use for rolling standard deviation.
 
         Returns
         -------
         test_info : tuple
             A tuple containing test information including var_name, qc variable name,
-            test_number, test_meaning, test_assessment
+            test_number, test_meaning, test_assessment.
 
         """
         test_meaning = 'Standard deviation of variable is greater than the mean standard deviation of other like variables'

act/retrievals/radiation.py

@@ -289,10 +289,10 @@ def calculate_irradiance_stats(
         Name of the second irradiance variable
     diff_output_variable : str
         Variable name to store the difference results
-        Defaults to 'diff_' + variable
+        Defaults to ``diff_ + variable``
     ratio_output_variable : str
         Variable name to store the ratio results
-        Defaults to 'ratio_' + variable
+        Defaults to ``ratio_ + variable``
 
     Returns
     -------

docs/source/conf.py

@@ -266,6 +266,6 @@
     'python': ('https://docs.python.org/3/', None),
     'numpy': ('https://docs.scipy.org/doc/numpy/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
-    'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None),
     'matplotlib': ('https://matplotlib.org', None),
 }

examples/discovery/plot_improve.py

@@ -1,6 +1,6 @@
 """
 IMPROVE Data
------------
+------------
 
 This example shows how to get IMPROVE data for the
 system located at ARM's Southern Great Plains site.