Fix Sphinx warnings related to whitespace (#197)

* Ensure API docs are generated to gitignored doc/source/_icepyx folder
* Fix whitespace issues in *.rst files
* Fix whitespace issues in Earthdata.py and variables.py
Adding or removing spaces so that Sphinx stops complaining like "WARNING: Explicit markup ends without a blank line".

ATTRIBUTION.rst

@@ -1,14 +1,15 @@
 .. _attribution_ref_label:
+
 Attribution Guidelines
 ======================
 
 We are extremely grateful to everyone who has contributed to the success of the icepyx community, whether through direct contributions to or feedback about icepyx or as developers or maintainers of complimentary resources that are included within the icepyx ecosystem. This document outlines our goals to give appropriate attribution to all contributors to icepyx in ways that are fair and diverse and supportive of professional goals. To do so, we define broadly *contributions* as:
 
     Efforts towards achieving icepyx's goals, including writing code, tests, or documentation,
-    development of example workflows, development, significant contributions, or maintenance of 
-    a tailored package that broadens the functionality of icepyx, feedback and suggestions, 
+    development of example workflows, development, significant contributions, or maintenance of
+    a tailored package that broadens the functionality of icepyx, feedback and suggestions,
     community building, etc.
-    
+
 We use the terms "contributors", "developers", and "authors" interchangeably. We will recognize contributions in the following ways.
 
 Contributors List
@@ -39,11 +40,11 @@ Authorship on scientific papers currently constitutes an important metric for as
   2. Add themself to the `Contributors List`_.
   3. Contribute ideas, participate in authorship discussions (see next paragraph), write, read, and review the manuscript in a timely manner, and provide feedback (acknowledgement of review is sufficient, but we'd prefer more).
 
-Author order will be determined based on co-author discussion, led by the lead author, during the initial planning stages of manuscript preparation (i.e. as soon as an idea matures into a potential manuscript and before writing begins). Authorship will continue to be evaluated throughout the manuscript preparation process. Discussions will consider authorship norms (e.g. How does author order convey participation and prestige? How critical is first authorship to career advancement for each member of the team? Do an individual's contributions meet authorship criteria or are they more suited to acknowledgements?). Author order determination will also consider metrics such as the number of commits since the last major release with an associated paper (``git shortlog vX.0.0...HEAD -sne``), contributions that do not have associated commits, and contributions to the preparation of the manuscript. 
+Author order will be determined based on co-author discussion, led by the lead author, during the initial planning stages of manuscript preparation (i.e. as soon as an idea matures into a potential manuscript and before writing begins). Authorship will continue to be evaluated throughout the manuscript preparation process. Discussions will consider authorship norms (e.g. How does author order convey participation and prestige? How critical is first authorship to career advancement for each member of the team? Do an individual's contributions meet authorship criteria or are they more suited to acknowledgements?). Author order determination will also consider metrics such as the number of commits since the last major release with an associated paper (``git shortlog vX.0.0...HEAD -sne``), contributions that do not have associated commits, and contributions to the preparation of the manuscript.
 
 
 
-    Disclaimer: These policies are not permanent or fixed and may change to accomodate community growth, 
+    Disclaimer: These policies are not permanent or fixed and may change to accomodate community growth,
     best practices, and feedback.
 
-Copyright notice: This document was inspired by the `authorship guidelines <https://github.com/fatiando/contributing/blob/master/AUTHORSHIP.md>`_ provided by `Fatiando a Terra <https://github.com/fatiando>`_ and encourages potential co-authors to consider the resources provided by the `NASA High Mountain Asia Team (HiMAT) <https://highmountainasia.github.io/team-collaboration/authorship/>`_.
+Copyright notice: This document was inspired by the `authorship guidelines <https://github.com/fatiando/contributing/blob/master/AUTHORSHIP.md>`_ provided by `Fatiando a Terra <https://github.com/fatiando>`_ and encourages potential co-authors to consider the resources provided by the `NASA High Mountain Asia Team (HiMAT) <https://highmountainasia.github.io/team-collaboration/authorship/>`_.

doc/source/community/contact.rst

@@ -1,4 +1,5 @@
 .. _contact_ref_label:
+
 Contact Us
 ==========
 
@@ -20,4 +21,4 @@ We meet on:
 
 Additional information about logging in to the meetings can be found on `this Discourse post <https://discourse.pangeo.io/t/icepyx-team-meetings/722/2?u=jessicas11>`_.
 
-Absolutely NO previous software development experience is necessary to attend any meeting. Think of them more like coffee hour mixed with office hours than a conference call. We look forward to seeing you there!
+Absolutely NO previous software development experience is necessary to attend any meeting. Think of them more like coffee hour mixed with office hours than a conference call. We look forward to seeing you there!

doc/source/community/resources.rst

@@ -1,4 +1,5 @@
 .. _resource_ref_label:
+
 ICESat-2 Open-Source Resources Guide
 ====================================
 

doc/source/user_guide/documentation/icepyx.rst

@@ -1,11 +1,10 @@
 icepyx Documentation (API Reference)
 ====================================
 
-
-
 .. image:: icepyx_class_diagram.png
   :width: 600
   :alt: PlantUML Class Diagram illustrating the public-facing classes within icepyx, their attributes and methods, their relationships (e.g. component classes).
+
 icepyx class diagram illustrating the library's public-facing classes, their attributes and methods, and their relationships.
 
 

doc/source/user_guide/documentation/query.rst

@@ -8,7 +8,7 @@ Constructor
 -----------
 
 .. autosummary::
-   :toctree: ../_icepyx/
+   :toctree: ../../_icepyx/
 
    Query
 
@@ -17,7 +17,7 @@ Attributes
 ----------
 
 .. autosummary::
-   :toctree: ../_icepyx/
+   :toctree: ../../_icepyx/
 
    Query.CMRparams
    Query.cycles
@@ -38,7 +38,7 @@ Methods
 -------
 
 .. autosummary::
-   :toctree: ../_icepyx/
+   :toctree: ../../_icepyx/
 
    Query.avail_granules
    Query.dataset_all_info

icepyx/core/Earthdata.py

@@ -28,7 +28,11 @@ class Earthdata:
     """
 
     def __init__(
-        self, uid, email, capability_url, pswd=None,
+        self,
+        uid,
+        email,
+        capability_url,
+        pswd=None,
     ):
 
         assert isinstance(uid, str), "Enter your login user id as a string"
@@ -63,7 +67,9 @@ def _start_session(self):
 
         response = None
         response = requests.post(
-            token_api_url, json=data, headers={"Accept": "application/json", "Client-Id": "icepyx"}
+            token_api_url,
+            json=data,
+            headers={"Accept": "application/json", "Client-Id": "icepyx"},
         )
 
         # check for a valid login
@@ -102,7 +108,9 @@ def login(self):
         Then change the permissions of that file to 600
         This will allow you to have read and write access to the file
         No other user can access the file
+
             $ chmod 600 ~/.netrc
+
         The function checks for this file to retrieve credentials, prior to
         prompting for manual input.
 

icepyx/core/variables.py

@@ -33,7 +33,7 @@ class Variables:
         Properly formatted string specifying a valid version of the ICESat-2 dataset
     source : string, default None
         For vartype file, a path to a directory or single input source files (not yet implemented)
-   """
+    """
 
     def __init__(
         self,
@@ -77,7 +77,7 @@ def avail(self, options=False, internal=False):
         >>> reg_a.earthdata_login(user_id,user_email)
         Earthdata Login password:  ········
         >>> reg_a.order_vars.avail()
-       ['ancillary_data/atlas_sdp_gps_epoch',
+        ['ancillary_data/atlas_sdp_gps_epoch',
         'ancillary_data/control',
         'ancillary_data/data_end_utc',
         'ancillary_data/data_start_utc',
@@ -140,39 +140,39 @@ def parse_var_list(varlist):
         >>> var_dict.keys()
         dict_keys(['atlas_sdp_gps_epoch', 'control', 'data_end_utc', 'data_start_utc',
         'end_cycle', 'end_delta_time', 'end_geoseg', 'end_gpssow', 'end_gpsweek',
-        'end_orbit', 'end_region', 'end_rgt', 'granule_end_utc', 'granule_start_utc', 
-        'qa_at_interval', 'release', 'start_cycle', 'start_delta_time', 'start_geoseg', 
-        'start_gpssow', 'start_gpsweek', 'start_orbit', 'start_region', 'start_rgt', 
-        'version', 'dt_hist', 'fit_maxiter', 'fpb_maxiter', 'maxiter', 'max_res_ids', 
-        'min_dist', 'min_gain_th', 'min_n_pe', 'min_n_sel', 'min_signal_conf', 'n_hist', 
-        'nhist_bins', 'n_sigmas', 'proc_interval', 'qs_lim_bsc', 'qs_lim_hrs', 'qs_lim_hsigma', 
-        'qs_lim_msw', 'qs_lim_snr', 'qs_lim_sss', 'rbin_width', 'sigma_beam', 'sigma_tx', 
-        't_dead', 'atl06_quality_summary', 'delta_time', 'h_li', 'h_li_sigma', 'latitude', 
-        'longitude', 'segment_id', 'sigma_geo_h', 'fpb_mean_corr', 'fpb_mean_corr_sigma', 
-        'fpb_med_corr', 'fpb_med_corr_sigma', 'fpb_n_corr', 'med_r_fit', 'tx_mean_corr', 
+        'end_orbit', 'end_region', 'end_rgt', 'granule_end_utc', 'granule_start_utc',
+        'qa_at_interval', 'release', 'start_cycle', 'start_delta_time', 'start_geoseg',
+        'start_gpssow', 'start_gpsweek', 'start_orbit', 'start_region', 'start_rgt',
+        'version', 'dt_hist', 'fit_maxiter', 'fpb_maxiter', 'maxiter', 'max_res_ids',
+        'min_dist', 'min_gain_th', 'min_n_pe', 'min_n_sel', 'min_signal_conf', 'n_hist',
+        'nhist_bins', 'n_sigmas', 'proc_interval', 'qs_lim_bsc', 'qs_lim_hrs', 'qs_lim_hsigma',
+        'qs_lim_msw', 'qs_lim_snr', 'qs_lim_sss', 'rbin_width', 'sigma_beam', 'sigma_tx',
+        't_dead', 'atl06_quality_summary', 'delta_time', 'h_li', 'h_li_sigma', 'latitude',
+        'longitude', 'segment_id', 'sigma_geo_h', 'fpb_mean_corr', 'fpb_mean_corr_sigma',
+        'fpb_med_corr', 'fpb_med_corr_sigma', 'fpb_n_corr', 'med_r_fit', 'tx_mean_corr',
         tx_med_corr', 'dem_flag', 'dem_h', 'geoid_h', 'dh_fit_dx', 'dh_fit_dx_sigma', '
-        dh_fit_dy', 'h_expected_rms', 'h_mean', 'h_rms_misfit', 'h_robust_sprd', 
-        'n_fit_photons', 'n_seg_pulses', 'sigma_h_mean', 'signal_selection_source', 
-        'signal_selection_source_status', 'snr', 'snr_significance', 'w_surface_window_final', 
-        ckgrd', 'bsnow_conf', 'bsnow_h', 'bsnow_od', 'cloud_flg_asr', 'cloud_flg_atm', 'dac', 
-        'e_bckgrd', 'layer_flag', 'msw_flag', 'neutat_delay_total', 'r_eff', 'solar_azimuth', 
-        'solar_elevation', 'tide_earth', 'tide_equilibrium', 'tide_load', 'tide_ocean', 
-        'tide_pole', 'ref_azimuth', 'ref_coelv', 'seg_azimuth', 'sigma_geo_at', 'sigma_geo_r', 
-        igma_geo_xt', 'x_atc', 'y_atc', 'bckgrd_per_m', 'bin_top_h', 'count', 'ds_segment_id', 
-        'lat_mean', 'lon_mean', 'pulse_count', 'segment_id_list', 'x_atc_mean', 'record_number', 
-        'reference_pt_lat', 'reference_pt_lon', 'signal_selection_status_all', 
-        'signal_selection_status_backup', 'signal_selection_status_confident', 'crossing_time', 
-        'cycle_number', 'lan', 'orbit_number', 'rgt', 'sc_orient', 'sc_orient_time', 
-        'qa_granule_fail_reason', 'qa_granule_pass_fail', 'signal_selection_source_fraction_0', 
-        'signal_selection_source_fraction_1', 'signal_selection_source_fraction_2', 
+        dh_fit_dy', 'h_expected_rms', 'h_mean', 'h_rms_misfit', 'h_robust_sprd',
+        'n_fit_photons', 'n_seg_pulses', 'sigma_h_mean', 'signal_selection_source',
+        'signal_selection_source_status', 'snr', 'snr_significance', 'w_surface_window_final',
+        ckgrd', 'bsnow_conf', 'bsnow_h', 'bsnow_od', 'cloud_flg_asr', 'cloud_flg_atm', 'dac',
+        'e_bckgrd', 'layer_flag', 'msw_flag', 'neutat_delay_total', 'r_eff', 'solar_azimuth',
+        'solar_elevation', 'tide_earth', 'tide_equilibrium', 'tide_load', 'tide_ocean',
+        'tide_pole', 'ref_azimuth', 'ref_coelv', 'seg_azimuth', 'sigma_geo_at', 'sigma_geo_r',
+        igma_geo_xt', 'x_atc', 'y_atc', 'bckgrd_per_m', 'bin_top_h', 'count', 'ds_segment_id',
+        'lat_mean', 'lon_mean', 'pulse_count', 'segment_id_list', 'x_atc_mean', 'record_number',
+        'reference_pt_lat', 'reference_pt_lon', 'signal_selection_status_all',
+        'signal_selection_status_backup', 'signal_selection_status_confident', 'crossing_time',
+        'cycle_number', 'lan', 'orbit_number', 'rgt', 'sc_orient', 'sc_orient_time',
+        'qa_granule_fail_reason', 'qa_granule_pass_fail', 'signal_selection_source_fraction_0',
+        'signal_selection_source_fraction_1', 'signal_selection_source_fraction_2',
         'signal_selection_source_fraction_3'])
         >>> import numpy
         >>> numpy.unique(paths)
         array(['ancillary_data', 'bias_correction', 'dem', 'fit_statistics',
-       'geophysical', 'ground_track', 'gt1l', 'gt1r', 'gt2l', 'gt2r',
-       'gt3l', 'gt3r', 'land_ice', 'land_ice_segments', 'none',
-       'orbit_info', 'quality_assessment', 'residual_histogram',
-       'segment_quality', 'signal_selection_status'], dtype='<U23')
+        'geophysical', 'ground_track', 'gt1l', 'gt1r', 'gt2l', 'gt2r',
+        'gt3l', 'gt3r', 'land_ice', 'land_ice_segments', 'none',
+        'orbit_info', 'quality_assessment', 'residual_histogram',
+        'segment_quality', 'signal_selection_status'], dtype='<U23')
         """
 
         # create a dictionary of variable names and paths
@@ -336,23 +336,23 @@ def _iter_paths(self, sum_varlist, req_vars, vgrp, beam_list, keyword_list):
     # DevGoal: we can ultimately add an "interactive" trigger that will open the not-yet-made widget. Otherwise, it will use the var_list passed by the user/defaults
     def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=None):
         """
-        Add to the list of desired variables using user specified beams and variable list. 
-        A pregenerated default variable list can be used by setting defaults to True. 
+        Add to the list of desired variables using user specified beams and variable list.
+        A pregenerated default variable list can be used by setting defaults to True.
         Note: The calibrated backscatter cab_prof is not in the default list for ATL09
-        
+
         Parameters
         ----------
         defaults : boolean, default False
-            Include the variables in the default variable list. Defaults are defined per-data product. 
+            Include the variables in the default variable list. Defaults are defined per-data product.
             When specified in conjuction with a var_list, default variables not on the user-
             specified list will be added to the order.
 
         var_list : list of strings, default None
-            A list of variables to request, if not all available variables are wanted. 
+            A list of variables to request, if not all available variables are wanted.
             A list of available variables can be obtained by entering `var_list=['']` into the function.
 
         beam_list : list of strings, default None
-            A list of beam strings, if only selected beams are wanted (the default value of None will automatically 
+            A list of beam strings, if only selected beams are wanted (the default value of None will automatically
             include all beams). For ATL09, acceptable values are ['profile_1', 'profile_2', 'profile_3'].
             For all other datasets, acceptable values are ['gt1l', 'gt1r', 'gt2l', 'gt2r', 'gt3l', 'gt3r'].
 
@@ -374,19 +374,19 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non
         Earthdata Login password:  ········
 
         To add all variables related to a specific ICESat-2 beam
-        
+
         >>> reg_a.order_vars.append(beam_list=['gt1r'])
-        
+
         To include the default variables:
-        
+
         >>> reg_a.order_vars.append(defaults=True)
 
         To add specific variables in orbit_info
-        
+
         >>> reg_a.order_vars.append(keyword_list=['orbit_info'],var_list=['sc_orient_time'])
 
         To add all variables and paths in ancillary_data
-        
+
         >>> reg_a.order_vars.append(keyword_list=['ancillary_data'])
         """
 
@@ -454,19 +454,19 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non
     def remove(self, all=False, var_list=None, beam_list=None, keyword_list=None):
         """
         Remove the variables and paths from the wanted list using user specified beam, keyword,
-         and variable lists. 
-        
+         and variable lists.
+
         Parameters:
         -----------
         all : boolean, default False
             Remove all variables and paths from the wanted list.
-        
+
         var_list : list of strings, default None
-            A list of variables to request, if not all available variables are wanted. 
+            A list of variables to request, if not all available variables are wanted.
             A list of available variables can be obtained by entering `var_list=['']` into the function.
 
         beam_list : list of strings, default None
-            A list of beam strings, if only selected beams are wanted (the default value of None will automatically 
+            A list of beam strings, if only selected beams are wanted (the default value of None will automatically
             include all beams). For ATL09, acceptable values are ['profile_1', 'profile_2', 'profile_3'].
             For all other datasets, acceptable values are ['gt1l', 'gt1r', 'gt2l', 'gt2r', 'gt3l', 'gt3r'].
 
@@ -487,19 +487,19 @@ def remove(self, all=False, var_list=None, beam_list=None, keyword_list=None):
         Earthdata Login password:  ········
 
         To clear the list of wanted variables
-        
+
         >>> reg_a.order_vars.remove(all=True)
-        
+
         To remove all variables related to a specific ICESat-2 beam
-        
+
         >>> reg_a.order_vars.remove(beam_list=['gt1r'])
 
         To remove specific variables in orbit_info
-        
+
         >>> reg_a.order_vars.remove(keyword_list=['orbit_info'],var_list=['sc_orient_time'])
 
         To remove all variables and paths in ancillary_data
-        
+
         >>> reg_a.order_vars.remove(keyword_list=['ancillary_data'])
         """