clean up a bunch of sphinx doc warnings

doc/docs.rst

@@ -12,17 +12,17 @@ Contents:
 
    download
    compilation/index
-   commandline/index
    apps
    stages/index
    pipeline
-   vagranttutorial
+   vagrant
    community
    faq
    development/index
    tutorial/index
    api/index
    metadata
+   vagrant
    copyright
 
 Indices and tables

doc/stages/filters.ferry.rst

@@ -1,7 +1,7 @@
 .. _filters.ferry:
 
 filters.ferry
-============
+================================================================================
 
 The ferry filter is used to stash intermediate variables as part of
 processing data. For example, a common scenario is to keep both the

doc/stages/filters.merge.rst

@@ -1,13 +1,13 @@
 .. _filters.merge:
 
 filters.merge
-============
+===============================================================================
 
 The merge filter combines input from multiple sources into a single output.
 No checks are made to ensure that points from the various sources have similar
 dimensions or are generally compatible.  Notably, dimensions are not
 initialized when points merged from various sources do not have dimensions in
-common. 
+common.
 
 Example
 -------

doc/stages/filters.mortonorder.rst

@@ -1,7 +1,7 @@
 .. _filters.mortonorder:
 
 filters.mortonorder
-===========
+================================================================================
 
 Sorts the XY data using `Morton ordering`_.
 

doc/stages/filters.splitter.rst

@@ -1,7 +1,7 @@
 .. _filters.splitter:
 
 filters.splitter
-===============
+===============================================================================
 
 The splitter filter breaks a point cloud into square tiles of a size that
 you choose.  The origin of the tiles is chosen arbitrarily unless specified
@@ -12,7 +12,7 @@ for each tile as its output.
 
 Splitting is usually applied to data read from files (which produce one large
 stream of points) before the points are written to a database (which prefer
-data segmented into smaller blocks). 
+data segmented into smaller blocks).
 
 Example
 -------
@@ -40,10 +40,10 @@ Options
 length
   Length of the sides of the tiles that are created to hold points.
   [Default: 1000]
-  
+
 origin_x
   X Origin of the tiles.  [Default: none (chosen arbitarily)]
 
 origin_y
   Y Origin of the tiles.  [Default: none (chosen arbitarily)]
-  
+

doc/stages/filters.stats.rst

@@ -1,7 +1,7 @@
 .. _filters.stats:
 
 filters.stats
-============
+===============================================================================
 
 The stats filter calculates the minimum, maximum and average (mean) values
 of dimensions.  On request it will also provide an enumeration of values of
@@ -41,7 +41,7 @@ Options
 dimensions
   A comma-separated list of dimensions whose statistics should be
   processed.  If not provided, statistics for all dimensions are calculated.
-  
+
 enumerate
   A comma-separated list of dimensions whose values should be enumerated.
   Note that this list does not add to the list of dimensions that may be

doc/stages/readers.buffer.rst

@@ -3,7 +3,7 @@
 readers.buffer
 ==============
 
-The `readers.buffer`_ stage is a special stage that allows
+The :ref:`readers.buffer`_ stage is a special stage that allows
 you to read data from your own PointView rather than
 fetching the data from a specific reader. In the :ref:`writing` example,
 it is used to take a simple listing of points and turn them into an
@@ -13,7 +13,7 @@ LAS file.
 Example
 -------
 
-See :ref:`writing` for an example usage scenario for `readers.buffer`.
+See :ref:`writing` for an example usage scenario for :ref:`readers.buffer`.
 
 Options
 -------

doc/stages/readers.geowave.rst

@@ -1,9 +1,11 @@
 .. _readers.geowave:
 
 readers.geowave
-============
+===============================================================================
 
-The **GeoWave reader** uses `GeoWave`_ to read from Accumulo.  GeoWave entries are stored using EPSG:4326.  Instructions for configuring the GeoWave plugin can be found `here`_
+The **GeoWave reader** uses `GeoWave`_ to read from Accumulo.  GeoWave entries
+are stored using EPSG:4326.  Instructions for configuring the GeoWave plugin
+can be found `here`_
 
 Example
 -------
@@ -57,7 +59,7 @@ pointsPerEntry
   Sets the maximum number of points per Accumulo entry when using FeatureCollectionDataAdapter. [Default: 5000u]
 
 bounds
-  The extent of the bounding rectangle to use to query points, expressed as a string, eg: “([xmin,xmax],[ymin,ymax],[zmin,zmax])”. [Default: unit cube] 
+  The extent of the bounding rectangle to use to query points, expressed as a string, eg: “([xmin,xmax],[ymin,ymax],[zmin,zmax])”. [Default: unit cube]
 
 
 .. _GeoWave: https://ngageoint.github.io/geowave/

doc/stages/writers.las.rst

@@ -35,7 +35,7 @@ filename
   the placeholder will be replaced with an incrementing integer.  If no
   placeholder is found, all PointViews provided to the writer are
   aggregated into a single file for output.  Multiple PointViews are usually
-  the result of using :ref:`filters.splitter` or :ref:`filters.chipper`. 
+  the result of using :ref:`filters.splitter` or :ref:`filters.chipper`.
   [Required]
 
 forward
@@ -65,7 +65,7 @@ forward
   output file as necessary.  Unlike header values, VLRs from multiple input
   files are accumulated and each is written to the output file.  Forwarded
   VLRs may contain duplicate User ID/Record ID pairs.
-  
+
 minor_version
   All LAS files are version 1, but the minor version (0 - 4) can be specified
   with this option. [Default: 3]
@@ -77,32 +77,32 @@ software_id
 creation_doy
   Number of the day of the year (January 1 == 0, Dec 31 == 365) this file is
   being created.
-  
+
 creation_year
   Year (Gregorian) this file is being created.
-  
+
 dataformat_id
   Controls whether information about color and time are stored with the point
   information in the LAS file. [Default: 3]
-  
+
   * 0 == no color or time stored
   * 1 == time is stored
   * 2 == color is stored
-  * 3 == color and time are stored 
+  * 3 == color and time are stored
   * 4 [Not Currently Supported]
   * 5 [Not Currently Supported]
   * 6 == time is stored (version 1.4+ only)
   * 7 == time and color are stored (version 1.4+ only)
   * 8 == time, color and near infrared are stored (version 1.4+ only)
   * 9 [Not Currently Supported]
   * 10 [Not Currently Supported]
-  
+
 system_id
   String identifying the system that created this LAS file. [Default: "PDAL"]
-  
+
 a_srs
   The spatial reference system of the file to be written. Can be an EPSG string (eg "EPSG:268910") or a WKT string. [Default: Not set]
-  
+
 global_encoding
   Various indicators to describe the data.  See the LAS documentation.  Note
   that PDAL will always set bit four when creating LAS version output.
@@ -131,7 +131,7 @@ offset_x, offset_y, offset_z
    dimension.  [Default: 0]
 
    Note: written value = (nominal value - offset) / scale.
-  
+
 filesource_id
   The file source id number to use for this file (a value between
   1 and 65535) [Default: 0]
@@ -145,11 +145,11 @@ extra_dims
   Extra dimensions to be written as part of each point beyond those specified
   by the LAS point format.  The format of the option is
   <dimension_name>=<type>, ... where type is one of:
-      int8, int16, int32, int64, uint8, uint16, uint32, uint64, float, double
+  int8, int16, int32, int64, uint8, uint16, uint32, uint64, float, double
   '_t' may be added to any of the type names as well (e.g., uint32_t).  When
   the version of the output file is specified as 1.4 or greater, an extra
   bytes VLR (User ID: LASF_Spec, Record ID: 4), is created that describes the
   extra dimensions specified by this option.
 
 .. _LAS format: http://asprs.org/Committee-General/LASer-LAS-File-Format-Exchange-Activities.html
-  
+

doc/stages/writers.null.rst

@@ -1,4 +1,4 @@
-.. _writers.text:
+.. _writers.null:
 
 writers.null
 ============

doc/stages/writers.text.rst

@@ -3,7 +3,9 @@
 writers.text
 ============
 
-The **text writer** writes out to a text file. This is useful for debugging or getting smaller files into an easily parseable format.  The text writer supports both `GeoJson`_ and `CSV`_ output.
+The **text writer** writes out to a text file. This is useful for debugging or
+getting smaller files into an easily parseable format.  The text writer
+supports both `GeoJSON`_ and `CSV`_ output.
 
 
 Example
@@ -33,27 +35,27 @@ filename
   File to write to, or "STDOUT" to write to standard out [Required]
 
 format
-  Output format to use. One of "geojson" or "csv". [Default: **csv**] 
+  Output format to use. One of "geojson" or "csv". [Default: **csv**]
 
 order
   Comma-separated list of dimension names, giving the desired column order in the output file, for example "X,Y,Z,Red,Green,Blue". [Default: none]
-  
+
 keep_unspecified
   Should we output any fields that are not specified in the dimension order? [Default: **true**]
 
 jscallback
   When producing GeoJSON, the callback allows you to wrap the data in a function, so the output can be evaluated in a <script> tag.
-  
+
 quote_header
   When producing CSV, should the column header named by quoted? [Default: **true**]
-  
+
 newline
   When producing CSV, what newline character should be used? (For Windows, "\\r\\n" is common.) [Default: **\\n**]
-  
+
 delimiter
-  When producing CSV, what character to use as a delimiter? [Default: **,**]  
+  When producing CSV, what character to use as a delimiter? [Default: **,**]
 
 
-.. _GeoJson: http://geojson.org
+.. _GeoJSON: http://geojson.org
 .. _CSV: http://en.wikipedia.org/wiki/Comma-separated_values
 

doc/tutorial/liblas_to_pdal.rst

@@ -68,9 +68,9 @@ pointer was used with libLAS:
 
 .. code-block:: cpp
 
-if (LAS_header == NULL) {
-    /* fail */
-}
+    if (LAS_header == NULL) {
+        /* fail */
+    }
 
 In general, PDAL will throw a ``pdal_error`` exception in case something
 is wrong and it can't recover such in the case when the file can't be opened.
@@ -79,11 +79,11 @@ in ``try-catch`` block:
 
 .. code-block:: cpp
 
-try {
-    /* actual code */
-} catch {
-    /* fail in your own way */
-}
+    try {
+        /* actual code */
+    } catch {
+        /* fail in your own way */
+    }
 
 
 Dataset properties

doc/tutorial/overview.rst

@@ -1,4 +1,4 @@
-.. _overview
+.. _overview:
 
 ******************************************************************************
 PDAL Architecture Overview