Merge PDAL/PDAL into tindex-threaded

.readthedocs.yaml

@@ -11,13 +11,13 @@ build:
     python: "mambaforge-latest"
   jobs:
     pre_build:
-      # - doxygen ./doc/doxygen/doxygen.conf 1> /dev/null
+      - doxygen ./doc/doxygen/doxygen.conf 1> /dev/null
       # Generate on-the-fly Sphinx configuration from Jupyter Book's _config.yml
       - "jupyter-book config sphinx doc/"
       - sed -i "1i\import os, sys; sys.path.append(os.path.abspath(\"./_ext\"))" doc/conf.py
 
-  # apt_packages:
-  #   - graphviz
+  apt_packages:
+    - graphviz
 
 sphinx:
   # builder: html

doc/_config.yml

@@ -2,7 +2,8 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: Point Data Abstraction Library (PDAL)
-author: PDAL team
+author: ''
+copyright: "2024"
 # logo: _static/pdal_logo.png
 
 # Force re-execution of notebooks on each build.
@@ -15,29 +16,75 @@ execute:
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:
-    targetname: book.tex
-
-# Add a bibtex file so that we can create citations
-# bibtex_bibfiles:
-  # - references.bib
+    targetname: pdal.tex
 
 # Information about where the book exists on the web
 repository:
   url: https://github.com/PDAL/PDAL  # Online location of your book
   path_to_book: book/  # Optional path to your book, relative to the repository root
-  branch: main  # Which branch of the repository should be used when creating links (optional)
+  branch: master  # Which branch of the repository should be used when creating links (optional)
 
 # Add GitHub buttons to your book
 # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
 html:
   use_issues_button: true
   use_repository_button: true
+  extra_navbar: ""
+  use_edit_page_button: true
+  favicon: './_static/logo/favicon.ico'
+  short_title: "Documentation"
+  html_show_copyright: false
+  html_short_title: PDAL
+  html_title: PDAL2
+  extra_footer: |
+    <a href="https://hobu.co/access.html"><img width="30px" src="./_static/logo/hobu.png" /></a> <a href="/copyright.html">Copyright</a> ©2024 <a href="https://github.com/abellgithub">Andrew Bell</a>, <a href="https://github.com/chambbj">Brad Chambers</a>, <a href="http://github.com/hobu">Howard Butler</a>, and <a href="https://github.com/PDAL/PDAL/graphs/contributors">others</a>
+
 
 sphinx:
   config:
+    html_show_copyright: false
     bibtex_bibfiles:
       - references.bib
     bibtex_reference_style: author_year
+    breathe_projects:
+      api: "doxygen/xml"
+    breathe_diagram:
+      - path: "./doxygen/html"
+      - html-path: "../../../doxygen/html"
+      - project: "api"
+      - no-link: false
+    breathe_domain_by_extension:
+      hpp: "cpp"
+      h: "cpp"
+    breathe_default_project: api
+    latex_logo: "./_static/logo/pdal_logo_only.png"
+    latex_use_parts: false
+    latex_show_urls: "inline"
+    latex_elements:
+      preamble: '
+  \makeatother
+  %\color {blue}
+  %\normalcolor {dark blue}
+  \definecolor{VerbatimColor}{RGB}{239, 239, 239}
+  \definecolor{VerbatimBorderColor}{RGB}{148, 148, 148}
+  \usepackage{geometry}
+   \geometry{
+   letterpaper,
+   left={30mm},
+  }
+  \raggedright'
+      figure_align: 'htbp'
+      releasename: ''
+      tocdepth: 4
+      pointsize: '12pt'
+      papersize: 'letterpaper'
+    pygments_style: "sphinx"
+#    latex_documents:
+#      - "index"
+#      - "pdal.tex"
+#      - "PDAL: Point cloud Data Abstraction Library"
+#      - 'Andrew Bell\\Brad Chambers\\Howard Butler\\Michael Gerlek\\PDAL Contributors'
+#      - "manual"
   local_extensions:
     embed: ./_ext
   extra_extensions:
@@ -51,16 +98,16 @@ sphinx:
 
 parse:
   myst_substitutions:
-    ASPRSLAS: '[ASPRS LAS](http://www.asprs.org/Committee-General/LASer-LAS-File-Format-Exchange-Activities.html)'
+    ASPRSLAS: '[ASPRS LAS](https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities)'
     Bash: '[Bash](https://en.wikipedia.org/wiki/Bash_(Unix_shell))'
-    CRREL: '[CRREL](http://www.erdc.usace.army.mil/Locations/ColdRegionsResearchandEngineeringLaboratory.aspx)'
+    CRREL: '[CRREL](https://www.erdc.usace.army.mil/Locations/CRREL/)'
     CSV: '[CSV](https://en.wikipedia.org/wiki/Comma-separated_values)'
     Docker: '[Docker](https://www.docker.com/)'
-    Entwine: '[Entwine](http://entwine.io/)'
+    Entwine: '[Entwine](https://entwine.io/)'
     GDAL: '[GDAL](http://gdal.org/)'
-    GEOS: '[GEOS](https://trac.osgeo.org/geos/)'
-    GRID: '[GRiD](http://lidar.io/)'
-    GeoTIFF: '[GeoTIFF](https://trac.osgeo.org/geotiff/)'
+    GEOS: '[GEOS](https://libgeos.org)'
+    GRID: '[GRiD](https://grid.nga.mil/grid/)'
+    GeoTIFF: '[GeoTIFF](https://github.com/OSGeo/libgeotiff)'
     Hobu: '[Hobu](https://hobu.co/)'
     JSON: '[JSON](https://en.wikipedia.org/wiki/JSON)'
     Julia: '[Julia](https://julialand.org)'
@@ -71,18 +118,18 @@ parse:
     Optech: '[Optech](http://www.teledyneoptech.com/)'
     PCL: '[PCL](http://pointclouds.org)'
     PDAL: '[PDAL](https://pdal.io/)'
-    Proj: '[Proj.4](http://proj4.org)'
-    Python: '[Python](http://python.org/)'
-    QGIS: '[QGIS](http://qgis.org)'
-    RIEGL: '[RIEGL](http://riegl.com/)'
+    PROJ: '[PROJ](https://proj4.org)'
+    Python: '[Python](https://python.org/)'
+    QGIS: '[QGIS](https://qgis.org)'
+    RIEGL: '[RIEGL](https://riegl.com/)'
     Terminal: '`Conda Shell`'
     USACE: U.S. Army Corps of Engineers
     UTM: '[UTM](https://en.wikipedia.org/wiki/Universal_Transverse_Mercator_coordinate_system)'
     WGS84: '[WGS84](https://en.wikipedia.org/wiki/Geodetic_datum)'
-    WellKnownText: '[Well Known Text](https://en.wikipedia.org/wiki/Well-known_text#Coordinate_reference_systems)'
+    WellKnownText: '[Well Known Text](https://en.wikipedia.org/wiki/Well-known_text_representation_of_coordinate_reference_systems)'
     XML: '[XML](https://en.wikipedia.org/wiki/XML)'
     jq: '[jq](https://stedolan.github.io/jq/)'
-    libLAS: '[libLAS](http://liblas.org/)'
+    libLAS: '[libLAS](https://liblas.org/)'
     nbsp: '&#160;'
     alpinestatus: "[![Alpine Status](https://github.com/PDAL/PDAL/workflows/Alpine/badge.svg)](https://github.com/PDAL/PDAL/actions?query=workflow%3AAlpine)"
     dockerstatus: "[![Docker Status](https://github.com/PDAL/PDAL/workflows/Docker/badge.svg)](https://github.com/PDAL/PDAL/actions?query=workflow%3ADocker)"
@@ -93,4 +140,4 @@ parse:
   myst_enable_extensions:
     - substitution
     - deflist
-    - dollarmath
+    - dollarmath

doc/about.md

@@ -190,7 +190,7 @@ a variety of raster and vector formats. PDAL provides the same capability for
 point cloud data types.
 
 PDAL evolved out of the development of database storage and access capabilities
-for the {{ USACE }} [CRREL](http://www.erdc.usace.army.mil/Media/Fact-Sheets/Fact-Sheet-Article-View/Article/476649/remote-sensinggeographic-information-systems-center/) {{ GRID }} project. Functionality that was creeping into {{ libLAS }}
+for the {{ USACE }} [CRREL](https://www.erdc.usace.army.mil/Locations/CRREL/) {{ GRID }} project. Functionality that was creeping into {{ libLAS }}
 was pulled into a new library, and it was designed from the ground up to mimic
 successful extract, transform, and load libraries in the geospatial software
 domain. PDAL has steadily attracted more contributors as other software
@@ -348,25 +348,24 @@ extensions. There are many open source software projects for interacting
 with point cloud data, and PDAL's niche is in processing, translation,
 and automation.
 
-[asprs las]: http://www.asprs.org/Committee-General/LASer-LAS-File-Format-Exchange-Activities.html
-[cloudcompare]: http://www.danielgm.net/cc/
+[asprs las]: https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities
+[cloudcompare]: https://www.danielgm.net/cc/
 [entwine]: https://entwine.io
 [entwine point tile]: https://entwine.io/entwine-point-tile.html
-[fusion]: http://www.idaholidar.org/tools/fusion-ldv/
-[greyhound]: http://greyhound.io
+[fusion]: https://research.fs.usda.gov/pnw/products/dataandtools/tools/fusion/ldv-lidar-processing-and-visualization-software-version-4.40
 [hobu, inc.]: https://hobu.co
 [json]: https://en.wikipedia.org/wiki/JSON
-[lastools]: http://lastools.org
-[laszip]: http://laszip.org
-[liblas]: http://liblas.org
-[martin isenburg]: https://www.cs.unc.edu/~isenburg/
-[numpy]: http://www.numpy.org/
+[lastools]: https://lastools.org
+[laszip]: https://laszip.org
+[liblas]: https://liblas.org
+[martin isenburg]: https://lidarmag.com/2021/10/30/in-memoriam-martin-isenburg-1972-2021/
+[numpy]: https://numpy.org/
 [orfeotoolbox]: https://www.orfeo-toolbox.org/
 [osi]: https://opensource.org/licenses
-[pcl]: http://pointclouds.org
+[pcl]: https://pointclouds.org
 [point cloud data]: https://en.wikipedia.org/wiki/Point_cloud
-[potree]: http://potree.org
-[python las]: https://pypi.python.org/pypi/laspy/1.4.1
+[potree]: https://potree.org
+[python las]: https://pypi.python.org/pypi/laspy/
 [untwine]: https://github.com/hobuinc/untwine
-[virtual raster format]: http://www.gdal.org/gdal_vrttut.html
+[virtual raster format]: https://gdal.org/en/latest/drivers/raster/vrt.html
 [webgl]: https://en.wikipedia.org/wiki/WebGL

doc/apps/density.md

@@ -27,4 +27,4 @@ $ pdal density <input> <output>
 --smooth           Smooth boundary output
 ```
 
-[ogr layer]: http://www.gdal.org/ogr_utilities.html
+[ogr layer]: https://gdal.org/en/latest/drivers/vector/index.html

doc/apps/tindex.md

@@ -36,7 +36,7 @@ The type of the index
 file can be specified by specifying the OGR code for the format using the
 `--ogrdriver` option.  If no driver is specified, the format defaults to "ESRI
 Shapefile".  Any filetype that can be handled by
-[OGR](http://www.gdal.org/ogr_formats.html) is acceptable.
+[OGR](https://gdal.org/en/latest/drivers/vector/) is acceptable.
 
 In vector file-speak, each file specified by `filespec` is stored as a
 feature in a layer in the index file. The `filespec` is a [glob pattern](http://man7.org/linux/man-pages/man7/glob.7.html).  and normally needs to be
@@ -85,6 +85,6 @@ $ pdal tindex create index.sqlite "*.las" -f "SQLite" --lyr_name "pdal" \
     --t_srs "EPSG:4326"
 ```
 
-[gdal]: http://www.gdal.org
-[gdaltindex]: http://www.gdal.org/gdaltindex.html
+[gdal]: https://gdal.org
+[gdaltindex]: https://gdal.org/en/latest/programs/gdaltindex.html
 [sqlite]: http://www.sqlite.org