Merge branch 'release/v2.1'

.gitignore

@@ -36,6 +36,9 @@ x86/
 /build
 /docs/_build
 
+# Vagrant
+.vagrant/
+
 # Balázs (Visual Studio etc)
 .vscode/
 .cproject

README.md

@@ -1,4 +1,4 @@
-# val3dity 
+# val3dity
 
 val3dity---pronounced 'val-three-dity'---allows us to validate 3D primitives according to the international standard ISO19107.
 Think of it as [PostGIS ST_IsValid](http://postgis.net/docs/ST_IsValid.html), but for 3D primitives (PostGIS only validates 2D primitives).
@@ -7,7 +7,7 @@ In short, it verifies whether a 3D primitive respects the definition as given in
 All the 3D primitives of GML are supported:
 
   - `<gml:MultiSurface>`
-  - `<gml:CompositeSurface>` 
+  - `<gml:CompositeSurface>`
   - `<gml:Solid>`
   - `<gml:MultiSolid>`
   - `<gml:CompositeSolid>`
@@ -17,16 +17,16 @@ However, as is the case for CityGML, only planar and linear primitives are allow
 
 val3dity accepts as input:
 
-  - [CityGML](https://www.citygml.org) 
+  - [CityGML](https://www.citygml.org)
   - [CityJSON](http://www.cityjson.org)
   - [GML files](https://en.wikipedia.org/wiki/Geography_Markup_Language) of any flavour
-  - [OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file) 
+  - [OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file)
   - [OFF](https://en.wikipedia.org/wiki/OFF_(file_format))
 
 
 ## Installation of the command-line tool
 
-We provide the source code that you need to compile with CMake. 
+We provide the source code that you need to compile with CMake.
 This is relatively easy under Mac and Linux.
 
 [For Windows, we offer an executable](https://github.com/tudelft3d/val3dity/releases), although it's also possible to compile val3dity yourself.
@@ -35,13 +35,13 @@ To compile val3dity yourself, you first need to install the following free libra
 
   1. [CGAL v4.10+](http://www.cgal.org) (<v4.10 will compile and run, but wrong results for one test (error 405))
   1. (CGAL needs to be compiled with the [Eigen library](http://eigen.tuxfamily.org))
-  1. [GEOS](http://trac.osgeo.org/geos/) 
+  1. [GEOS](http://trac.osgeo.org/geos/)
   1. [CMake](http://www.cmake.org)
 
 Under macOS, it's super easy, we suggest using [Homebrew](http://brew.sh/):
 
     $ brew install cgal --with-eigen
-    $ brew install cmake 
+    $ brew install cmake
     $ brew install geos
 
 Under Linux (at least Ubuntu), CGAL has to be compiled because apt-get doesn't give you a version with Eigen.
@@ -72,18 +72,22 @@ Finally, to see all the options possible:
 
     $ ./val3dity --help
 
+## Vagrant development environment
+
+If you are eager to contribute but do not want to fiddle with setting up the required libraries, Vagrant can take care of that. It creates a development environment in a virtual machine, which you can use to compile and run val3dity. For details see VAGRANT.md
+
 ## Web application
 
-If you don't want to go through the troubles of compiling and/or installing val3dity, we suggest you use the [web application](http://geovalidation.bk.tudelft.nl/val3dity). 
+If you don't want to go through the troubles of compiling and/or installing val3dity, we suggest you use the [web application](http://geovalidation.bk.tudelft.nl/val3dity).
 Simply upload your file to our server and get a validation report back.
 We delete the file as soon as it has been validated (promised!).
 However, a file is limited to 50MB.
-    
+
 ## Documentation and help
 
-Read the full documentation at [http://geovalidation.bk.tudelft.nl/val3dity/docs/](http://geovalidation.bk.tudelft.nl/val3dity/docs/). 
+Read the full documentation at [http://geovalidation.bk.tudelft.nl/val3dity/docs/](http://geovalidation.bk.tudelft.nl/val3dity/docs/).
 
-The primary channel to communicate with the developers is the Issues section. 
+The primary channel to communicate with the developers is the Issues section.
 
-If you have a question or came across a bug, please submit an issue there. 
-However we ask you check first whether your problem has already been solved by someone else.
+If you have a question or came across a bug, please submit an issue there.
+However we ask you check first whether your problem has already been solved by someone else.

VAGRANT.md

@@ -0,0 +1,63 @@
+# Installing Vagrant
+
+To download Vagrant for supported platforms, see [here](https://www.vagrantup.com/downloads.html)
+
+# Installing VirtualBox
+
+If choosing VirtualBox as your virtualization provider, see [here](https://www.virtualbox.org/wiki/Downloads).
+
+You may have to enable hardware virtualization extensions in your BIOS before using it.
+
+If running on Ubuntu, you may have to install a newer version of VirtualBox than what is available in the public repositories in order for it to work correctly with Vagrant.
+
+# Setting up val3dity with Vagrant & VirtualBox
+Once Vagrant has been installed, you can start an environment by checking out the val3dity code, then changing to the directory which contains the Vagrantfile by typing:
+
+    # Windows users will need to uncomment the line ending configuration option.
+    git clone [email protected]:tudelft3d/val3dity.git val3dity #--config core.autocrlf=input
+    cd val3dity
+    vagrant up
+
+# Other Virtualization Providers
+
+If you would like to use Parallels instead of VirtualBox, please run the following command:
+```
+vagrant up --provider=parallels
+```
+Please note that this requires the Parallels Vagrant plugin, which can be installed:
+```
+vagrant plugin install vagrant-parallels
+```
+
+Similarly, if you would like to use VMware Workstation instead of VirtualBox, please run the following command:
+```
+vagrant up --provider vmware_workstation
+```
+Please note that this requires the VMware Vagrant plugin, which can be installed:
+```
+vagrant plugin install vagrant-vmware-workstation
+```
+
+# Vagrant Provisioning
+
+The initialization of the vagrant vm (`vagrant up`) will take about an hour at first.
+
+You should be able to log into the running VM by typing:
+
+    vagrant ssh
+
+Within this login shell, you can build the code, run the server or the tests. For example, to run the tests:
+
+```
+    vagrant ssh
+    cd ~/val3dity_build
+    cmake ../val3dity
+    make
+    make install
+```
+
+The val3dity root folder (on host) is mapped to the `/home/vagrant/val3dity` folder on the guest. Note that # Vagrant shared folders (e.g. `/home/vagrant/val3dity`) incur a heavy performance penalty within the virtual machine when there is heavy I/O, so they should only be used for source files. Any compilation step, database files, and so on should be done outside the shared folder filesystem inside the guest filesystem itself.
+
+**Acknowledgement**
+
+The majority of this description was taken from the [Hootenanny project](https://github.com/ngageoint/hootenanny/blob/master/VAGRANT.md)

VagrantProvisionUbuntu1604.sh

@@ -0,0 +1,102 @@
+#!/usr/bin/env bash
+
+# Set environment variables
+BUILDS="/opt"
+HOME="/home/vagrant"
+echo HOME: $HOME
+
+apt-get update >/dev/null 2>&1
+
+# CMake, C/++ compiler ---------------------------------------------------------
+echo "Installing C/++ compiler and CMake..."
+apt-get install -y cmake gcc g++ >/dev/null 2>&1
+
+# pip --------------------------------------------------------------------------
+echo "Installing pip..."
+apt-get install -y python3-pip >/dev/null 2>&1
+
+# CGAL requirements ------------------------------------------------------------
+echo "Installing Eigen3, Boost, GMP, MPFR..."
+# get Boost
+apt-get install -y libboost-all-dev >/dev/null 2>&1
+# get Eigen3
+apt-get install -y libeigen3-dev >/dev/null 2>&1
+# get GMP and MPFR
+apt-get install -y libgmp10 libgmp-dev libmpfr-dev libmpfr4 >/dev/null 2>&1
+
+apt-get update >/dev/null 2>&1
+apt-get upgrade -y >/dev/null 2>&1
+
+# GEOS -------------------------------------------------------------------------
+echo "Downloading and building GEOS 3.6.2 ..."
+cd $BUILDS
+wget https://git.osgeo.org/gitea/geos/geos/archive/3.6.2.tar.gz >/dev/null 2>&1
+tar xf 3.6.2.tar.gz
+rm 3.6.2.tar.gz
+mkdir $BUILDS/geos/build && cd $BUILDS/geos/build
+cmake ..
+make
+geos_test=$(make check | grep -o '100% tests passed')
+if [ "$geos_test" = "100% tests passed" ]; then
+    make install
+    ldconfig
+    make clean
+else
+    echo "GEOS test failed, exiting provisioning"
+    exit 1
+fi
+
+
+# CGAL -------------------------------------------------------------------------
+# For some reason CGAL cannot link Eigen3 to boost_thread when the release tarball
+# is used for compilation. However, everything works when CGAL is compiled from
+# the source tarball (copy of GitHub master branch). Only the md5sum is not 
+# correct in the provided md5sum.txt
+echo "Downloading and building CGAL 4.10.2 ..."
+cd $BUILDS
+wget https://github.com/CGAL/cgal/archive/releases/CGAL-4.10.2.tar.gz >/dev/null 2>&1
+#wget https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-4.10.2/md5sum.txt >/dev/null 2>&1
+
+#CGAL_TAR=$(md5sum CGAL-4.10.2.tar.xz)
+#CGAL_MD5=$(cat md5sum.txt | grep CGAL-4.10.2.tar.xz)
+#if [ "$CGAL_TAR" = "$CGAL_MD5" ]; then
+#    tar -xf CGAL-4.10.2.tar.xz
+#    rm CGAL-4.10.2.tar.xz
+#    rm md5sum.txt
+#else
+#    echo "md5sum of CGAL not matching, exiting provisioning"
+#    exit 1
+#fi
+
+tar -xf CGAL-4.10.2.tar.gz
+rm CGAL-4.10.2.tar.gz
+
+mkdir $BUILDS/cgal-releases-CGAL-4.10.2/build && cd $BUILDS/cgal-releases-CGAL-4.10.2/build
+cmake .. -DWITH_Eigen3=ON
+make
+make install
+make clean
+ldconfig
+
+
+# pytest -----------------------------------------------------------------------
+echo "Installing pytest..."
+pip3 install pytest
+
+# val3dity ---------------------------------------------------------------------
+echo "Building val3dity..."
+# Vagrant shared folders incur a heavy performance penalty within the
+# virtual machine when there is heavy I/O, so they should only be used for
+# source files. Any compilation step, database files, and so on should be done
+# outside the shared folder filesystem inside the guest filesystem itself.
+mkdir $HOME/val3dity_build && cd $HOME/val3dity_build
+cmake $HOME/val3dity
+make
+make install
+cd $HOME
+
+val3dity --version
+
+chown vagrant:vagrant $HOME/val3dity_build
+
+echo "See VAGRANT.md for additional configuration instructions and then run 'vagrant ssh' to log into the val3dity virtual machine."

Vagrantfile

@@ -0,0 +1,74 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# All Vagrant configuration is done below. The "2" in Vagrant.configure
+# configures the configuration version (we support older styles for
+# backwards compatibility). Please don't change it unless you know what
+# you're doing.
+Vagrant.configure("2") do |config|
+  # The most common configuration options are documented and commented below.
+  # For a complete reference, please see the online documentation at
+  # https://docs.vagrantup.com.
+
+  # Every Vagrant development environment requires a box. You can search for
+  # boxes at https://vagrantcloud.com/search.
+#  config.vm.box = "debian/stretch64"
+  config.vm.box = "ubuntu/xenial64"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # VirtualBox Guest Additions plugin
+  config.vbguest.auto_update = true
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # NOTE: This will enable public access to the opened port
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine and only allow access
+  # via 127.0.0.1 to disable public access
+  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  config.vm.synced_folder ".", "/vagrant", disabled: true
+  config.vm.synced_folder ".", "/home/vagrant/val3dity"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+
+  config.vm.provider "virtualbox" do |vb|
+    # Display the VirtualBox GUI when booting the machine
+    # vb.gui = true
+
+    # Customize the amount of memory and CPUs on the VM:
+    vb.memory = 2048
+    vb.cpus = 2
+  end
+
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # Enable provisioning with a shell script. Additional provisioners such as
+  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
+  # documentation for more information about their specific syntax and use.
+#  config.vm.provision "shell", path: "VagrantProvisionDebian9.sh"
+  config.vm.provision "shell", path: "VagrantProvisionUbuntu1604.sh"
+end

changelog.md

@@ -1,6 +1,15 @@
 
 # Changelog
 
+## [Unreleased]
+- validation of IndoorGML features 
+
+## [2.1.0] - 2018-02-14
+### Changed
+- the report is slightly changed: the CityObjects/Primitives subdivision in the report is replaced by Features having Primitives, where Features are the top-level objects, containing one or many Primitives. This is done to allow other data model to be used as input, eg IndoorGML is coming soon!
+### Added
+- pytest allows to specify the binary to use if not under 'build/'
+
 ## [2.0.4] - 2018-01-26
 ### Changed
 - fixed bug where inner rings of gml:Polygon wasn't read properly when that polygon is referenced by an XLink.