Merge of Shingle 2.0 branch

.gitignore

@@ -0,0 +1,40 @@
+RTopo105b_50S.nc
+libspud.so
+*.pyc
+*.pkl
+*.shc
+spud/
+tool/spud-preprocess
+lib
+ref
+bin
+shingle.log
+.DS_Store
+
+dataset
+test/Amundsen_Sea/Amundsen_Sea.geo
+test/Antarctica_all/Antarctica_all.geo
+test/Antarctica_main_landmass/Antarctica_main_landmass.geo
+test/Antarctica_main_landicemass/Antarctica_main_landicemass.geo
+test/Antarctica_main_landicemass_30s/Antarctica_main_landicemass_30s.geo
+test/Filchner-Ronne/Filchner-Ronne.geo
+test/Filchner-Ronne_back/Filchner-Ronne_back.geo
+
+test/legacy/amundsen_sea/
+test/legacy/antarctica_all/
+test/legacy/filchner-ronne/
+test/legacy/antarctica_main_landicemass/
+test/legacy/antarctica_main_landicemass_30s/
+test/legacy/filchner-ronne_back/
+
+test/*/*.geo
+test/*/*.msh
+test/*/*.png
+test/*/data/*.nc
+
+test/Caribbean/data/Caribbean_valid.geo
+test/Caribbean_main_coastline/data/Caribbean_main_coastline_valid.geo
+
+shingle/unittest/output.brml
+shingle/unittest/output.msh
+

.travis.yml

@@ -1,9 +1,45 @@
 language: python
 python:
   - "2.7"
+sudo: required
+#install: "pip install -r requirements.txt"
+#before_install:
+#  - sudo apt-get -qq update
+#  - sudo apt-get install -y -qq python-numpy python-scientific python-matplotlib
+addons:
+  apt:
+    packages:
+      - python-numpy
+      - python-scientific
+      - python-matplotlib
+      - gcc
+      - g++
+      - gfortran
+      - tree
 virtualenv:
   system_site_packages: true
-before_install:
- - sudo apt-get install -qq python-numpy python-scientific python-matplotlib
-#install:
-script: make testwithdatadownload
+install:
+  - pip install numpy matplotlib pyproj Pydap shapely Pillow
+before_script:
+  - sudo apt-get install -qq python-numpy python-scientific python-matplotlib gmsh
+  - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/:$HOME/build/shingleproject/Shingle/lib/spud/:$HOME/build/shingleproject/Shingle/spud/.libs/:$HOME/build/lib.linux-x86_64-2.7/"
+  - export LIBRARY_PATH="$LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/:$HOME/build/shingleproject/Shingle/spud/:$HOME/build/shingleproject/Shingle/spud/.libs/:$HOME/build/lib.linux-x86_64-2.7/"
+# - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/"
+# - export LIBRARY_PATH="$LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/"
+script:
+  - pip install numpy matplotlib pyproj Pydap shapely Pillow pytest
+  - python -c 'import Scientific.IO'
+  - ./configure
+  - make
+  - make installpackage
+  - make unittest
+  - make test
+#before_script:
+#  - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/"
+#  - export LIBRARY_PATH="$LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/"
+# - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/:$HOME/build/shingleproject/Shingle/lib/spud/:$HOME/build/shingleproject/Shingle/spud/.libs/:$HOME/build/lib.linux-x86_64-2.7/"
+# - export LIBRARY_PATH="$LIBRARY_PATH:$HOME/build/shingleproject/Shingle/lib/:$HOME/build/shingleproject/Shingle/spud/:$HOME/build/shingleproject/Shingle/spud/.libs/:$HOME/build/lib.linux-x86_64-2.7/"
+#script:
+#  - ./configure
+#  - make 
+#  - find . -iname libspud* -print -exec nm -g {} \; 

COPYING

@@ -0,0 +1,45 @@
+Except as noted below, Shingle is copyright (C) 2011 - 2017
+Adam S. Candy and others. For a full list of contributors see the
+AUTHORS file.
+
+Shingle is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 3.0 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+The complete text of the GNU Lesser General Public License can be
+found in the file `LGPL-3.0'.
+
+-----
+
+Copyright and licence information for libspud is to be found in the
+file spud/COPYING.  Libspud makes use of Tinyxml and its notice is
+provided below.
+
+-----
+
+Tinyxml is copyright (c) 2000-2006 Lee Thomason (www.grinninglizard.com)
+
+This software is provided 'as-is', without any express or implied
+warranty. In no event will the authors be held liable for any
+damages arising from the use of this software.
+
+Permission is granted to anyone to use this software for any
+purpose, including commercial applications, and to alter it and
+redistribute it freely, subject to the following restrictions:
+
+1. The origin of this software must not be misrepresented; you must
+not claim that you wrote the original software. If you use this
+software in a product, an acknowledgment in the product documentation
+would be appreciated but is not required.
+
+2. Altered source versions must be plainly marked as such, and
+must not be misrepresented as being the original software.
+
+3. This notice may not be removed or altered from any source
+distribution.

MANIFEST.in

@@ -0,0 +1,13 @@
+include MANIFEST MANIFEST.in README.md AUTHORS COPYING LGPL-3.0
+include setup.py
+include schema/shingle_options.rng
+recursive-include shingle/ *.py
+recursive-include shingle/ *.so
+
+recursive-include spud/include/ *.h
+include spud/include/*.h
+
+prune dataset
+recursive-exclude dataset/ *
+
+

Makefile

@@ -66,16 +66,28 @@ manual:
 package:
 	@$(ECHO) 'PACKAGE shingle'
 	@python setup.py sdist bdist_wheel
-	@$(ECHO) 'PACKAGE diamond'
-	@cd spud/diamond; python setup.py sdist; cp -rp dist/* ../../dist/; cd ../..
+	@$(ECHO) 'PACKAGE dxdiff'
+	@cd spud/dxdiff; python setup.py sdist; cp -rp dist/* ../../dist/; cd ../..
+	#@$(ECHO) 'PACKAGE diamond'
+	#@cd spud/diamond; python setup.py sdist; cp -rp dist/* ../../dist/; cd ../..
 
 packageupload:
 	@$(ECHO) 'PACKAGE UPLOAD shingle'
 	@python setup.py register -r $(PYPI)
 	@python setup.py sdist bdist_wheel upload -r $(PYPI)
+	@$(ECHO) 'PACKAGE UPLOAD dxdiff'
+	@cd spud/dxdiff; python setup.py register -r $(PYPI); python setup.py sdist upload -r $(PYPI); cp -rp dist/* ../../dist/; cd ../..
 	@$(ECHO) 'PACKAGE UPLOAD diamond'
 	@cd spud/diamond; python setup.py register -r $(PYPI); python setup.py sdist upload -r $(PYPI); cp -rp dist/* ../../dist/; cd ../..
 
+installpackage: package
+	@$(ECHO) 'INSTALL shingle Python library'
+	@pip install ./dist/shingle-*.tar.gz
+	@$(ECHO) 'INSTALL dxdiff'
+	@pip install ./dist/dxdiff-*.tar.gz
+	#@$(ECHO) 'INSTALL diamond'
+	#@pip install ./dist/spud-diamond-*.tar.gz
+
 test: bin/shingle datalocal
 	@./bin/shingle -t test
 
@@ -110,7 +122,7 @@ datalink:
 testwithdatadownload:
 	@$(MAKE) -s -C test/legacy testwithdatadownload
 
-.PHONY: test testlegacy data datalink testwithdatadownload schema doc datalocal
+.PHONY: test testlegacy data datalink testwithdatadownload schema doc datalocal package
 
 # ------------------------------------------------------------------------
 
@@ -120,8 +132,11 @@ libspud: lib/libspud.so
 lib/libspud.so:
 	@mkdir -p lib
 	@$(MAKE) -C spud install-pyspud
-	@cp lib/python*/site-packages/libspud.so lib/
-	@cp lib/python*/site-packages/libspud.so shingle/
+	@cd lib; ln -sf libspud.so libspud.so.0; cd ..
+	@cd shingle; ln -sf libspud.so libspud.so.0; cd ..
+
+#@cp lib/python*/site-packages/libspud.so lib/
+#@cp lib/python*/site-packages/libspud.so shingle/
 
 # ------------------------------------------------------------------------
 

README.md

@@ -1,91 +1,50 @@
 Shingle
 =======
 
-Generation of boundary representation from arbitrary geophysical fields.
-
-For further information and updates, please contact the author Dr Adam S. Candy at [email protected].
+Generalised self-consistent and automated domain discretisation for multi-scale geophysical models.
 
 ![Shingle](./data/shingle.png?raw=true "Shingle")
 
-Outline web page: [http://adamcandy.github.io/Shingle](http://adamcandy.github.io/Shingle "Shingle")
+LibShingle: Computational research software library providing a high-level abstraction to spatial discretisation, or mesh generation, for domains containing complex, fractal-like boundaries that characterise those in numerical simulations of geophysical dynamics.  This is accompanied by a compact, shareable and necessarily complete description of the domain discretisation.
+
+Geophysical model domains typically contain irregular, complex fractal-like boundaries and physical processes that act over a wide range of scales. Constructing geographically constrained boundary-conforming spatial discretisations of these domains with flexible use of anisotropic, fully unstructured meshes is a challenge. The problem contains a wide range of scales and a relatively large, heterogeneous constraint parameter space. Approaches are commonly ad hoc, model or application specific and insufficiently described. Development of new spatial domains is frequently time-consuming, hard to repeat, error prone and difficult to ensure consistent due to the significant human input required. As a consequence, it is difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. Moreover, for flexible unstructured meshes, there is additionally a greater potential for inconsistencies in model initialisation and forcing parameters. This library introduces a consistent approach to unstructured mesh generation for geophysical models, that is automated, quick-to-draft and repeat, and provides a rigorous and robust approach that is consistent to the source data throughout. The approach is enabling further new research in complex multi-scale domains, difficult or not possible to achieve with existing methods.
+
+Outline web page: [http://shingleproject.org](http://shingleproject.org "Shingle")
+
+Further details are provided in the library source and [Shingle project manual](http://homepage.tudelft.nl/w8w0h/4fcf65d8/shingle_manual.pdf "Shingle manual").
+
+For further information and updates, please contact the lead author Dr Adam S. Candy at [email protected].
 
 Build status
 ------------
 
-[![Build Status](https://secure.travis-ci.org/adamcandy/Shingle.png)](http://travis-ci.org/adamcandy/Shingle)
+[![Build Status](https://travis-ci.org/shingleproject/Shingle.svg?branch=master)](http://travis-ci.org/shingleproject/Shingle)
 
 Example geophysical domains
 ---------------------------
 
-A selection of geophysical domains where Shingle has been applied to generate the boundary representation.
-This description is then meshed using [Gmsh](http://geuz.org/gmsh "Gmsh").
+A selection of geophysical domains where Shingle has been applied to describe and generate geophysical domain spatial discretisation.
 
 ![Shingle examples](./data/shingleexamples.jpg?raw=true "Shingle examples")
 
-Outline
--------
-
-A new meshing approach for realistic domains.
-
-This code generates boundary representations with elemernt identifications from arbitrary geophysical fields.  It was originally used  mask to generate a boundary along the coastlines and grounding line* (which is not positioned at a constant depth).  The code is easily applied to boundaries along depth contours and to work with other NetCDF sources.
-
-The new approach uses contouring routines (as opposed to the GSHHS Gmsh plugin, or a GMT approach).  It would be useful to test this new code on a wide range of regions - particularly to check the contouring routines are behaving satisfactorily.  It works very well in the Antarctic region (including the region inside ice shelf cavities). 
-
-The dependencies are all Python modules (e.g. GMT is not required).
-
- * which involves a neat trick with modulo arithmetic to keep calculation time down significantly.
-
-Supported features
-------------------
-
-  - Generate boundary representation from raw raster input (e.g. a NetCDF data file),
-  - Regions defined by arbitrary functions of longitude and latitude (given on the command line),
-  - Simpler definition of regions by boxes (such as 'longmin:longmax,latmin:longmax'),
-  - Define included paths by Gmsh ID number (useful to include or exclude  specific islands/land masses),
-  - Deals with multiple open boundaries,
-  - Islands and boundaries split by the global boundary are treated,
-  - Automatically closes boundaries with parallels and meridians (with a prescribed length step),
-  - Applies different boundary IDs on open and closed boundaries,
-  - Exclude smaller islands - restricted by a given minimum area,
-  - Option to extend domain in latitude on open boundaries (e.g. for sponge regions, or large open regions in the open ocean),
-  - Command line used is saved in the Gmsh .geo file for reference,
-  - Projection type (e.g. options to generate a mesh to UTM coordinates, 
-  - Option to generate the ACC average track line (and then to refine the mesh to this).
-  - Ice shelf inclusion options
-
-Development version
--------------------
-
-A development version of the code also has:
-  - Caching of contours (which can save a lot of processing time)
-  - Graphical output of contouring stage, to aid in contour selection
-
-
-Other updates
--------------
-
-  - Consistent use of dx_default,
-  - The Antarctica main example contour can now be meshed (uses dx=10 in the parallel creation now),
-  - Renamed the variables associated with the inclusion of the ice shelf ocean cavities to be more intuitive.
-
-Test suite
+Objectives
 ----------
 
-Currently there are six tests in the test suite:
-  - amundsen_sea
-  - antarctica_all
-  - antarctica_main_landmass
-  - antarctica_main_landmass_30s
-  - filchner-ronne
-  - filchner-ronne_iceshelf
+1. Introduce a consistent approach to the generation of boundary representation to arbitrary geoid bounds.
+2. A user-friendly, accessible and extensible framework for model-independent geophysical domain mesh generation.
+3. An intuitive, hierarchical formal grammar to fully describe and share the full heterogeneous set of constraints for the spatial discretisation of geophysical model domains.
+4. Natural language basis for describing geophysical domain features.
+5. Self-consistent, scalable, automated and efficient mesh prototyping.
+6. Platform for iterative development that is repeatable, reproducible with a provenance history of generation.
+7. Enabling rigorous unstructured mesh generation in general, for a wide range of geophysical applications, in a process that is automated, quick-to-draft and repeat, rigorous and robust, and consistent to the source data throughout.
+
+Verification test engine
+------------------------
+
+Includes a selection of examples, from a relatively straight-forward high-level GUI-driven interaction accessible to modellers new to mesh generation, to complex low-level development communicating with the LibShingle library.  Python interaction is used within the source, in generating documentation and in example Jupyter notebooks.
 
-Datasets
---------
+A verification test engine is continuously run in response to source code changes, some of which is tested under [http://travis-ci.org/shingleproject/Shingle](Travis "Travis").
 
-The above tests use the RTopo dataset, described in detail at: [http://doi.pangaea.de/10.1594/PANGAEA.741917](http://doi.pangaea.de/10.1594/PANGAEA.741917 "RTopo").
+An earlier version of the library Shingle 1.0 is available at: [https://github.com/shingleproject/Shingle1.0](https://github.com/shingleproject/Shingle1.0 "Shingle1.0"), with details on the [Shingle1.0 webpage](http://shingleproject.org/index_shingle1.0.html "Shingle1.0 webpage").
 
-Timmermann, R et al. (2010): Antarctic ice sheet topography, cavity geometry, and global bathymetry (RTopo 1.0.5-beta). doi:10.1594/PANGAEA.741917,
-Supplement to: Timmermann, Ralph; Le Brocq, Anne M; Deen, Tara J; Domack, Eugene W; Dutrieux, Pierre; Galton-Fenzi, Ben; Hellmer, Hartmut H; Humbert, Angelika; Jansen, Daniela; Jenkins, Adrian; Lambrecht, Astrid; Makinson, Keith; Niederjasper, Fred; Nitsche, Frank-Oliver; Nøst, Ole Anders; Smedsrud, Lars Henrik; Smith, Walter (2010): A consistent dataset of Antarctic ice sheet topography, cavity geometry, and global bathymetry. Earth System Science Data, 2(2), 261-273, doi:10.5194/essd-2-261-2010
 
-[![githalytics.com alpha](https://cruel-carlota.pagodabox.com/5494cf3263af78dea92487d951d530a8 "githalytics.com")](http://githalytics.com/adamcandy/Shingle)
-[![Bitdeli Badge](https://d2weczhvl823v0.cloudfront.net/adamcandy/shingle/trend.png)](https://bitdeli.com/free "Bitdeli Badge")

configure

@@ -0,0 +1,7 @@
+#! /bin/sh
+
+cd spud
+./configure --prefix=${PWD}/..
+#./configure
+cd ..
+

doc/Makefile

@@ -0,0 +1,31 @@
+
+MAKE = make
+ECHO = echo
+
+default: shingle_manual
+
+
+shingle_manual: verification_figures.tex
+	@echo BUILD shingle_manual
+	@$(MAKE) -s shingle_manual.pdf
+
+verification_figures.tex:
+	@echo BUILD verification_figures
+	@./compile_verification_test_images.py 
+
+%.pdf: %.tex
+	pdflatex -shell-escape $^
+	if fgrep "Rerun to" $*.log; then $(MAKE) --assume-new $^ $@;fi
+ifndef NOBIBTEX
+	if fgrep "There were undefined"  $*.log;\
+	then bibtex $*; \
+	$(MAKE) NOBIBTEX=true --assume-new $^ $@;fi
+endif
+
+clean: 
+	@rm -f *.{aux,log,bbl,blg,out,toc,pyg,thm}
+	@rm -f verification_figures.tex shingle_manual.pdf
+	@rm -rf _minted-shingle_manual
+
+.PHONY: verification_figures shingle_manual
+