r.pops.spread: Update to PoPS version 1.0.0 (#269)

Update to PoPS 1.0.0 release, i.e., the tag v1.0.0 in the ncsu-landscape-dynamics/r.pops.spread repo which in turn uses tag v1.0.0 in PoPS Core (ncsu-landscape-dynamics/pops-core).

https://github.com/ncsu-landscape-dynamics/r.pops.spread/releases/tag/v1.0.0
https://github.com/ncsu-landscape-dynamics/pops-core/releases/tag/v1.0.0

grass7/raster/r.pops.spread/CHANGELOG.md

@@ -4,6 +4,16 @@ All notable changes to this project should be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## 2020-04-16 - SEI model
+
+### Added
+
+- Add SEI modeling using model_type and latency_period parameters. (Vaclav Petras)
+
+### Changed
+
+- Reduced scope of mortality_simulation_year variable. (Vaclav Petras)
+
 ## 2018-09-18 - July 2019 improvements
 
 ### Changed

grass7/raster/r.pops.spread/CITATION.cff

@@ -1,5 +1,5 @@
 cff-version: 1.0.3
-message: If you use this software, please cite it as below.
+message: If you use this software, please cite it using the references in the readme (this file is outdated).
 authors:
   - family-names: Petras
     given-names: Vaclav

grass7/raster/r.pops.spread/Makefile

@@ -5,8 +5,8 @@ PGM = r.pops.spread
 LIBES = $(RASTERLIB) $(GISLIB) $(MATHLIB) $(VECTORLIB) $(DATETIMELIB)
 DEPENDENCIES = $(RASTERDEP) $(GISDEP) $(VECTORDEP) $(DATETIMEDEP)
 EXTRA_LIBS = $(GDALLIBS) $(OMPLIB)
-EXTRA_CFLAGS = $(GDALCFLAGS) -std=c++11 -Wall -Wextra -fpermissive $(OMPCFLAGS) $(VECT_CFLAGS)
-EXTRA_INC = $(VECT_INC)
+EXTRA_CFLAGS = $(GDALCFLAGS) -std=c++11 -Wall -Wextra -Werror=return-type -fpermissive $(OMPCFLAGS) $(VECT_CFLAGS)
+EXTRA_INC = $(VECT_INC) -Ipops-core/include
 
 include $(MODULE_TOPDIR)/include/Make/Module.make
 

grass7/raster/r.pops.spread/README.md

@@ -1,38 +1,75 @@
 # r.pops.spread
 
 This is a GRASS GIS module *r.pops.spread* for simulating spread of
-pests and pathogens.
+pests and pathogens. The module is a GRASS GIS interface to the PoPS
+(Pest or Pathogen Spread) model implemented in C++ library maintained
+in the [PoPS Core repository](https://github.com/ncsu-landscape-dynamics/pops-core).
 
-This is a GRASS GIS interface to PoPS (Pest or Pathogen Spread) model
-which is a C++ library maintained in this repository:
+The purpose of the *r.pops.spread* module is to provide easy way of
+running the model in GRASS GIS environment once you have calibrated
+the model for your purposes. You can obtain the calibration from a
+colleague or published work or you can calibrate the model manually (in
+GRASS GIS) or use the R interface to PoPS called
+[rpops](https://github.com/ncsu-landscape-dynamics/rpops) to do that.
 
-https://github.com/ncsu-landscape-dynamics/PoPS
+Note: Earlier versions of this module were called *r.spread.pest* and
+*r.spread.sod*.
 
-Note: Former names of the r.pops.spread are r.spread.pest and r.spread.sod.
+## How to cite
 
-## References
+If you use this software or code, please cite the following papers:
 
-Please, in addition to citing or acknowledging this software, cite the
-following papers:
+* Ross K. Meentemeyer, Nik J. Cunniffe, Alex R. Cook, Joao A. N. Filipe,
+  Richard D. Hunter, David M. Rizzo, and Christopher A. Gilligan, 2011.
+  Epidemiological modeling of invasion in heterogeneous landscapes:
+  spread of sudden oak death in California (1990–2030).
+  *Ecosphere* 2:art17.
+  [DOI: 10.1890/ES10-00192.1](https://doi.org/10.1890/ES10-00192.1)
 
-Ross K. Meentemeyer, Nik J. Cunniffe, Alex R. Cook, Joao A. N. Filipe,
-Richard D. Hunter, David M. Rizzo, and Christopher A. Gilligan 2011.
-Epidemiological modeling of invasion in heterogeneous landscapes:
-spread of sudden oak death in California (1990–2030).
-*Ecosphere* 2:art17.
-[DOI: 10.1890/ES10-00192.1](https://doi.org/10.1890/ES10-00192.1)
+* Tonini, Francesco, Douglas Shoemaker, Anna Petrasova, Brendan Harmon,
+  Vaclav Petras, Richard C. Cobb, Helena Mitasova,
+  and Ross K. Meentemeyer, 2017.
+  Tangible geospatial modeling for collaborative solutions
+  to invasive species management.
+  *Environmental Modelling & Software* 92: 176-188.
+  [DOI: 10.1016/j.envsoft.2017.02.020](https://doi.org/10.1016/j.envsoft.2017.02.020)
 
-Tonini, Francesco, Douglas Shoemaker, Anna Petrasova, Brendan Harmon,
-Vaclav Petras, Richard C. Cobb, Helena Mitasova,
-and Ross K. Meentemeyer.
-Tangible geospatial modeling for collaborative solutions
-to invasive species management.
-*Environmental Modelling & Software* 92 (2017): 176-188.
-[DOI: 10.1016/j.envsoft.2017.02.020](https://doi.org/10.1016/j.envsoft.2017.02.020)
+In case you are using the automatic management feature in rpops or the
+steering version of r.pops.spread (from the branch steering), please
+cite also:
 
-## Obtaining the latest code
+* Petrasova, A., Gaydos, D.A., Petras, V., Jones, C.M., Mitasova, H. and
+  Meentemeyer, R.K., 2020.
+  Geospatial simulation steering for adaptive management.
+  *Environmental Modelling & Software* 133: 104801.
+  [DOI: 10.1016/j.envsoft.2020.104801](https://doi.org/10.1016/j.envsoft.2020.104801)
 
-The PoPS library is in a submodule, so use `--recursive` when cloning,
+In addition to citing the above paper, we also encourage you to
+reference, link, and/or acknowledge specific version of the software
+you are using for example:
+
+* *We have used rpops R package version 1.0.0 from
+  <https://github.com/ncsu-landscape-dynamics/rpops>*.
+
+## Download
+
+### Download and install
+
+The latest release of the *r.pops.spread* module is available in GRASS GIS Addons repository
+and can be installed directly in GRASS GIS through graphical user
+interface or using the following command:
+
+```
+g.extension r.pops.spread
+```
+
+Alternatively, you can obtain latest source code here and install it
+from this repository (see below).
+
+### Source code download
+
+Just use Git, but note that the
+PoPS Core library is in a submodule, so use `--recursive` when cloning,
 for example:
 
 ```
@@ -45,7 +82,16 @@ If you have already cloned, you can obtain the submodules using:
 git submodule update --init
 ```
 
-## Updating submodule to latest version
+Note that downloading as ZIP won't include the source code for the submodule,
+so downloading as ZIP is not useful for this repo.
+
+## Contributing
+
+Please see the [pops-core](https://github.com/ncsu-landscape-dynamics/pops-core#readme) repository
+for contributing best practices and release policies.
+Other than that, just open pull requests against this repo.
+
+### Updating submodule to latest version
 
 To update the submodule, i.e. update submodule's commit used in this
 repository, use:
@@ -61,7 +107,7 @@ particular commit in the submodule repository (rather than the latest
 version). Git works this way to avoid breaking things unexpectedly due
 to changes in the submodule repository.
 
-## Updating the code of the submodule
+### Updating the code of the submodule
 
 ```
 cd pops
@@ -77,21 +123,20 @@ git commit pops -m "update to latest pops commit"
 git push
 ```
 
-
-
 ## The files
 
-The main.cpp contains the main program to run.
+The `main.cpp` file contains the main program to run.
+The model is in `pops-core/include/pops-core` directory.
 
 ## To run the model
 
 You can use Linux to run the model in the following way.
 
 Open an terminal and install dependencies:
 
-    sudo apt-get install grass-dev
+    sudo apt-get install grass grass-dev
 
-Download the model code as ZIP or using Git:
+Download this repo using Git (see above):
 
     git clone ...
 
@@ -103,20 +148,36 @@ Compile:
 
     grass --tmp-location XY --exec g.extension module=r.pops.spread url=.
 
-Run:
+Run (assuming you checked how to create a GRASS GIS mapset with our data):
 
     grass .../modeling/scenario1 --exec r.pops.spread ...
 
-## Authors
+## Authors and contributors
+
+### Authors
+
+_(alphabetical order)_
+
+* Chris Jones
+* Margaret Lawrimore
+* Vaclav Petras
+* Anna Petrasova
+
+### Previous contributors
+
+_(alphabetical order)_
 
-* Francesco Tonini (original R version)
-* Zexi Chen (initial C++ version)
-* Vaclav Petras (parallelization, GRASS interface, raster handling, ...)
-* Anna Petrasova (single species simulation)
+* Zexi Chen
+* Devon Gaydos
+* Francesco Tonini
 
-See [CHANGELOG.md](CHANGELOG.md) for details about contributions.
+See Git commit history, GitHub insights, or CHANGELOG.md file (if present)
+for details about contributions.
 
 ## License
 
-This program is free software under the GNU General Public License
-(>=v2). Read the file LICENSE for details.
+Permission to use, copy, modify, and distribute this software and its documentation
+under the terms of the GNU General Public License version 2 or higher is hereby
+granted. No representations are made about the suitability of this software for any
+purpose. It is provided "as is" without express or implied warranty.
+See the GNU General Public License for more details.