Release version 0.6.0

.clang-format.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+
+SPDX-License-Identifier: CC0-1.0

.editorconfig

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+#
+# SPDX-License-Identifier: CC0-1.0
+
 # EditorConfig is awesome: https://EditorConfig.org
 
 # top-most EditorConfig file

.gitignore

@@ -1,3 +1,10 @@
+# SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+#
+# SPDX-License-Identifier: CC0-1.0
+
 /build
 /build/
 valgrind_memcheck.log
+
+# Config for [YouCompleteMe](http://ycm-core.github.io/YouCompleteMe/#intro)
+.ycm_extra_conf.py

.gitlab-ci.yml

@@ -1,4 +1,9 @@
+# SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
+
 stages:
+  - lint
   - build
   - test
   - postprocess
@@ -10,6 +15,15 @@ variables:
 # The documentation and the source code are compiled separately so that the
 # pipeline can continue with the unit tests even if doxygen fails.
 
+# Check whether the project is REUSE compliant (https://reuse.software).
+check_license:
+  image:
+    name: fsfe/reuse:latest
+    entrypoint: [""]
+  stage: lint
+  script:
+    - reuse lint
+
 compile:
   image: gcc:latest
   stage: build

.reuse/dep5

@@ -0,0 +1,8 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Modular Megafauna Model (MMM)
+Upstream-Contact: Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+Source: https://github.com/wtraylor/modular_megafauna_model
+
+Files: external/cpptoml/*
+Copyright: 2014 Chase Geigle and CPPToml contributors
+License: MIT

CHANGELOG.md

@@ -1,7 +1,27 @@
+<!--
+SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+
 # Changelog
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) by Olivier Lacan, and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+The format is based on [Keep a Changelog][] by Olivier Lacan, and this project adheres to [Semantic Versioning][].
+
+[Keep a Changelog]: <https://keepachangelog.com/en/1.0.0/>
+[Semantic Versioning]: <https://semver.org/spec/v2.0.0.html>
+
+## [0.6.0] - 2021-04-08
+
+### Added
+- Invitation to Matrix room in README.
+
+### Fixed
+- Add licensing information. [#22]
+
+### Removed
+- Nitrogen retention by herbivores. The function `Habitat::add_excreted_nitrogen()` has been removed. The vegetation model must now handle recycling of nitrogen itself. This simplifies the code and reduces the number of parameters. Compare [#15]
 
 ## [0.5.5] - 2020-08-04
 
@@ -151,7 +171,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 - TOML instruction file reader.
 - Demo simulator with simple logistic grass growth.
 
-[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.5...develop
+[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/0.6.0...develop
+[0.6.0]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.5...0.6.0
 [0.5.5]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.4...0.5.5
 [0.5.4]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.3...0.5.4
 [0.5.3]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.2...0.5.3
@@ -174,6 +195,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 [#8]: https://github.com/wtraylor/modular_megafauna_model/issues/8
 [#9]: https://github.com/wtraylor/modular_megafauna_model/issues/9
 [#10]: https://github.com/wtraylor/modular_megafauna_model/issues/10
+[#15]: https://github.com/wtraylor/modular_megafauna_model/issues/15
+[#22]: https://github.com/wtraylor/modular_megafauna_model/issues/22
 [#25]: https://github.com/wtraylor/modular_megafauna_model/issues/25
 [#26]: https://github.com/wtraylor/modular_megafauna_model/issues/26
 [#28]: https://github.com/wtraylor/modular_megafauna_model/issues/28

CMakeLists.txt

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
+
 cmake_minimum_required (VERSION 3.10)
 project ("Modular Megafauna Model"
   VERSION 0.5.1
@@ -74,8 +78,6 @@ set (SOURCE_FILES
   src/Fauna/mortality_factors.h
   src/Fauna/net_energy_models.cpp
   src/Fauna/net_energy_models.h
-  src/Fauna/nitrogen.cpp
-  src/Fauna/nitrogen.h
   src/Fauna/parameters.cpp
   src/Fauna/parameters.h
   src/Fauna/population_interface.cpp
@@ -145,7 +147,6 @@ if (BUILD_TESTING)
     src/Fauna/insfile_reader.test.cpp
     src/Fauna/mortality_factors.test.cpp
     src/Fauna/net_energy_models.test.cpp
-    src/Fauna/nitrogen.test.cpp
     src/Fauna/parameters.test.cpp
     src/Fauna/reproduction_models.test.cpp
     src/Fauna/world.test.cpp

CONTRIBUTING.md

@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2020 Wolfgang Traylor <wolfgang.traylor@senckenberg.de>
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+
 # Contributing to the Codebase
 
 This document is a guide for developers who want to contribute to the megafauna library.
@@ -6,22 +12,27 @@ This document is only about *syntax* only.
 
 ## Table of Contents
 
-- [Version Control](#version-control)
-    - [Branches](#branches)
-    - [Release Versioning](#release-versioning)
-    - [Commit Messages](#commit-messages)
-    - [Continuous Integration](#continuous-integration)
-- [Coding Guidelines](#coding-guidelines)
-    - [Repository Structure](#repository-structure)
-    - [Code Format](#code-format)
-        - [Naming Code Elments](#naming-code-elements)
-        - [Ordering](#ordering)
-        - [File Header](#file-header)
-    - [Unit Tests](#unit-tests)
-    - [Code Checkers](#code-checkers)
-    - [Doxygen Documentation](#doxygen-documentation)
-        - [Markdown](#markdown)
-        - [BibTeX Bibliography](#bibtex-bibliography)
+<!-- vim-markdown-toc GFM -->
+
+* [Version Control](#version-control)
+    * [Branches](#branches)
+    * [Release Versioning](#release-versioning)
+    * [Commit Messages](#commit-messages)
+    * [Continuous Integration](#continuous-integration)
+* [Licensing](#licensing)
+* [Coding Guidelines](#coding-guidelines)
+    * [Repository Structure](#repository-structure)
+    * [Code Format](#code-format)
+        * [Naming Code Elements](#naming-code-elements)
+        * [Ordering](#ordering)
+        * [File Header](#file-header)
+    * [Unit Tests](#unit-tests)
+    * [Code Checkers](#code-checkers)
+    * [Doxygen Documentation](#doxygen-documentation)
+        * [Markdown](#markdown)
+        * [BibTeX Bibliography](#bibtex-bibliography)
+
+<!-- vim-markdown-toc -->
 
 ## Version Control
 
@@ -60,6 +71,15 @@ The CI script also runs [Valgrind](https://valgrind.org) memory check.
 With the bash script `tools/run_valgrind_memcheck` you can execute a memory check manually on your local machine.
 **Always make sure contributions to the codebase don’t have memory leaks.**
 
+## Licensing
+- Familiarize yourself with the REUSE standard in this tutorial: <https://reuse.software/tutorial/>
+- When you create a new file, add a REUSE license header with the same license as similar files in the project.
+- When you contribute to a file, add yourself as a copyright holder to the REUSE license header.
+- When you create a commit with Git, use the `-s/--signoff` flag in order to sign the [Developer Certificate of Origin][DCO]. This way you certify that you wrote or otherwise have the right to submit the code you’re contributing to the project.
+    - Just come into the habit of writing `git commit -s`.
+
+[DCO]: https://developercertificate.org/
+
 ## Coding Guidelines
 
 ### Repository Structure
@@ -151,11 +171,13 @@ Ususally the brief description will be the same for a `.h` and its `.cpp` file.
 If it is only one class in the header file, you can also copy the `\brief` description from that class.
 Here is an example:
 
+<!--TODO: REUSE header-->
+
 ```cpp
 /**
  * \file
  * \brief Management classes of herbivore populations.
- * \copyright <TODO: fill in license of the project>
+ * \copyright LGPL-3.0-or-later
  * \date <current year>
  */
 ```

LICENSES/BSL-1.0.txt

@@ -0,0 +1,23 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute, execute,
+and transmit the Software, and to prepare derivative works of the Software,
+and to permit third-parties to whom the Software is furnished to do so, all
+subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer, must
+be included in all copies of the Software, in whole or in part, and all derivative
+works of the Software, unless such copies or derivative works are solely in
+the form of machine-executable object code generated by a source language
+processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES
+OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.