Release version 1.0.2

.gitlab-ci.yml

@@ -24,11 +24,27 @@ check_license:
   script:
     - reuse lint
 
+# The develop branch should reset the version to "0.0.0" so that there can
+# never be a confusion with a released version. Compare CONTRIBUTING.md.
+check_develop_version:
+  image: debian:stable-slim
+  stage: lint
+  rules:
+    # Only execute on tags that look like a version, e.g.: "0.5.1"
+    - if: '$CI_COMMIT_BRANCH == "develop"'
+      when: always
+  script:
+    - echo "If this fails, check the version is reset to '0.0.0' in CITATION.cff and CMakeLists.txt."
+    - test "0.0.0" == $(grep "^\s*VERSION" CMakeLists.txt | grep -oP '\d+\.\d+\.\d+.*')
+    - test "0.0.0" == $(grep "^version\s*:" CITATION.cff | grep -oP '\d+\.\d+\.\d+.*')
+    - echo "'date-released:' in CITATION.cff should be unset."
+    - grep --silent "^date-released\s*:\s*$" CITATION.cff
+
 # Check that the tag matches the version in the CMakeLists.txt file.
 # If the tag doesn’t match, you will need to change CMakeLists.txt and
 # forcefully move the tag to the corrected commit.
-check_version:
-  image: ubuntu:latest
+check_release_version:
+  image: debian:stable-slim
   stage: lint
   rules:
     # Only execute on tags that look like a version, e.g.: "0.5.1"
@@ -37,6 +53,8 @@ check_version:
   script:
     - echo "If this fails, check that the Git tag matches VERSION in CMakeLists.txt."
     - test "$CI_COMMIT_TAG" == $(grep "^\s*VERSION" CMakeLists.txt | grep -oP '\d+\.\d+\.\d+.*')
+    - echo "If this fails, check that the Git tag matches version in CITATION.cff"
+    - test "$CI_COMMIT_TAG" == $(grep "^version\s*:" CITATION.cff | grep -oP '\d+\.\d+\.\d+.*')
 
 # Check that all files are correctly formatted according to ".clang-format".
 # Exclude the "external/" directory because they will use different formatting.
@@ -76,6 +94,11 @@ compile:
       - build/megafauna_unit_tests
     expire_in: 20 minutes
 
+# Compare the Sphinx instructions in "docs/sphinx/conf.py".
+# TODO: Currently (2021-05-05), the Docker image "readthedocs/build:latest"
+# (7.0) is based on Ubuntu 18.04. It does not contain the required Doxygen
+# version 1.8.16 yet. As soon as the readthedocs image is properly updated,
+# we should use it here in the CI.
 doxygen:
   image: ubuntu:latest
   stage: build
@@ -102,7 +125,7 @@ doxygen:
       - build/docs/html/
 
 unit_tests:
-  image: ubuntu:latest
+  image: gcc:latest
   stage: test
   needs: ["compile"]
   script:
@@ -112,7 +135,7 @@ unit_tests:
 # Check that the linter works and that the example instruction files are
 # correct.
 linter:
-  image: ubuntu:latest
+  image: gcc:latest
   stage: test
   needs: ["compile"]
   script:
@@ -138,7 +161,7 @@ linter:
     - (./build/megafauna_insfile_linter tests/bad_insfiles/two_hfts_with_same_name.toml 2>&1 || true) | grep -iq 'HFT.*is defined twice'
 
 memcheck:
-  image: ubuntu:latest
+  image: gcc:latest
   stage: test
   needs: ["compile"]
   before_script:
@@ -167,7 +190,7 @@ memcheck:
       - build/memcheck.log
 
 demo_simulation:
-  image: ubuntu:latest
+  image: gcc:latest
   stage: test
   needs: ["compile"]
   script:

CHANGELOG.md

@@ -12,6 +12,15 @@ The format is based on [Keep a Changelog][] by Olivier Lacan, and this project a
 [Keep a Changelog]: <https://keepachangelog.com/en/1.0.0/>
 [Semantic Versioning]: <https://semver.org/spec/v2.0.0.html>
 
+## [1.0.2] - 2021-05-05
+
+### Changed
+- Increase demo simulation years so we can see some population ups and downs.
+
+### Fixed
+- The unit tests were broken after the last release.
+- cpptoml wouldn’t compile with latest `g++` (11.1.0).
+
 ## [1.0.1] - 2021-04-29
 
 ### Fixed
@@ -203,7 +212,8 @@ The format is based on [Keep a Changelog][] by Olivier Lacan, and this project a
 [Illius & O’Connor (2000)]: <https://doi.org/10.2307/3800911>
 [Taylor et al. (1981)]: <https://doi.org/10.1017/S0003356100040617>
 
-[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.1...develop
+[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.2...develop
+[1.0.1]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.1...1.0.2
 [1.0.1]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.0...1.0.1
 [1.0.0]: https://github.com/wtraylor/modular_megafauna_model/compare/0.6.0...1.0.0
 [0.6.0]: https://github.com/wtraylor/modular_megafauna_model/compare/0.5.5...0.6.0

CITATION.cff

@@ -10,9 +10,9 @@ authors:
     affiliation: Senckenberg Biodiversity and Climate Research Centre
     orcid: https://orcid.org/0000-0003-4925-7248
 title: "Modular Megafauna Model"
-version: 1.0.1
+version: 1.0.2
 # This DOI represents all versions, and will always resolve to the latest one.
 doi: 10.5281/zenodo.4710254
-date-released: 2021-04-29
+date-released: 2021-05-05
 license: LGPL-3.0-or-later
 repository-code: https://github.com/wtraylor/modular_megafauna_model

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required (VERSION 3.10)
 project ("Modular Megafauna Model"
   # This version must match exactly the Git tag!
   # Compare the "check_version" job in ".gitlab-ci.yml".
-  VERSION 1.0.1
+  VERSION 1.0.2
   DESCRIPTION "A physiological, dynamic herbivore simulator in C++."
   LANGUAGES CXX
   )

README.md

@@ -7,6 +7,7 @@ SPDX-License-Identifier: CC-BY-4.0
 [![LGPL logo](docs/images/lgpl.svg)](https://choosealicense.com/licenses/lgpl-3.0/)
 [![REUSE-compliant](docs/images/reuse-compliant.svg)][REUSE]
 [![Documentation Status](https://readthedocs.org/projects/modular-megafauna-model/badge/?version=latest)](https://modular-megafauna-model.readthedocs.io/en/latest/?badge=latest)
+[![Pipeline Status](https://gitlab.com/wtraylor/modular_megafauna_model/badges/master/pipeline.svg)](https://gitlab.com/wtraylor/modular_megafauna_model/-/commits/master)
 [![DOI](docs/images/zenodo_doi.svg)](https://zenodo.org/badge/latestdoi/228426088)
 
 [REUSE]: https://reuse.software
@@ -43,8 +44,7 @@ This project follows the [Pitchfork Layout](https://github.com/vector-of-bool/pi
 - `include/`: Public API header files.
 - `LICENSES/`: Folder with licenses, compliant with [REUSE][].
 - `src/`: Source and (private) header files of the project. Subdirectories correspond to C++ namespaces.
-- `tests/`: Unit tests.
-    - `tests/bad_insfiles/`: Example erroneous example files, each of which should throw an error.
+- `tests/`: Unit tests and test scripts.
 - `tools/`: Different helper tools for the developer.
 
 Usage

examples/demo_simulation.toml

@@ -9,7 +9,7 @@
 [general]
 
 # Number of simulation years. [1,∞)
-years = 20
+years = 100
 
 # Number of habitat groups.
 habitat_groups = 2

external/cpptoml/include/cpptoml.h

@@ -14,6 +14,7 @@
 #include <cstring>
 #include <fstream>
 #include <iomanip>
+#include <limits>
 #include <map>
 #include <memory>
 #include <sstream>

src/Fauna/get_forage_demands.test.cpp

@@ -22,9 +22,6 @@ TEST_CASE("Fauna::calc_allometry()") {
 
   // Typical case without error.
   REQUIRE_NOTHROW(calc_allometry(GivenPointAllometry({0.75, Y}), 10, 8));
-  // Exponent <= 0
-  CHECK_THROWS(calc_allometry(GivenPointAllometry({-0.1, Y}), 10, 10));
-  CHECK_THROWS(calc_allometry(GivenPointAllometry({0, Y}), 10, 10));
   // Body mass <= 0
   CHECK_THROWS(calc_allometry(GivenPointAllometry({0.75, Y}), 0, 10));
   CHECK_THROWS(calc_allometry(GivenPointAllometry({0.75, Y}), 10, 0));

src/Fauna/hft.h

@@ -432,7 +432,7 @@ struct Hft {
   /** @{ \name "digestion": Digestion-related parameters. */
   /// Parameters for \ref DigestiveLimit::Allometric
   /** See documentation in \ref DigestiveLimit::Allometric.*/
-  GivenPointAllometry digestion_allometric = {0.05, -0.25};
+  GivenPointAllometry digestion_allometric = {-0.25, 0.05};
 
   /// Factor to change ruminant digestibility for other digestion types.
   /**
@@ -530,7 +530,7 @@ struct Hft {
    * \see \ref ExpenditureComponent::FieldMetabolicRate
    * \see \ref DigestiveLimit::FixedFraction
    */
-  GivenPointAllometry expenditure_basal_rate = {7.5, 0.75};
+  GivenPointAllometry expenditure_basal_rate = {0.75, 7.5};
 
   /// Energy expenditure components, summing up to actual expenditure.
   std::set<ExpenditureComponent> expenditure_components = {