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.gitlab-ci.yml
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# SPDX-FileCopyrightText: 2020 W. Traylor <[email protected]>
#
# SPDX-License-Identifier: LGPL-3.0-or-later
stages:
- lint
- build
- test
- postprocess
variables:
# Install packages without user interaction.
DEBIAN_FRONTEND: "noninteractive"
# 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
# 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:
- test "0.0.0" == $(grep "^version\s*:" CITATION.cff | grep -oP '\d+\.\d+\.\d+.*')
- grep --silent "^date-released\s*:\s*$" CITATION.cff
- test "0.0.0" == $(grep '"version"' codemeta.json | grep -oP '\d+\.\d+\.\d+')
- grep --silent '"dateModified":\s*""' codemeta.json
- test "0.0.0" == $(grep "^\s*VERSION" CMakeLists.txt | grep -oP '\d+\.\d+\.\d+.*')
# Check that the tag matches the version in the CMakeLists.txt file.
# If the tag doesn’t match, you will need to change CMakeLists.txt and
# forcefully move the tag to the corrected commit.
check_release_version:
image: debian:stable-slim
stage: lint
rules:
# Only execute on tags that look like a release version, e.g., "0.5.1".
# Prerelease versions (e.g., "1.2.0-alpha.1" or "1.2.0-beta.3") are not
# required to have the version as metadata.
- if: '$CI_COMMIT_TAG =~ /^\d+\.\d+\.\d+/'
when: always
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" == $(grep "^version\s*:" CITATION.cff | grep -oP '\d+\.\d+\.\d+.*')
- echo "If this fails, check that the Git tag matches version in codemeta.json."
- test "$CI_COMMIT_TAG" == $(grep '"version"' codemeta.json | 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.
clang-format:
image:
name: mikedld/clang-format:12-latest # Update this to later clang versions as necessary.
entrypoint: [""]
stage: lint
script:
# We need to use simple BusyBox `find` syntax here.
- >
clang-format --dry-run --Werror
$(find src/ -iname '*.cpp' -or -iname '*.h')
$(find docs/ -iname '*.cpp' -or -iname '*.h')
$(find include/ -iname '*.cpp' -or -iname '*.h')
$(find tests/ -iname '*.cpp' -or -iname '*.h')
$(find tools/ -iname '*.cpp' -or -iname '*.h')
compile:
image: gcc:latest
stage: build
before_script:
- apt-get update -qq
- apt-get install -y -qq cmake
script:
- mkdir --parents build
- cp examples/demo_simulation.toml build/
- cd build
- cmake
-DBUILD_TESTING=ON
-DBUILD_DEMO_SIMULATOR=ON
-DBUILD_DOC=OFF ..
- make --jobs=6
megafauna_demo_simulator
megafauna_insfile_linter
megafauna_unit_tests
artifacts:
paths:
- build/demo_results.Rmd
- build/demo_simulation.toml
- build/megafauna.toml
- build/megafauna_demo_simulator
- build/megafauna_insfile_linter
- build/megafauna_unit_tests
expire_in: 20 minutes
# Compare the Sphinx instructions in "docs/sphinx/conf.py".
doxygen:
image: readthedocs/build:latest
stage: build
before_script:
- conda install --yes cmake
- conda install --yes --channel conda-forge doxygen
- PATH=$HOME/.conda/bin:$PATH
script:
- mkdir --parents build
- cd build
- cmake
-DSTOP_DOXYGEN_ON_WARNING=ON
-DBUILD_TESTING=OFF
-DBUILD_DEMO_SIMULATOR=OFF
-DBUILD_DOC=ON ..
- make --jobs=6 megafauna_docs
artifacts:
paths:
- build/docs/html/
unit_tests:
image: gcc:latest
stage: test
needs: ["compile"]
script:
- cd build
- ./megafauna_unit_tests
# Test coverage for codecov.io
# The environment variable "CODECOV_TOKEN" must be provided. Compare:
# <https://docs.codecov.io/docs/about-the-codecov-bash-uploader#upload-token>
# <https://docs.gitlab.com/ce/ci/variables/README.html#project-cicd-variables>
code_coverage:
image: gcc:latest
stage: test
needs: ["compile"]
before_script:
- apt-get update -qq
- apt-get install -y -qq cmake gcovr
script:
- mkdir --parents build
- cd build
- cmake -DBUILD_TESTING=ON -DENABLE_COVERAGE=ON -DBUILD_DOC=OFF ..
- make --jobs=6 megafauna_unit_tests
- ./megafauna_unit_tests
- make --jobs=6 gcov
- bash <(curl -s https://codecov.io/bash) -X gcov
# Check that the linter works and that the example instruction files are
# correct.
linter:
image: gcc:latest
stage: test
needs: ["compile"]
script:
# Create a symbolic link in order to shorten instructions.
- ln -s ./build/megafauna_insfile_linter lint
# GOOD FILES:
- ./lint examples/megafauna.toml
- for f in tests/good_insfiles/*.toml; do ./lint $f; done
- ./lint tests/good_insfiles/legacy_massdensity_per_hft.toml 2>&1 | grep -i 'mass_density_per_hft.*deprecated'
# BAD FILES:
# These checks could be done with the catch framework, too
# (CHECK_THROWS_AS). That would be more flexible than checking for a
# specific error message in STDERR.
# Check *all* bad instruction files:
- for f in tests/bad_insfiles/*.toml; do
echo;
echo $f;
(! ./lint $f);
done
# Check for specific error messages:
# Note that commands that expected to fail need to be executed in a
# subshell like this: `(command || true)`
- (./lint tests/bad_insfiles/breeding_start_ambiguous.toml 2>&1 || true) | grep -iq 'breeding_season\.start.*ambiguous'
- (./lint tests/bad_insfiles/wrong_type_01.toml 2>&1 || true) | grep -iq 'body_mass\.female.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_02.toml 2>&1 || true) | grep -iq 'body_mass\.female.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_03.toml 2>&1 || true) | grep -iq 'output\.text_tables\.tables.*wrong type.*expected array of string'
- (./lint tests/bad_insfiles/wrong_type_04.toml 2>&1 || true) | grep -iq 'expenditure\.components.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_05.toml 2>&1 || true) | grep -iq 'mortality\.factors.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_06.toml 2>&1 || true) | grep -iq 'simulation\.establishment_interval.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_07.toml 2>&1 || true) | grep -iq 'output\.text_tables\.precision.*wrong type'
- (./lint tests/bad_insfiles/wrong_type_08.toml 2>&1 || true) | grep -iq 'body_mass\.female.*wrong type'
- (./lint tests/bad_insfiles/two_groups_with_same_name.toml 2>&1 || true) | grep -iq 'group.*is defined twice'
- (./lint tests/bad_insfiles/two_hfts_with_same_name.toml 2>&1 || true) | grep -iq 'HFT.*is defined twice'
memcheck:
image: gcc:latest
stage: test
needs: ["compile"]
before_script:
- apt-get update -qq
- apt-get install -y -qq valgrind
script:
- cd build
# Only run two years:
- sed -e 's/^\s*years\s*=.*/years = 2/' --in-place
demo_simulation.toml
# The following command needs to be quoted as a whole so that the YAML
# parser does not interpret the "|" special character.
- "valgrind
--leak-check=full
--show-leak-kinds=all
--track-origins=yes
--verbose
./megafauna_demo_simulator
megafauna.toml
demo_simulation.toml
| tee memcheck.log"
# If the error summary has not zero errors, the grep command will fail.
# Note that the "!" doesn’t work without starting a subshell with
# parentheses. Compare <https://stackoverflow.com/a/53753605>.
- "(! grep --silent 'ERROR SUMMARY: 0 errors' memcheck.log)"
artifacts:
paths:
- build/memcheck.log
demo_toml_files:
image: gcc:latest
stage: test
needs: ["compile"]
script:
- (! ./build/megafauna_demo_simulator
"tests/good_insfiles/two_hfts_01.toml"
"tests/bad_demosim_insfiles/habitats_not_multiple_of_hfts_01.toml");
- "rm -f *.tsv"
# Without HFTs, the option "one_hft_per_habitat" has no effect.
- ./build/megafauna_demo_simulator
"tests/good_insfiles/no_hfts_02.toml"
"tests/bad_demosim_insfiles/habitats_not_multiple_of_hfts_01.toml";
- "rm -f *.tsv"
- (! ./build/megafauna_demo_simulator
"good_insfiles/two_hfts_01.toml"
"tests/bad_demosim_insfiles/habitats_not_multiple_of_hfts_02.toml");
- "rm -f *.tsv"
- ./build/megafauna_demo_simulator
"tests/good_insfiles/two_hfts_01.toml"
"tests/good_demosim_insfiles/habitats_is_multiple_of_hfts_01.toml";
- "rm -f *.tsv"
# A simulation should run without HFTs and still produce (non-herbivore)
# output.
- ./build/megafauna_demo_simulator
"tests/good_insfiles/no_hfts_01.toml"
"tests/good_demosim_insfiles/minimal.toml";
- test -f available_forage.tsv
- test -f digestibility.tsv
- (! test -f body_fat.tsv)
- (! test -f eaten_forage_per_ind.tsv)
- (! test -f eaten_nitrogen_per_ind.tsv)
- (! test -f individual_density.tsv)
- (! test -f mass_density.tsv)
demo_simulation:
image: gcc:latest
stage: test
needs: ["compile"]
script:
- cd build
- ./megafauna_demo_simulator
"megafauna.toml"
"demo_simulation.toml"
artifacts:
paths:
- build/demo_results.Rmd
# All output files necessary for plotting demo results:
- build/available_forage.tsv
- build/body_fat.tsv
- build/digestibility.tsv
- build/eaten_forage_per_ind.tsv
- build/eaten_nitrogen_per_ind.tsv
- build/individual_density.tsv
- build/mass_density.tsv
expire_in: 20 minutes
plot_demo_results:
# This job should match the quickstart guide in the README.md.
image: r-base:latest
stage: postprocess
needs: ["demo_simulation"]
before_script:
- apt-get update -qq
- apt-get install -y -qq pandoc
- Rscript -e 'install.packages("rmarkdown")'
script:
- cd build
- Rscript -e "rmarkdown::render('demo_results.Rmd')"
- test -f "demo_results.html"
artifacts:
paths:
- build/demo_results.html