Merge branch 'develop' into optimize_transpose

.github/workflows/test_install.yml

@@ -33,10 +33,6 @@ jobs:
       run: |
         scripts/buildSundials.sh
 
-    - name: Build cpputest
-      run: |
-        scripts/buildCpputest.sh
-
     - name: Build AMICI
       run: |
         scripts/buildAmici.sh

.github/workflows/test_python_cplusplus.yml

@@ -69,7 +69,7 @@ jobs:
 
     - name: C++ tests
       run: |
-        scripts/run-cpputest.sh
+        scripts/run-cpp-tests.sh
 
     - name: Install python package
       run: |
@@ -85,7 +85,7 @@ jobs:
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
           --cov-append \
           ${AMICI_DIR}/python/tests
-          
+
     - name: example notebooks
       run: |
         scripts/runNotebook.sh python/examples/example_*/
@@ -96,7 +96,7 @@ jobs:
 
     - name: Codecov Python
       uses: codecov/codecov-action@v1
-      with: 
+      with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./build/coverage_py.xml
         flags: python
@@ -163,4 +163,4 @@ jobs:
 
     - name: C++ tests
       run: |
-        scripts/run-cpputest.sh
+        scripts/run-cpp-tests.sh

.gitignore

@@ -4,9 +4,9 @@ build/*
 build-debug/*
 build_xcode/*
 swig/python/build/*
-tests/cpputest/build/*
-tests/cpputest/build_xcode/*
-tests/cpputest/Testing/*
+tests/cpp/build/*
+tests/cpp/build_xcode/*
+tests/cpp/Testing/*
 
 doc-venv/*
 doc/*
@@ -136,8 +136,8 @@ tests/test/*
 */tests/fricker_2010_apoptosis_amici/*
 */tests/explicit_amici/*
 */tests/fixed_initial_amici/*
-tests/cpputest/writeResults.h5
-tests/cpputest/writeResults.h5.bak
+tests/cpp/writeResults.h5
+tests/cpp/writeResults.h5.bak
 tests/sbml-test-suite/*
 tests/sbml-test-suite/
 tests/sedml-test-suite/
@@ -171,7 +171,6 @@ AMICI_guide.pdf
 
 ThirdParty/bionetgen.tar.gz
 ThirdParty/BioNetGen-*
-ThirdParty/cpputest-master*
 ThirdParty/doxygen/*
 ThirdParty/mtocpp-master*
 ThirdParty/sundials/build/*

CMakeLists.txt

@@ -268,7 +268,7 @@ if(BUILD_TESTS)
     if(ENABLE_HDF5)
         enable_testing()
 
-        add_subdirectory(tests/cpputest)
+        add_subdirectory(tests/cpp)
     else()
         message(WARNING "Cannot build tests with ENABLE_HDF5=OFF.")
     endif()

documentation/CI.md

@@ -18,7 +18,7 @@ tests are integrated with CMake, see `make help` in the build directory.
 ## C++ unit and integration tests
 
 To run C++ tests, build AMICI with `make` or `scripts/buildAll.sh`,
-then run `scripts/run-cpputest.sh`.
+then run `scripts/run-cpp-tests.sh`.
 
 
 ## Python unit and integration tests
@@ -58,7 +58,7 @@ To execute the Matlab test suite, run `tests/testModels.m`.
 
 Many of our integration tests are model simulations. The simulation results
 obtained from the Python and C++ are compared to results saved in an HDF5 file
-(`tests/cpputest/expectedResults.h5`).
+(`tests/cpp/expectedResults.h5`).
 Settings and data for the test simulations are also specified in this file.
 
 **Note:** The C++ code for the models is included in the repository under 
@@ -73,7 +73,7 @@ the Matlab model import routines change.
 
 This is done with
 
-    tests/cpputest/wrapTestModels.m
+    tests/cpp/wrapTestModels.m
 
 **Note:** This is currently only possible from Matlab < R2018a. This should
 change as soon as 1) all second-order sensitivity code is ported to C++/Python,
@@ -84,13 +84,13 @@ for Python.
 ### Regenerating expected results
 
 To update test results, run `make test` in the build directory,
-replace `tests/cpputest/expectedResults.h5` by 
-`tests/cpputest/writeResults.h5.bak` 
+replace `tests/cpp/expectedResults.h5` by 
+`tests/cpp/writeResults.h5.bak` 
 [ONLY DO THIS AFTER TRIPLE CHECKING CORRECTNESS OF RESULTS]
 Before replacing the test results, confirm that only expected datasets have
 changed, e.g. using 
 
-    h5diff -v --relative 1e-8 tests/cpputest/expectedResults.h5 tests/cpputest/writeResults.h5.bak | less
+    h5diff -v --relative 1e-8 tests/cpp/expectedResults.h5 tests/cpp/writeResults.h5.bak | less
 
 
 ## Adding/Updating tests

documentation/cpp_installation.rst

@@ -24,8 +24,8 @@ To use AMICI from C++, run the
 
 .. code-block:: bash
 
+    ./scripts/buildSuiteSparse.sh
     ./scripts/buildSundials.sh
-    ./scripts/buildSuitesparse.sh
     ./scripts/buildAmici.sh
 
 script to build the AMICI library.

documentation/development.rst

@@ -60,18 +60,18 @@ process described below:
    (our CI pipeline will do this for you)
 
 -  When adding new functionality, please also provide test cases (see
-   ``tests/cpputest/`` and
+   ``tests/cpp/`` and
    `documentation/CI.md <documentation/CI.md>`__)
 
 -  Write meaningful commit messages
 
 -  Run all tests to ensure nothing was broken (`more
    details <documentation/CI.md>`__)
 
-   -  Run ``scripts/buildAll.sh && scripts/run-cpputest.sh``.
+   -  Run ``scripts/buildAll.sh && scripts/run-cpp-tests.sh``.
 
    -  If you made changes to the Matlab or C++ code and have a Matlab
-      license, please also run ``tests/cpputest/wrapTestModels.m`` and
+      license, please also run ``tests/cpp/wrapTestModels.m`` and
       ``tests/testModels.m``
 
    -  If you made changes to the Python or C++ code, run

matlab/tests/testModels.m

@@ -18,18 +18,18 @@ function testModels()
 
     model_dir = [fileparts(mfilename('fullpath')) '/../../models/'];
     cd(fileparts(mfilename('fullpath')))
-    addpath(genpath('../../tests/cpputest'));
+    addpath(genpath('../../tests/cpp'));
     addpath(genpath('../examples'));
     % wrapTestModels()
 
     cd(fileparts(mfilename('fullpath')))
     hdf5file = fullfile(fileparts(mfilename('fullpath')), ...
-        '../../tests/cpputest', 'expectedResults.h5');
-    
+        '../../tests/cpp', 'expectedResults.h5');
+
     info = h5info(hdf5file);
     for imodel = 1:length(info.Groups)
         modelname = info.Groups(imodel).Name(2:end);
-      
+
         if(~isempty(regexp(modelname,'^model_neuron')))
             model_atol = 1e-9;
             model_rtol = 1e-4;
@@ -42,18 +42,18 @@ function testModels()
             if(ismember(testname, ignoredTests))
                 continue
             end
-            
+
             display(testname);
 
             [results,options,data,t,theta,kappa] = readDataFromHDF5(info.Groups(imodel).Groups(itest),hdf5file);
-            
+
             % rebuild model
             old_path = addpath([model_dir modelname]);
             old_pwd = cd([model_dir modelname]);
             rebuild = str2func(['rebuild_' modelname]);
             rebuild();
             cd(old_pwd);
-            
+
             sol = getResults(modelname,options,data,t,theta,kappa);
             compareResults(sol,results);
             path(old_path);

python/tests/test_pregenerated_models.py

@@ -3,19 +3,18 @@
 """Run simulations with Matlab-AMICI pre-generated models and verify using
 saved expectations."""
 
-import h5py
-import amici
 import os
-from amici.gradient_check import check_derivatives, check_results
-import pytest
+from pathlib import Path
 
+import amici
+import h5py
 import numpy as np
+import pytest
+from amici.gradient_check import check_derivatives, check_results
 
-
-options_file = os.path.join(os.path.dirname(__file__), '..', '..',
-                            'tests', 'cpputest', 'testOptions.h5')
-expected_results_file = os.path.join(os.path.dirname(__file__), '..', '..',
-                                     'tests', 'cpputest', 'expectedResults.h5')
+cpp_test_dir = Path(__file__).parents[2] / 'tests' / 'cpp'
+options_file = str(cpp_test_dir / 'testOptions.h5')
+expected_results_file = str(cpp_test_dir / 'expectedResults.h5')
 expected_results = h5py.File(expected_results_file, 'r')
 
 model_cases = [(sub_test, case)
@@ -43,10 +42,9 @@ def test_pregenerated_model(sub_test, case):
     else:
         model_name = sub_test
 
-    model_swig_folder = \
-        os.path.join(os.path.dirname(__file__), '..', '..', 'build', 'tests',
-                     'cpputest', f'external_{model_name}-prefix',
-                     'src', f'external_{model_name}-build', 'swig')
+    model_swig_folder = str(Path(__file__).parents[2] / 'build' / 'tests'
+                            / 'cpp' / f'external_{model_name}-prefix' / 'src'
+                            / f'external_{model_name}-build' / 'swig')
 
     test_model_module = amici.import_model_module(
         module_name=model_name, module_path=model_swig_folder)
@@ -64,7 +62,7 @@ def test_pregenerated_model(sub_test, case):
     edata = None
     if 'data' in expected_results[sub_test][case].keys():
         edata = amici.readSimulationExpData(
-            expected_results_file,
+            str(expected_results_file),
             f'/{sub_test}/{case}/data', model.get()
         )
     rdata = amici.runAmiciSimulation(model, solver,

scripts/README.md

@@ -14,12 +14,7 @@ This directory contains a number of build, installation, and CI scripts.
 
    Download and build 
    [BioNetGen](https://www.csb.pitt.edu/Faculty/Faeder/?page_id=409) (required for some tests)
-
-* `buildCpputest.sh`
-
-   Download and build [CppUTest](https://cpputest.github.io/)
-   (required for C++ test suite)
-
+
 * `buildSuiteSparse.sh`
 
    Build [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
@@ -64,7 +59,7 @@ This directory contains a number of build, installation, and CI scripts.
 
   Run static code analysis
 
-* `run-cpputest.sh`
+* `run-cpp-tests.sh`
 
   Run C++ unit and integration tests
 

scripts/buildAmici.sh

@@ -2,7 +2,8 @@
 #
 # Build libamici
 #
-set -e
+set -eou pipefail
+
 cmake=${CMAKE:-cmake}
 make=${MAKE:-make}
 
@@ -12,28 +13,26 @@ amici_build_dir="${amici_path}/build"
 mkdir -p "${amici_build_dir}"
 cd "${amici_build_dir}"
 
-cpputest_build_dir="${amici_path}/ThirdParty/cpputest-master/build/"
-
-if [[ $TRAVIS = true ]] || [[ $GITHUB_ACTIONS = true ]] || [[ $ENABLE_AMICI_DEBUGGING = TRUE ]];
-then
+if [ "${TRAVIS:-}" = true ] ||
+  [ "${GITHUB_ACTIONS:-}" = true ] ||
+  [ "${ENABLE_AMICI_DEBUGGING:-}" = TRUE ]; then
   # Running on CI server
   build_type="Debug"
 else
   build_type="RelWithDebInfo"
 fi
 
-CppUTest_DIR=${cpputest_build_dir} \
-  ${cmake} \
-    -DCMAKE_CXX_FLAGS="-Wall -Wextra -Werror" \
-    -DCMAKE_BUILD_TYPE=$build_type \
-    -DPython3_EXECUTABLE="$(command -v python3)" ..
+${cmake} \
+  -DCMAKE_CXX_FLAGS="-Wall -Wextra -Werror" \
+  -DCMAKE_BUILD_TYPE=$build_type \
+  -DPython3_EXECUTABLE="$(command -v python3)" ..
 
 # build, with or without sonarcloud wrapper
-if [[ "$CI_SONARCLOUD" == "TRUE" ]]; then
+if [ "${CI_SONARCLOUD:-}" = "TRUE" ]; then
   build-wrapper-linux-x86-64 \
     --out-dir "${amici_path}/bw-output" \
     cmake --build . --parallel
-elif [[ "$TRAVIS" == "true" ]]; then
+elif [ "${TRAVIS:-}" = "true" ]; then
   cmake --build .
   ${make} python-sdist
 else

scripts/buildDependencies.sh

@@ -9,5 +9,4 @@ script_path=$(cd "$script_path" && pwd)
 
 "${script_path}/buildSuiteSparse.sh"
 "${script_path}/buildSundials.sh"
-"${script_path}/buildCpputest.sh"
 "${script_path}/buildBNGL.sh"

scripts/buildXcode.sh

@@ -12,18 +12,16 @@ CMAKE=${CMAKE:-cmake}
 ${AMICI_PATH}/scripts/buildSuiteSparse.sh
 ${AMICI_PATH}/scripts/buildSundials.sh
 ${AMICI_PATH}/scripts/buildAmici.sh
-${AMICI_PATH}/scripts/buildCpputest.sh
 
 
-cp ${AMICI_PATH}/tests/cpputest/expectedResults.h5 ./expectedResults.h5
+cp ${AMICI_PATH}/tests/cpp/expectedResults.h5 ./expectedResults.h5
 
 mkdir -p ${AMICI_PATH}/build_xcode
 cd ${AMICI_PATH}/build_xcode
-CPPUTEST_BUILD_DIR=${AMICI_PATH}/ThirdParty/cpputest-master/build/
-CppUTest_DIR=${CPPUTEST_BUILD_DIR} ${CMAKE} -G"Xcode" -DCMAKE_BUILD_TYPE=Debug ..
+${CMAKE} -G"Xcode" -DCMAKE_BUILD_TYPE=Debug ..
 
 for model in steadystate robertson neuron neuron_o2 jakstat_adjoint jakstat_adjoint_o2 dirac events nested_events
 do
-    cp ${AMICI_PATH}/build/tests/cpputest/external_model_${model}-prefix/src/external_model_${model}-build/libmodel_${model}.a \
-       ${AMICI_PATH}/build_xcode/tests/cpputest/external_model_${model}-prefix/src/external_model_${model}-build/libmodel_${model}.a
+    cp ${AMICI_PATH}/build/tests/cpp/external_model_${model}-prefix/src/external_model_${model}-build/libmodel_${model}.a \
+       ${AMICI_PATH}/build_xcode/tests/cpp/external_model_${model}-prefix/src/external_model_${model}-build/libmodel_${model}.a
 done