Merge pull request #1079 from ICB-DCM/release_0.11.0

Release 0.11.0
AMICI-dev · May 10, 2020 · a5f30d5 · a5f30d5
2 parents 390305f + 2ad2e36
commit a5f30d5
Show file tree

Hide file tree

Showing 656 changed files with 113,244 additions and 32,286 deletions.
diff --git a/.github/workflows/sbml-semantic-test-suite.yml b/.github/workflows/sbml-semantic-test-suite.yml
@@ -5,8 +5,13 @@ on:
       - develop
       - master
   pull_request:
-    branches:
-      - master
+    paths:
+      - python/amici/sbml_import.py
+      - python/amici/ode_export.py
+      - scripts/run-SBMLTestsuite.sh
+      - tests/testSBMLSuite.py
+  check_suite:
+   types: [requested]
 
 jobs:
   build:

diff --git a/.github/workflows/test_cplusplus.yml b/.github/workflows/test_cplusplus.yml
@@ -0,0 +1,107 @@
+name: C++ testsuite / Ubuntu
+on: [push]
+
+jobs:
+  build:
+    name: _
+
+    # TODO: prepare image with more deps preinstalled
+    runs-on: ubuntu-latest
+
+    env:
+      ENABLE_GCOV_COVERAGE: TRUE
+      CI_SONARCLOUD: TRUE
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+    - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
+
+      # sonar cloud
+    - run: echo "::set-env name=SONAR_SCANNER_VERSION::4.2.0.1873"
+    - run: echo "::set-env name=SONAR_SCANNER_HOME::$HOME/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux"
+    - run: echo "::set-env name=SONAR_SCANNER_OPTS::-server"
+    - run: echo "::add-path::${SONAR_SCANNER_HOME}/bin"
+    - run: echo "::add-path::$HOME/.sonar/build-wrapper-linux-x86"
+
+    # TODO: add to ci image
+    - name: Install sonarcloud tools
+      run: |
+        sudo apt install nodejs curl unzip \
+        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
+          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
+        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
+        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
+          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
+        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+
+    # install amici dependencies
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            g++ \
+            libatlas-base-dev \
+            libboost-serialization-dev \
+            libhdf5-serial-dev \
+            python3-dev \
+            swig
+
+    - name: Build suitesparse
+      run: |
+        scripts/buildSuiteSparse.sh
+
+    - name: Build sundials
+      run: |
+        scripts/buildSundials.sh
+
+    - name: Build cpputest
+      run: |
+        scripts/buildCpputest.sh
+
+    - name: Build cpputest
+      run: |
+        scripts/buildBNGL.sh
+
+    - name: Build AMICI
+      run: |
+        CI_SONARCLOUD=TRUE scripts/buildAmici.sh
+
+    - name: Cache sonar files
+      id: cache-sonar
+      uses: actions/cache@v1
+      with:
+        path: sonar_cache
+        key: ${{ runner.os }}-sonar_cache
+
+    - name: C++ tests
+      run: |
+        scripts/run-cpputest.sh
+
+    - name: gcov
+      run: cd build && gcov CMakeFiles/amici.dir/src/*.o
+
+    - name: Install python package
+      run: scripts/installAmiciSource.sh
+
+    - name: Python tests
+      run: |
+        source build/venv/bin/activate \
+        && pip3 install coverage pytest pytest-cov \
+        && pytest \
+          --ignore-glob=*petab* \
+          --cov=amici \
+          --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
+          --cov-append \
+          ${AMICI_DIR}/python/tests
+
+    - name: Run sonar-scanner
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        sonar-scanner \
+         -Dsonar.cfamily.build-wrapper-output=bw-output \
+         -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
diff --git a/.github/workflows/test_cplusplus_valgrind.yml b/.github/workflows/test_cplusplus_valgrind.yml
@@ -0,0 +1,54 @@
+name: C++ testsuite / Valgrind / Ubuntu
+on:
+  push:
+    branches:
+      - develop
+      - master
+      - feature_1053_sonarcloud
+
+
+jobs:
+  build:
+    name: _
+
+    # TODO: prepare image with more deps preinstalled
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    # install amici dependencies
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            g++ \
+            libatlas-base-dev \
+            libboost-serialization-dev \
+            libhdf5-serial-dev \
+            swig \
+            valgrind
+
+    - name: Build suitesparse
+      run: |
+        scripts/buildSuiteSparse.sh
+
+    - name: Build sundials
+      run: |
+        scripts/buildSundials.sh
+
+    - name: Build cpputest
+      run: |
+        scripts/buildCpputest.sh
+
+    - name: Build AMICI
+      # TODO: should get rid of having to install numpy before
+      run: |
+        pip3 install numpy \
+        && scripts/buildAmici.sh
+
+    - name: C++ tests / Valgrind
+      run: |
+        scripts/run-valgrind.sh
diff --git a/.gitignore b/.gitignore
@@ -108,6 +108,8 @@ tests/test/*
 */tests/test_model_presimulation/*
 */tests/test_model_presimulation_pysb/*
 */tests/test_model_presimulation_sbml/*
+*/tests/model_constant_species_cl/*
+*/tests/model_constant_species/*
 */tests/test_likelihoods/*
 */tests/bax_pore_sequential_amici/*
 */tests/bax_pore_amici/*
@@ -136,6 +138,7 @@ tests/sedml-test-suite/
 tests/SBMLTestModels/
 tests/benchmark-models/test_bmc
 tests/petab_test_suite
+petab_test_suite
 /python/test/amici-SBMLTest*/
 
 python/examples/example_steadystate/model_steadystate_scaled/*

diff --git a/.travis.yml b/.travis.yml
@@ -94,7 +94,6 @@ matrix:
         - travis_wait brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
         - brew link --overwrite python # https://github.com/ICB-DCM/AMICI/issues/894
         - export -f travis_fold travis_nanoseconds travis_time_start travis_time_finish
-        - pip3 install --user -U numpy
       after_success:
         - cd $BASE_DIR # cd to base dir for correct relative path in deploy
 
@@ -149,7 +148,6 @@ matrix:
         - choco install python --version 3.7.5
         - choco install swig
         - python -m pip install --upgrade pip
-        - pip install --user -U numpy
         - git clone -c core.symlinks=true https://github.com/ICB-DCM/AMICI.git && cd AMICI
         - if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then git checkout -qf $TRAVIS_COMMIT; elif [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then git fetch --update-head-ok origin pull/$TRAVIS_PULL_REQUEST/head:$TRAVIS_BRANCH && git checkout $TRAVIS_BRANCH; fi
         # run BLAS installation script

diff --git a/README.md b/README.md
@@ -37,8 +37,8 @@ constrained optimization problems.
   <img src="https://travis-ci.com/ICB-DCM/AMICI.svg?branch=master"></a>
 <a href="https://codecov.io/gh/ICB-DCM/AMICI" alt="CodeCov">
   <img src="https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg"></a>
-<a href="https://www.codacy.com/app/FFroehlich/AMICI" alt="Codacy">
-  <img src="https://api.codacy.com/project/badge/Grade/945235766e344a7fa36278feab915ff6"></a>
+<a href="https://sonarcloud.io/dashboard?id=ICB-DCM_AMICI&branch=master" alt="SonarCloud">
+  <img src="https://sonarcloud.io/api/project_badges/measure?branch=master&project=ICB-DCM_AMICI&metric=sqale_index"></a>
 <a href="https://zenodo.org/badge/latestdoi/43677177" alt="Zenodo">
   <img src="https://zenodo.org/badge/43677177.svg"></a>
 <a href="https://amici.readthedocs.io/en/latest/?badge=latest" alt="RTD">
@@ -130,7 +130,7 @@ When presenting work that employs AMICI, feel free to use one of the icons in
 
 ## Status of SBML support in Python-AMICI
 
-Python-AMICI currently passes 500 out of the 1780 (~28%) test cases from
+Python-AMICI currently passes 696 out of the 1780 (~39%) test cases from
 the semantic
 [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite/)
 ([current status](https://github.com/ICB-DCM/AMICI/actions)).
@@ -139,10 +139,7 @@ In addition, we currently plan to add support for the following features
 (see corresponding issues for details and progress):
 
 - Events (currently Matlab-only)
-- Rate rules
 - Algebraic rules
-- Species assignment rules
-- Compartment assignment rules
 - Models without species
 
 contributions are welcome.

diff --git a/ThirdParty/SuiteSparse/AMD/Doc/License.txt b/ThirdParty/SuiteSparse/AMD/Doc/License.txt
@@ -1,37 +1,14 @@
 AMD, Copyright (c), 1996-2015, Timothy A. Davis,
 Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
 
-AMD License: At the user's option, you may use AMD under either the LGPL
-version 2.1 license, or the BSD 3-clause license.  You may not use both
-licenses, nor may you mix-and-match clauses from each license.  To use a
-license, in the documentation for your application simply state either of the
-following, replacing <YOUR APPLICATION> with the name of your application:
-
-    AMD, Copyright (c), 1996-2015, Timothy A. Davis,
-    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
-    Used in <YOUR APPLICATION> under the BSD 3-clause license.
-
-or
-
-    AMD, Copyright (c), 1996-2015, Timothy A. Davis,
-    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
-    Used in <YOUR APPLICATION> under the LGPL v2.1 license.
-
-In the event that your package <A> includes another package <B> by another
-author, and <A> and <B> use AMD under different licenses, you may select
-one license to apply to both uses of AMD in the combined application.
-
 Availability:
 
     http://www.suitesparse.com
 
 -------------------------------------------------------------------------------
-BSD 3-clause:
+AMD License: BSD 3-clause:
 -------------------------------------------------------------------------------
 
-    Copyright (c), 1996-2015, Timothy A. Davis,
-    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
-
     Redistribution and use in source and binary forms, with or without
     modification, are permitted provided that the following conditions are met:
         * Redistributions of source code must retain the above copyright
@@ -56,36 +33,3 @@ BSD 3-clause:
     OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
     DAMAGE.
 
--------------------------------------------------------------------------------
-LGPL version 2.1:
--------------------------------------------------------------------------------
-
-    Your use or distribution of AMD or any modified version of
-    AMD implies that you agree to this License.
-
-    This library is free software; you can redistribute it and/or
-    modify it under the terms of the GNU Lesser General Public
-    License as published by the Free Software Foundation; either
-    version 2.1 of the License, or (at your option) any later version.
-
-    This library is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-    Lesser General Public License for more details.
-
-    You should have received a copy of the GNU Lesser General Public
-    License along with this library; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
-    USA
-
-    Permission is hereby granted to use or copy this program under the
-    terms of the GNU LGPL, provided that the Copyright, this License,
-    and the Availability of the original version is retained on all copies.
-    User documentation of any code that uses this code or any modified
-    version of this code must cite the Copyright, this License, the
-    Availability note, and "Used by permission." Permission to modify
-    the code and to distribute modified code is granted, provided the
-    Copyright, this License, and the Availability note are retained,
-    and a notice that the code was modified is included.
-
--------------------------------------------------------------------------------
diff --git a/ThirdParty/SuiteSparse/AMD/Doc/Makefile b/ThirdParty/SuiteSparse/AMD/Doc/Makefile
@@ -23,9 +23,9 @@ distclean: clean
 #------------------------------------------------------------------------------
 
 AMD_UserGuide.pdf: AMD_UserGuide.tex AMD_UserGuide.bib ../Include/amd.h
-	echo '\begin{verbatim}' > amd_h.tex
+	echo '\\begin{verbatim}' > amd_h.tex
 	expand -8 ../Include/amd.h >> amd_h.tex
-	echo '\end{verbatim}' >> amd_h.tex
+	echo '\\end{verbatim}' >> amd_h.tex
 	pdflatex AMD_UserGuide
 	bibtex AMD_UserGuide
 	pdflatex AMD_UserGuide

diff --git a/ThirdParty/SuiteSparse/CAMD/Doc/License.txt b/ThirdParty/SuiteSparse/CAMD/Doc/License.txt
@@ -3,38 +3,33 @@ Yanqing Chen,
 Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
 CAMD is available under alternate licenses, contact T. Davis for details.
 
-CAMD License:
-
-    Your use or distribution of CAMD or any modified version of
-    CAMD implies that you agree to this License.
-
-    This library is free software; you can redistribute it and/or
-    modify it under the terms of the GNU Lesser General Public
-    License as published by the Free Software Foundation; either
-    version 2.1 of the License, or (at your option) any later version.
-
-    This library is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-    Lesser General Public License for more details.
-
-    You should have received a copy of the GNU Lesser General Public
-    License along with this library; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
-    USA
-
-    Permission is hereby granted to use or copy this program under the
-    terms of the GNU LGPL, provided that the Copyright, this License,
-    and the Availability of the original version is retained on all copies.
-    User documentation of any code that uses this code or any modified
-    version of this code must cite the Copyright, this License, the
-    Availability note, and "Used by permission." Permission to modify
-    the code and to distribute modified code is granted, provided the
-    Copyright, this License, and the Availability note are retained,
-    and a notice that the code was modified is included.
+CAMD License: BSD 3-clause
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above copyright
+          notice, this list of conditions and the following disclaimer in the
+          documentation and/or other materials provided with the distribution.
+        * Neither the name of the organizations to which the authors are
+          affiliated, nor the names of its contributors may be used to endorse
+          or promote products derived from this software without specific prior
+          written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+    ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
+    DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+    LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+    DAMAGE.
 
 Availability:
 
     http://www.suitesparse.com
 
--------------------------------------------------------------------------------