Merge pull request #1028 from sys-bio/develop

Release 2.2.2

CMakeLists.txt

@@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16)
 
 set(ROADRUNNER_VERSION_MAJOR 2)
 set(ROADRUNNER_VERSION_MINOR 2)
-set(ROADRUNNER_VERSION_PATCH 1)
+set(ROADRUNNER_VERSION_PATCH 2)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 
@@ -114,10 +114,6 @@ option(BUILD_LLVM "Build the LLVM back end" ON)
 # note I've tried using the C backend and it no longer compiles. Could be useful to keep though
 option(BUILD_LEGACY_C "Build the legacy C code generating backend (deprecated)" OFF)
 
-if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "../roadrunner-${CMAKE_GENERATOR_PLATFORM}-${CMAKE_BUILD_TYPE}" CACHE PATH "..." FORCE)
-endif()
-
 # should we build the swig python wrapper?
 option(BUILD_PYTHON "Build the SWIG generated python wrapper" OFF)
 if (BUILD_PYTHON)
@@ -360,6 +356,11 @@ endif ()
 
 set(CMAKE_DEBUG_POSTFIX "d")
 
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "../install-${CMAKE_BUILD_TYPE}" CACHE PATH "..." FORCE)
+endif()
+
+
 ####################################################
 #   Dependencies
 
@@ -394,12 +395,55 @@ else ()
 endif (WIN32)
 
 
-find_package(Threads) # for libxml2, FindThreads.cmake is shipped with cmake
-find_package(LibLZMA) # for libxml2, LibLZMA.cmake is shipped with cmake
+#find_package(Threads) # for libxml2, FindThreads.cmake is shipped with cmake
+#find_package(LibLZMA) # for libxml2, LibLZMA.cmake is shipped with cmake
 find_package(zlib CONFIG REQUIRED)
-find_package(bzip2 CONFIG REQUIRED)
-find_package(iconv CONFIG REQUIRED)
-find_package(libxml2 CONFIG REQUIRED)
+#find_package(bzip2 CONFIG REQUIRED)
+#find_package(iconv CONFIG REQUIRED)
+
+find_package(expat CONFIG REQUIRED)
+
+## https://stackoverflow.com/questions/32183975/how-to-print-all-the-properties-of-a-target-in-cmake/56738858#56738858
+## https://stackoverflow.com/a/56738858/3743145
+
+## Get all properties that cmake supports
+execute_process(COMMAND cmake --help-property-list OUTPUT_VARIABLE CMAKE_PROPERTY_LIST)
+## Convert command output into a CMake list
+STRING(REGEX REPLACE ";" "\\\\;" CMAKE_PROPERTY_LIST "${CMAKE_PROPERTY_LIST}")
+STRING(REGEX REPLACE "\n" ";" CMAKE_PROPERTY_LIST "${CMAKE_PROPERTY_LIST}")
+
+list(REMOVE_DUPLICATES CMAKE_PROPERTY_LIST)
+
+function(print_target_properties tgt)
+    if(NOT TARGET ${tgt})
+      message("There is no target named '${tgt}'")
+      return()
+    endif()
+
+    foreach (prop ${CMAKE_PROPERTY_LIST})
+        string(REPLACE "<CONFIG>" "${CMAKE_BUILD_TYPE}" prop ${prop})
+        get_target_property(propval ${tgt} ${prop})
+        if (propval)
+            message ("${tgt} ${prop} = ${propval}")
+        endif()
+    endforeach(prop)
+endfunction(print_target_properties)
+
+cmake_language(CALL print_target_properties zlib::zlibstatic)
+cmake_language(CALL print_target_properties expat::expat)
+
+#libsbml now needs to know that we found expat, so we set the relevant flags
+set(EXPAT_LIBRARY "expat::expat")
+get_target_property(EXPAT_INCLUDE_DIR expat::expat INTERFACE_INCLUDE_DIRECTORIES)
+get_target_property(EXPAT_LIBRARY expat::expat LOCATION)
+message(STATUS "EXPAT_LIBRARY: ${EXPAT_LIBRARY}")
+set(ZLIB_LIBRARY "zlib::zlibstatic")
+get_target_property(ZLIB_LIBRARY zlib::zlibstatic LOCATION)
+set(ZLIB_INCLUDE_DIR "${RR_DEPENDENCIES_INSTALL_PREFIX}/include/")
+
+message(STATUS "ZLIB_LIBRARY: ${ZLIB_LIBRARY}")
+message(STATUS "ZLIB_INCLUDE_DIR: ${ZLIB_INCLUDE_DIR}")
+
 find_package(${SBML_TARGET_NAME} CONFIG REQUIRED)
 find_package(rr-libstruct CONFIG REQUIRED)
 find_package(clapack CONFIG REQUIRED)

azure-pipelines.yml

@@ -1,4 +1,4 @@
-# Starter pipeline
+# Starter pipeline 
 # Start with a minimal pipeline that you can customize to build and deploy your code.
 # Add steps that build, run tests, deploy, and more:
 # https://aka.ms/yaml
@@ -117,10 +117,6 @@ stages:
               $(CondaExecutable) create --quiet --yes --name $(PythonName) python=$(PythonVersion)
             displayName: InstallCondaEnv
 
-          - script: |
-               brew install ncurses
-            displayName: install ncurses
-
           - script: |
               $(PipExecutable) install requests
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
@@ -200,9 +196,6 @@ stages:
           vmImage: 'macOS-10.15'
         strategy:
           matrix:
-            py37:
-              PythonVersion: 3.7
-              PythonName: py37
             py38:
               PythonVersion: 3.8
               PythonName: py38
@@ -261,8 +254,6 @@ stages:
           - script: |
               mkdir $(DEPS_INSTALL_PREFIX)
             displayName: Make Directories
-          - script: brew install ncurses
-            displayName: install ncurses
           - script: |
               $(PipExecutable) install requests
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
@@ -566,9 +557,6 @@ stages:
           vmImage: 'windows-2019'
         strategy:
           matrix:
-            py37:
-              PythonVersion: 3.7
-              PythonName: py37
             py38:
               PythonVersion: 3.8
               PythonName: py38
@@ -629,11 +617,12 @@ stages:
 
               echo "pip install requests:"
               $(PipExecutable) install requests
+              $(PipExecutable) install numpy
             displayName: "Setup conda"
 
           - script: |
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
-            displayName: "Get LLVM and NumPy"
+            displayName: "Get LLVM"
             condition: ne(variables.LLVM_CACHE, 'true')
 
           - task: DownloadPipelineArtifact@2
@@ -784,6 +773,7 @@ stages:
           PythonLibDir: '$(PythonRoot)/lib'
           PythonExecutable: '$(PythonRoot)/bin/python'
           PipExecutable: '$(PythonRoot)/bin/pip'
+          SphinxExecutable: '$(PythonRoot)/bin/sphinx-build'
           PythonName: 'py39'
           PythonVersion: '3.9'
           LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm13-ubuntu-gcc10-rel.tar.gz'
@@ -845,13 +835,15 @@ stages:
               echo "g++ $(g++ --version)"
               sudo add-apt-repository ppa:ubuntu-toolchain-r/test
               sudo apt-get update
-              sudo apt-get install -y gcc-10 g++-10 doxygen python3-sphinx
+              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils textlive-latex-extra
               sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 1
-            displayName: Install g++10
+            displayName: Install g++10 and doxygen
           - script: |
               eval "$(conda shell.bash hook)"
               conda create -y --name $(PythonName) python=$(PythonVersion)
               $(PipExecutable) install requests
+            displayName: "Install Python via conda"
+          - script: |
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
               echo "give execute permissions to llvm-config using chmod 777"
               chmod 777 $(LLVM_INSTALL_PREFIX)/bin/llvm-config
@@ -920,9 +912,28 @@ stages:
               rm -r $(Build.ArtifactStagingDirectory)/*
             displayName: Clear staging area
             condition: eq(variables.BuildType, 'Release')
+          - script: |
+              echo "cd to docs dir"
+              cd $(SOURCE_DIR)/docs/
+              echo "pip install dependencies"
+              $(PipExecutable) install -r requirements.txt
+              export SPHINXBUILD=$(SphinxExecutable)
+              echo "make html"
+              make html
+              echo "list build/html"
+              ls build/html
+              echo "move docs to installation"
+              cd
+              pwd
+              mkdir $(INSTALL_DIR)/docs
+              mv $(SOURCE_DIR)/docs/build/html '$(INSTALL_DIR)/docs/docs-build'
+              mv $(SOURCE_DIR)/docs/doxygen-output '$(INSTALL_DIR)/docs/doxygen-output'
+              ls '$(INSTALL_DIR)/docs'
+            displayName: Make Docs
+            condition: eq(variables.BuildType, 'Release')
           - task: CopyFiles@2
             inputs:
-              contents: '$(SOURCE_DIR)/docs/docs-build/**'
+              contents: '$(INSTALL_DIR)/docs/**'
               targetFolder: $(Build.ArtifactStagingDirectory)
             displayName: Copy docs to Staging Area
             condition: eq(variables.BuildType, 'Release')
@@ -941,9 +952,6 @@ stages:
       - job:
         strategy:
           matrix:
-            py37:
-              PythonVersion: 3.7
-              PythonName: py37
             py38:
               PythonVersion: 3.8
               PythonName: py38
@@ -1050,8 +1058,8 @@ stages:
               $(PipExecutable) install -r $(SOURCE_DIR)/requirements.txt
               $(PipExecutable) install -r $(SOURCE_DIR)/test-requirements.txt
 
-              echo "cmake command: cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) .."
-              cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) ..
+              echo "cmake command: cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release .."
+              cmake -DLLVM_INSTALL_PREFIX=/install-llvm-13.x -DRR_DEPENDENCIES_INSTALL_PREFIX=/libroadrunner-deps/install-libroadrunner-deps -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIRECTORY) -DBUILD_PYTHON=ON -DBUILD_RR_PLUGINS=ON -DBUILD_TESTS=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SwigExecutable) -DCMAKE_BUILD_TYPE=Release ..
               cmake --build . --target install --config Release -j 12
 
             displayName: Build With Python
@@ -1071,8 +1079,8 @@ stages:
 
               echo "cd'ing to build dir $(BUILD_DIR)"
               cd $(BUILD_DIR)
-              # ctest --tests-regex python_tests_RunStochasticTestSuite .
-            displayName: (DISABLED) Run Stochastic test suite
+              ctest --tests-regex python_tests_RunStochasticTestSuite .
+            displayName: Run Stochastic test suite
 
           - script: |
               echo "cd to $(INSTALL_DIRECTORY)"

docs/docs-build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e3a0f48672f347564e56dd04b049664c
+config: 6fe8ded2a92374737db879ef72778739
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/docs-build/C++APIReference/CVODEIntegrator.html

@@ -1,7 +1,8 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>CVODEIntegrator &mdash; libRoadRunner 1.1.16 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -129,11 +130,11 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="cvodeintegrator">
+  <section id="cvodeintegrator">
 <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalink to this headline"></a></h1>
 <dl class="cpp class">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegratorE">
-<span id="_CPPv3N2rr15CVODEIntegratorE"></span><span id="_CPPv2N2rr15CVODEIntegratorE"></span><span id="rr::CVODEIntegrator"></span><span class="target" id="classrr_1_1CVODEIntegrator"></span><span class="k"><span class="pre">class</span></span><span class="w"> </span><span class="sig-prename descclassname"><span class="n"><span class="pre">rr</span></span><span class="p"><span class="pre">::</span></span></span><span class="sig-name descname"><span class="n"><span class="pre">CVODEIntegrator</span></span></span><span class="w"> </span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="k"><span class="pre">public</span></span><span class="w"> </span><span class="n"><span class="pre">rr</span></span><span class="p"><span class="pre">::</span></span><a class="reference internal" href="Integrator.html#_CPPv4N2rr10IntegratorE" title="rr::Integrator"><span class="n"><span class="pre">Integrator</span></span></a><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegratorE" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3N2rr15CVODEIntegratorE"></span><span id="_CPPv2N2rr15CVODEIntegratorE"></span><span id="rr::CVODEIntegrator"></span><span class="target" id="classrr_1_1CVODEIntegrator"></span><span class="k"><span class="pre">class</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">CVODEIntegrator</span></span></span><span class="w"> </span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="k"><span class="pre">public</span></span><span class="w"> </span><span class="n"><span class="pre">rr</span></span><span class="p"><span class="pre">::</span></span><a class="reference internal" href="Integrator.html#_CPPv4N2rr10IntegratorE" title="rr::Integrator"><span class="n"><span class="pre">Integrator</span></span></a><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegratorE" title="Permalink to this definition"></a><br /></dt>
 <dd><p>A <a class="reference internal" href="rrRoadRunner.html#classrr_1_1RoadRunner"><span class="std std-ref">RoadRunner</span></a> integrator based on CVODE; serves as <a class="reference internal" href="rrRoadRunner.html#classrr_1_1RoadRunner"><span class="std std-ref">RoadRunner</span></a>’s main integrator for ODEs. </p>
 <p>
 Provides a wrapper around CVODE from the SUNDIALS suite. CVODE has two main solvers: an Adams-Moulton solver for non-stiff problems, and a backward differentiation formula (BDF) solver for stiff problems. See: <a class="reference external" href="https://computation.llnl.gov/casc/sundials/documentation/toms_sundials.pdf">https://computation.llnl.gov/casc/sundials/documentation/toms_sundials.pdf</a> <dl class="simple">
@@ -651,7 +652,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 </div>
 </dd></dl>
 
-</div>
+</section>
 
 
            </div>
@@ -664,7 +665,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2013-2018, Andy Somogyi, J Kyle Medley, Kiri Choi, Herbert Suaro.</p>
+    <p>&#169; Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/docs-build/C++APIReference/Dictionary.html

@@ -1,7 +1,8 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Dictionary &mdash; libRoadRunner 1.1.16 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -129,11 +130,11 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="dictionary">
+  <section id="dictionary">
 <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this headline"></a></h1>
 <dl class="cpp class">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr10DictionaryE">
-<span id="_CPPv3N2rr10DictionaryE"></span><span id="_CPPv2N2rr10DictionaryE"></span><span id="rr::Dictionary"></span><span class="target" id="classrr_1_1Dictionary"></span><span class="k"><span class="pre">class</span></span><span class="w"> </span><span class="sig-prename descclassname"><span class="n"><span class="pre">rr</span></span><span class="p"><span class="pre">::</span></span></span><span class="sig-name descname"><span class="n"><span class="pre">Dictionary</span></span></span><a class="headerlink" href="#_CPPv4N2rr10DictionaryE" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3N2rr10DictionaryE"></span><span id="_CPPv2N2rr10DictionaryE"></span><span id="rr::Dictionary"></span><span class="target" id="classrr_1_1Dictionary"></span><span class="k"><span class="pre">class</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">Dictionary</span></span></span><a class="headerlink" href="#_CPPv4N2rr10DictionaryE" title="Permalink to this definition"></a><br /></dt>
 <dd><p>This class is frozen, no new features A dictionary interface that objects can implement. </p>
 <p>These are automatically mapped to python dictionaries. </p>
 <p>Subclassed by rr::BasicDictionary, <a class="reference internal" href="rrNLEQ1Interface.html#classrr_1_1NLEQ1Interface"><span class="std std-ref">rr::NLEQ1Interface</span></a>, <a class="reference internal" href="rrNLEQ2Interface.html#classrr_1_1NLEQ2Interface"><span class="std std-ref">rr::NLEQ2Interface</span></a></p>
@@ -195,7 +196,7 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
 </div>
 </dd></dl>
 
-</div>
+</section>
 
 
            </div>
@@ -208,7 +209,7 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2013-2018, Andy Somogyi, J Kyle Medley, Kiri Choi, Herbert Suaro.</p>
+    <p>&#169; Copyright 2013-2021, Andy Somogyi, J Kyle Medley, Kiri Choi, Ciaran Welsh, Lucian Smith, Herbert Sauro.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a