Merge pull request #1170 from sys-bio/develop

Update docs.
sys-bio · Dec 13, 2023 · 4ed3408 · 4ed3408
2 parents ea600f8 + 4d8807a
commit 4ed3408
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Showing 73 changed files with 4,821 additions and 1,685 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ cmake_minimum_required(VERSION 3.16)
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 4)
+set(ROADRUNNER_VERSION_MINOR 5)
 set(ROADRUNNER_VERSION_PATCH 0)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
@@ -472,9 +472,9 @@ find_package(SUNDIALS CONFIG REQUIRED)
 # not for windows. So not required, but we throw error if not win and not found.
 find_package(Curses)
 
-if (NOT WIN32 AND NOT ${CURSES_FOUND})
-    message(FATAL_ERROR "ncurses library not found. Please install it with your native package manager")
-endif ()
+#if (NOT WIN32 AND NOT ${CURSES_FOUND})
+#    message(FATAL_ERROR "ncurses library not found. Please install it with your native package manager")
+#endif ()
 
 
 set(BUILD_SHARED_LIBS OFF)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -137,8 +137,7 @@ stages:
               # for example, it looks like this:
               # - https://dev.azure.com/TheRoadrunnerProject/libroadrunner-deps/_build?definitionId=9
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-$(BuildType)
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts
@@ -272,8 +271,7 @@ stages:
               source: 'specific'
               project: 'libroadrunner-deps'
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-Release
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts
@@ -503,8 +501,7 @@ stages:
               source: 'specific'
               project: 'libroadrunner-deps'
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-$(BuildType)
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts
@@ -594,7 +591,7 @@ stages:
           - powershell: |
               where.exe conda
               where.exe python
-              conda update conda -y -c conda-forge
+              # conda update conda -y -c conda-forge
               conda install numpy
               conda install python=3.11 -c conda-forge
               conda --version
@@ -637,8 +634,7 @@ stages:
               source: 'specific'
               project: 'libroadrunner-deps'
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-Release
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts
@@ -776,13 +772,13 @@ stages:
               BuildDocs: OFF
         variables:
           MinicondaRoot : '/usr/share/miniconda'
-          PythonRoot: '$(MinicondaRoot)/envs/$(PythonName)'
+          PythonRoot: '$(MinicondaRoot)/'
           PythonLibDir: '$(PythonRoot)/lib'
           PythonExecutable: '$(PythonRoot)/bin/python'
           PipExecutable: '$(PythonRoot)/bin/pip'
           SphinxExecutable: '$(PythonRoot)/bin/sphinx-build'
-          PythonName: 'py39'
-          PythonVersion: '3.9'
+          PythonName: 'py311'
+          PythonVersion: '3.11'
           LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm13-ubuntu-gcc10-rel.tar.gz'
         steps:
           - checkout: self
@@ -849,7 +845,7 @@ stages:
             displayName: Install g++10 and doxygen
           - script: |
               eval "$(conda shell.bash hook)"
-              conda create -y --name $(PythonName) python=$(PythonVersion)
+              # conda create -y --name $(PythonName) python=$(PythonVersion)
               $(PipExecutable) install requests
             displayName: "Install Python via conda"
           - script: |
@@ -867,8 +863,7 @@ stages:
               source: 'specific'
               project: 'libroadrunner-deps'
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-$(BuildType)
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts

diff --git a/cmake/FindLLVM.cmake b/cmake/FindLLVM.cmake
@@ -210,13 +210,13 @@ correct location. ")
         #message("UNIX true")
         #        message("LLVM VERSION >= 3.4, looking for curses library")
         # sudo apt-get install libncurses5-dev libncursesw5-dev
-        find_package(Curses REQUIRED)
+        #find_package(Curses REQUIRED)
         #        message(STATUS "curses: ${CURSES_FOUND}")
         #        message(STATUS "curdir: ${CURSES_INCLUDE_DIR}")
         #        message(STATUS "curlib: ${CURSES_LIBRARIES}")
         #        message(STATUS "LLVM_LIBRARIES: ${LLVM_LIBRARIES}")
 
-        set(LLVM_LIBRARIES "${LLVM_LIBRARIES};${CURSES_LIBRARIES}")
+        #set(LLVM_LIBRARIES "${LLVM_LIBRARIES};${CURSES_LIBRARIES}")
 
 
         # LLVM 3.5 seems to require zlib, at least on OSX 10.9.

diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -416,9 +416,9 @@ set(INCLUDE_DIRS "$<BUILD_INTERFACE:${LLVM_INCLUDE_DIRS}>"
         "$<BUILD_INTERFACE:${DEPENDENCY_INCLUDE_DIR}/libexpat>"
         "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
         "$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>")
-if (NOT WIN32)
-    set(INCLUDE_DIRS ${INCLUDE_DIRS} "$<BUILD_INTERFACE:${CURSES_INCLUDE_DIRS}>")
-endif ()
+#if (NOT WIN32)
+#    set(INCLUDE_DIRS ${INCLUDE_DIRS} "$<BUILD_INTERFACE:${CURSES_INCLUDE_DIRS}>")
+#endif ()
 
 target_include_directories(
         ${target}-static PUBLIC ${INCLUDE_DIRS}
@@ -430,12 +430,12 @@ target_include_directories(
 set(PLATFORM_SPECIFIC_LIBS)
 if (UNIX)
     #    icui18n icuuc (can be used instead of iconv)
-    set(PLATFORM_SPECIFIC_LIBS ${PLATFORM_SPECIFIC_LIBS} pthread dl m ${CURSES_LIBRARIES})
+    set(PLATFORM_SPECIFIC_LIBS ${PLATFORM_SPECIFIC_LIBS} pthread dl m)
 elseif (WIN32)
     set(PLATFORM_SPECIFIC_LIBS ${PLATFORM_SPECIFIC_LIBS} Ws2_32)
 
 elseif (APPLE AND NOT UNIX)
-    set(PLATFORM_SPECIFIC_LIBS ${PLATFORM_SPECIFIC_LIBS} ${CURSES_LIBRARIES})
+    set(PLATFORM_SPECIFIC_LIBS ${PLATFORM_SPECIFIC_LIBS})
 
 endif ()
 

diff --git a/source/CVODEIntegrator.h b/source/CVODEIntegrator.h
@@ -243,7 +243,7 @@ namespace rr {
          * 
          * The absolute tolerance vector is either set directly by the user as a vector, or is generated from the single absolute tolerance value (either default or set by the user) multiplied by the initial value of every element in the state vector (independent floating species, and elements controlled by rate rules).  If that initial value is zero, the corresponding element of the absolute tolerance vector is the single value multiplied by the compartment volume for species, or by one for all other values.
          */
-        virtual std::vector<double> getAbsoluteToleranceVector();
+        std::vector<double> getAbsoluteToleranceVector() override;
 
 
     private:

diff --git a/source/GillespieIntegrator.cpp b/source/GillespieIntegrator.cpp
@@ -61,23 +61,13 @@ namespace rr
 
         assert(floatingSpeciesStart >= 0);
 
-        // get rows and columns
-        mModel->getStoichiometryMatrix(&stoichRows, &stoichCols, nullptr);
-        stoichData = new double[stoichRows * stoichCols];
-
-        // fill stoichData
-        mModel->getStoichiometryMatrix(&stoichRows, &stoichCols, &stoichData);
-
         setEngineSeed(getValue("seed").get<std::uint64_t>());
 	}
 
 	GillespieIntegrator::GillespieIntegrator(ExecutableModel* m)
 	    :   Integrator(m),
 			timeScale(1.0),
 			stoichScale(1.0),
-			stoichRows(0),
-			stoichCols(0),
-			stoichData(nullptr),
 			reactionRates(nullptr),
 			reactionRatesBuffer(nullptr),
 			stateVector(nullptr),
@@ -98,12 +88,10 @@ namespace rr
             delete[] reactionRatesBuffer;
             delete[] stateVector;
             delete[] stateVectorRate;
-            delete[] stoichData;
             reactionRates = nullptr;
             reactionRatesBuffer = nullptr;
             stateVector = nullptr;
             stateVectorRate = nullptr;
-            stoichData = nullptr;
         }
 	}
 
@@ -114,12 +102,10 @@ namespace rr
         delete[] reactionRatesBuffer;
         delete[] stateVector;
         delete[] stateVectorRate;
-        delete[] stoichData;
         reactionRates = nullptr;
         reactionRatesBuffer = nullptr;
         stateVector = nullptr;
         stateVectorRate = nullptr;
-        stoichData = nullptr;
 
         mModel = m;
         mModel->reset();
@@ -130,10 +116,6 @@ namespace rr
         timeScale = 1.;
         stoichScale = 1.;
 
-        stoichRows = 0;
-        stoichCols = 0;
-        stoichData = nullptr;
-
         initializeFromModel();
     }
 

diff --git a/source/GillespieIntegrator.h b/source/GillespieIntegrator.h
@@ -133,11 +133,6 @@ namespace rr
         int stateVectorSize;
         double* stateVector;
         double* stateVectorRate;
-        // m rows x n cols
-        // offset = row*NUMCOLS + column
-        int stoichRows;
-        int stoichCols;
-        double* stoichData;
         std::vector<unsigned char> eventStatus;
         std::vector<unsigned char> previousEventStatus;
 
@@ -146,11 +141,10 @@ namespace rr
 
         double urand();
         void setEngineSeed(std::uint64_t seed);
-        std::uint64_t getSeed() const;
 
         inline double getStoich(uint species, uint reaction)
         {
-            return stoichData[species * stoichCols + reaction];
+            return mModel->getStoichiometry(species, reaction);
         }
 
         /**

diff --git a/source/SBMLValidator.cpp b/source/SBMLValidator.cpp
@@ -140,6 +140,9 @@ namespace rr
                 if (err)
                 {
                     errmsg = "  Error from libsbml:\n" + err->getMessage();
+                    if (err->getErrorId() == 10103) {
+                        throw std::domain_error("Invalid SBML, but valid XML.  It's possible that this is not an SBML file at all, but something else.");
+                    }
                 }
                 throw std::runtime_error("SBML document unable to be read." + errmsg);
             }

diff --git a/source/conservation/ConservedMoietyConverter.cpp b/source/conservation/ConservedMoietyConverter.cpp
@@ -19,7 +19,6 @@
 #include "rrRoadRunner.h"
 
 #include <sbml/math/ASTNode.h>
-#include <sbml/AlgebraicRule.h>
 #include <sbml/AssignmentRule.h>
 #include <sbml/RateRule.h>
 #include <sbml/InitialAssignment.h>

diff --git a/source/llvm/AssignmentRuleEvaluator.h b/source/llvm/AssignmentRuleEvaluator.h
@@ -12,7 +12,6 @@
 
 #include <sbml/Model.h>
 #include <sbml/SBMLVisitor.h>
-#include <sbml/AlgebraicRule.h>
 #include <sbml/AssignmentRule.h>
 
 namespace rrllvm

diff --git a/source/llvm/EvalInitialConditionsCodeGen.cpp b/source/llvm/EvalInitialConditionsCodeGen.cpp
@@ -189,7 +189,7 @@ void EvalInitialConditionsCodeGen::codeGenStoichiometry(
     Value *stoich = builder.CreateLoad(stoichEP, "stoichiometry");
 
     std::list<LLVMModelDataSymbols::SpeciesReferenceInfo> stoichEntries =
-            dataSymbols.getStoichiometryIndx();
+            dataSymbols.getStoichiometryList();
 
     for (std::list<LLVMModelDataSymbols::SpeciesReferenceInfo>::iterator i =
             stoichEntries.begin(); i != stoichEntries.end(); i++)