Merge pull request #143 from SwissTPH/develop

Merge develop for release 'schema-34.0'

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "zlib"]
+	path = zlib
+	url = https://github.com/commontk/zlib.git
+[submodule "gsl"]
+	path = gsl
+	url = https://github.com/ampl/gsl

.travis.yml

@@ -1,28 +1,75 @@
+env:
+  global:
+    - BASE_URL="https://github.com/SwissTPH/openmalaria"
+
+os:
+  - linux
+  - osx
+
+matrix:
+  allow_failures:
+    - os: osx
+    - compiler: clang
+
+sudo: false
+
 language: cpp
 
-compiler: gcc
+compiler:
+  - gcc
+  - clang
+
+addons:
+  apt:
+    packages:
+    - build-essential
+    - cmake
+    - python
+    - libboost-all-dev
+    - libgsl0-dev
+    - libxerces-c2-dev
+    - xsdcxx
+    - zlib1g-dev
 
 before_install:
-  - sudo apt-get -qq install cmake build-essential python libgsl0-dev libboost-all-dev libxerces-c2-dev xsdcxx zlib1g-dev
+  - test "$TRAVIS_OS_NAME" == "osx" && util/install-dep-osx.sh || echo "not installing osx dependencies"
 
 install:
-  - mkdir build && cd build
+  - mkdir build && pushd build
   - cmake -DCMAKE_BUILD_TYPE=Release ..
 
 script:
   - make -j2
-  - ctest -j2
+  - ./openMalaria --version
+  - test "$TRAVIS_OS_NAME" == "linux" && ldd openMalaria || otool -L openMalaria
+  - ctest
+  - popd
 
-notifications:
-  email:
-    - [email protected]
+after_success:
+  - util/generate-checksums.sh build
+  - util/build-info.sh | tee travis-build.json
+
+before_deploy:
+  - mv -v build/schema/scenario_current.xsd .
+  - mv -v build/openMalaria* .
+  - tar cvzf openMalaria-$TRAVIS_OS_NAME.tar.gz openMalaria* scenario_current.xsd test/autoRegressionParameters.csv test/densities.csv travis-build.json
 
 deploy:
   provider: releases
   api_key:
     secure: dOTDLZ10UHm3JoKODtlBMxChFaXOekUM69S2f6eoAt0ctjFPZXHic2aEUvabeZJqq8UX83xO1I0tGTX7DWMvxd7zPTQHcW9N3XxWvgChKxs4OSqRL7GnunI3iZPH8125ZCeMNuh+oCgf1DdfOy0uOgdygGKzvIYEFhd7c5gOH/I=
   skip_cleanup: true
-  file:
-    openMalaria
+  file: openMalaria-$TRAVIS_OS_NAME.tar.gz
   on:
     tags: true
+
+# blacklist
+branches:
+  except:
+    - appveyor-build
+    - binary-archive
+
+notifications:
+  email:
+    - [email protected]
+

CMakeLists.txt

@@ -19,12 +19,14 @@ set (CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
 # -----  Compile options  -----
 
 # C++11 would be nice, but we have to compile for relatively old platforms
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++98")
+if (NOT MSVC)
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++98")
+endif (NOT MSVC)
 
 set (OM_STD_LIBS )
 
 # Statically link libgcc; isn't going to work when other C++ libraries are dynamically linked
-IF( ${CMAKE_COMPILER_IS_GNUCXX} )
+if( ${CMAKE_COMPILER_IS_GNUCXX} )
   # This doesn't show up in the cache, but it is passed to gcc:
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall")
 
@@ -39,13 +41,13 @@ IF( ${CMAKE_COMPILER_IS_GNUCXX} )
     link_directories (${CMAKE_SOURCE_DIR}/lib)
     # Note: -static-libstdc++ is only available since GCC 4.5
     # See: http://www.trilithium.com/johan/2005/06/static-libstdc/
-    ADD_DEFINITIONS(-static-libgcc -static-libstdc++)
-    SET(CMAKE_CXX_LINK_EXECUTABLE "${CMAKE_CXX_LINK_EXECUTABLE} -static-libgcc -static-libstdc++")
+    add_definitions(-static-libgcc -static-libstdc++)
+    set(CMAKE_CXX_LINK_EXECUTABLE "${CMAKE_CXX_LINK_EXECUTABLE} -static-libgcc -static-libstdc++")
   endif (OM_STATICALLY_LINK)
-ENDIF( ${CMAKE_COMPILER_IS_GNUCXX} )
+endif( ${CMAKE_COMPILER_IS_GNUCXX} )
 
 option (BUILD_SHARED_LIBS "Link xsdcxx, model, etc. libraries dynamically instead of statically (almost certainly not wanted)." OFF)
-MARK_AS_ADVANCED (BUILD_SHARED_LIBS)
+mark_as_advanced (BUILD_SHARED_LIBS)
 
 if (MSVC)
   # This is now the OM_STATICALLY_LINK for windows
@@ -153,7 +155,7 @@ endif (OM_BOINC_INTEGRATION)
 # -----  Compile-time optional features  -----
 # (must come before add_subdirectory (model))
 
-option (OM_STREAM_VALIDATOR "Compile in StreamValidator (see include/util/StreamValidator.h for usage notes)" OFF)
+option (OM_STREAM_VALIDATOR "Compile in StreamValidator (see model/util/StreamValidator.h for usage notes)" OFF)
 if (OM_STREAM_VALIDATOR)
   add_definitions (-DOM_STREAM_VALIDATOR)
 endif (OM_STREAM_VALIDATOR)
@@ -191,9 +193,6 @@ include_directories (
   ${CMAKE_SOURCE_DIR}/model ${CMAKE_BINARY_DIR}
 )
 
-file(STRINGS version.txt OM_VERSION)
-configure_file(model/util/version.h.in ../model/util/version.h	@ONLY)
-
 add_executable (openMalaria model/openMalaria.cpp)
 
 target_link_libraries (openMalaria

FindXERCESC.cmake

@@ -14,7 +14,9 @@ FIND_PATH(XERCESC_INCLUDE_DIRS xercesc/dom/DOMNode.hpp
   "C:/Program Files/CodeSynthesis XSD 3.2/include"
   "D:/Program Files/CodeSynthesis XSD 3.2/include"
   "C:/Program Files/CodeSynthesis XSD 3.3/include"
+  "C:/Program Files/CodeSynthesis XSD 4.0/include"
   "C:/Program Files (x86)/CodeSynthesis XSD 3.3/include"
+  "C:/Program Files (x86)/CodeSynthesis XSD 4.0/include"
   ${CMAKE_SOURCE_DIR}/../xsd/libxsd
 )
 
@@ -23,7 +25,9 @@ set (XERCESC_LIB_PATHS
   "C:/Program Files/CodeSynthesis XSD 3.2/lib/vc-8.0"
   "D:/Program Files/CodeSynthesis XSD 3.2/lib/vc-8.0"
   "C:/Program Files/CodeSynthesis XSD 3.3/lib/vc-8.0"
+  "C:/Program Files/CodeSynthesis XSD 4.0/lib64/vc-12.0"
   "C:/Program Files (x86)/CodeSynthesis XSD 3.3/lib/vc-8.0"
+  "C:/Program Files (x86)/CodeSynthesis XSD 4.0/lib/vc-12.0"
 )
 find_library (XERCESC_LIB_OPT NAMES xerces-c xerces-c_3 xerces-c_2 xerces-c_static xerces-c_static_3 xerces-c_static_2
   ${XERCESC_LIB_PATHS}

FindXSD.cmake

@@ -17,7 +17,11 @@ FIND_PATH(XSD_INCLUDE_DIRS xsd/cxx/parser/elements.hxx
   "C:/Program Files/CodeSynthesis XSD 3.2/include"
   "D:/Program Files/CodeSynthesis XSD 3.2/include"
   "C:/Program Files/CodeSynthesis XSD 3.3/include"
+  "C:/Program Files/CodeSynthesis XSD 4.0/include"
   "C:/Program Files (x86)/CodeSynthesis XSD 3.3/include"
+  "C:/Program Files (x86)/CodeSynthesis XSD 4.0/include"
+  "/usr/local/Cellar/xsd/4.0.0/include"
+  ${CMAKE_SOURCE_DIR}/../xsd/include
   ${CMAKE_SOURCE_DIR}/../xsd/libxsd
 )
 
@@ -27,7 +31,11 @@ FIND_PROGRAM(XSD_EXECUTABLE
   "C:/Program Files/CodeSynthesis XSD 3.2/bin"
   "D:/Program Files/CodeSynthesis XSD 3.2/bin"
   "C:/Program Files/CodeSynthesis XSD 3.3/bin"
+  "C:/Program Files/CodeSynthesis XSD 4.0/bin"
   "C:/Program Files (x86)/CodeSynthesis XSD 3.3/bin"
+  "C:/Program Files (x86)/CodeSynthesis XSD 4.0/bin"
+  "/usr/local/Cellar/xsd/4.0.0/bin"
+  ${CMAKE_SOURCE_DIR}/../xsd/bin
 )
 
 if (NOT XSD_INCLUDE_DIRS)

README.md

@@ -6,25 +6,28 @@ This git-repository contains source-code for Open Malaria, a simulator program f
 
 For further documentation, take a look at our [wiki](https://github.com/SwissTPH/openmalaria/wiki).
 
-The stable version of OpenMalaria supports schema [schema version 33](https://github.com/SwissTPH/openmalaria/wiki/GeneratedSchema33Doc) and is currently maintained in the __['master' branch](https://github.com/SwissTPH/openmalaria/tree/master)__.
+Also find our code on zenodo, with DOI-references: [![DOI](https://zenodo.org/badge/15670/SwissTPH/openmalaria.svg)](https://zenodo.org/badge/latestdoi/15670/SwissTPH/openmalaria)
 
-You can download the latest build [#200](https://travis-ci.org/SwissTPH/openmalaria/builds/73175741) here: [schema-33.1](https://github.com/SwissTPH/openmalaria/tree/schema-33.1)
+The stable version of OpenMalaria supports schema [schema version 34](https://github.com/SwissTPH/openmalaria/wiki/GeneratedSchema34Doc) and is currently maintained in the __['master' branch](https://github.com/SwissTPH/openmalaria/tree/master)__.
+
+You can download the latest build here: [schema-34.0](https://github.com/SwissTPH/openmalaria/releases/tag/schema-34.0)
 
 Status of __[master](https://github.com/SwissTPH/openmalaria/tree/master)__ builds:
 
 [![Linux Build Status](https://travis-ci.org/SwissTPH/openmalaria.svg?branch=master)](https://travis-ci.org/SwissTPH/openmalaria) [![Windows Build Status](https://ci.appveyor.com/api/projects/status/8el77m2gg4aqqnqg/branch/master?svg=true)](https://ci.appveyor.com/project/tph-thuering/openmalaria/branch/master)
 
-The development version of OpenMalaria supports the upcoming [schema version 34](https://github.com/SwissTPH/openmalaria/wiki/GeneratedSchema34Doc) and is currently maintained in the __['develop' branch](https://github.com/SwissTPH/openmalaria/tree/develop)__.
-
 Status of __[develop](https://github.com/SwissTPH/openmalaria/tree/develop)__ builds:
 
 
-[![Build Status](https://travis-ci.org/SwissTPH/openmalaria.svg?branch=develop)](https://travis-ci.org/SwissTPH/openmalaria)
-![Coverage Status](https://coveralls.io/repos/SwissTPH/openmalaria/badge.svg)
+[![Build Status](https://travis-ci.org/SwissTPH/openmalaria.svg?branch=develop)](https://travis-ci.org/SwissTPH/openmalaria) [![Windows Build Status](https://ci.appveyor.com/api/projects/status/8el77m2gg4aqqnqg/branch/develop?svg=true)](https://ci.appveyor.com/project/tph-thuering/openmalaria/branch/develop)
 
+Code Coverage: ![Coverage Status](https://coveralls.io/repos/SwissTPH/openmalaria/badge.svg)
 
 License: [GPL v2](http://opensource.org/licenses/GPL-2.0) (see COPYING).
 
+Installation instructions:
+==================
+See [INSTALLATION](https://github.com/openmalaria/wiki/Installation).
 
 Build instructions:
 ===================

appveyor.yml

@@ -0,0 +1,56 @@
+clone_depth: 30
+
+environment:
+  VisualStudioVersion: 14.0
+
+os: Visual Studio 2015
+
+cache:
+  - xsd-4.0.msi -> appveyor.yml
+  - boost_1_55_0.zip -> appveyor.yml
+  - gsl-libs.zip -> appveyor.yml
+  - gsl-headers.zip -> appveyor.yml
+  - zlib.lib.zip -> appveyor.yml
+
+install:
+  - git submodule init && git submodule update
+  - pushd util\install-dep-windows\ && install-dependencies-win.bat & popd
+  - pushd gsl && cmake . & popd
+  - pushd zlib && cmake . & popd
+  - cmd: echo "Dependencies installed and configured"
+  - cmd: echo "Configure openMalaria build and generate solution file 'OpenMalaria.sln' with CMake"
+  - mkdir build-win && pushd build-win && cmake .. -DGSL_LIB_OPT:FILEPATH="%APPVEYOR_BUILD_FOLDER%/lib/gsl.lib" -DZ_LIBRARIES:FILEPATH="%APPVEYOR_BUILD_FOLDER%/lib/zlib.lib" -DXERCESC_LIB_OPT:FILEPATH="%APPVEYOR_BUILD_FOLDER%/xsd/lib/vc-12.0/xerces-c_3.lib" -DZ_INCLUDE_DIRS:PATH="%APPVEYOR_BUILD_FOLDER%/zlib" -DXERCESC_INCLUDE_DIRS:PATH="%APPVEYOR_BUILD_FOLDER%/xsd/include/xercesc" -DBoost_INCLUDE_DIR:PATH="%APPVEYOR_BUILD_FOLDER%/boost_1_55_0" -DGSL_INCLUDE_DIR:PATH="%APPVEYOR_BUILD_FOLDER%/gsl" -DGSL_INCLUDE_DIR2:PATH="%APPVEYOR_BUILD_FOLDER%/gsl/gsl" -DGSL_CBLAS_LIB_OPT:FILEPATH="%APPVEYOR_BUILD_FOLDER%/lib/gslcblas.lib" -DXSD_INCLUDE_DIRS:PATH="%APPVEYOR_BUILD_FOLDER%/xsd/include" -DXSD_EXECUTABLE:FILEPATH="%APPVEYOR_BUILD_FOLDER%/xsd/bin/xsd.exe" & popd
+
+configuration: Release
+
+build:
+  project: build-win\OpenMalaria.sln
+  parallel: true
+  verbosity: normal
+
+after_build:
+  - cmd: ECHO build-log":" https://ci.appveyor.com/project/tph-thuering/openmalaria/build/%APPVEYOR_BUILD_VERSION% >> %APPVEYOR_BUILD_FOLDER%\appveyor.log
+  - cmd: ECHO build-id":" %APPVEYOR_BUILD_ID% >> %APPVEYOR_BUILD_FOLDER%\appveyor.log
+  - cmd: ECHO build-name":" %APPVEYOR_BUILD_NAME% >> %APPVEYOR_BUILD_FOLDER%\appveyor.log
+  - ps: pushd "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin"; .\dumpbin.exe /dependents $env:APPVEYOR_BUILD_FOLDER"\build-win\Release\openMalaria.exe" > $env:APPVEYOR_BUILD_FOLDER"\dependencies.txt"; popd
+  - 7z a openMalaria-windows.zip "%APPVEYOR_BUILD_FOLDER%\build-win\Release\openMalaria.exe" "%APPVEYOR_BUILD_FOLDER%\xsd\bin\xerces-c_3_1_vc120.dll" "%APPVEYOR_BUILD_FOLDER%\README.md" "%APPVEYOR_BUILD_FOLDER%\build-win\schema\scenario_current.xsd" "%APPVEYOR_BUILD_FOLDER%\appveyor.log" "%APPVEYOR_BUILD_FOLDER%\dependencies.txt" "%APPVEYOR_BUILD_FOLDER%\test\autoRegressionParameters.csv" "%APPVEYOR_BUILD_FOLDER%\test\densities.csv"
+
+artifacts:
+- path: openMalaria-windows.zip
+
+notifications:
+- provider: Email
+  to:
+  - [email protected]
+  on_build_success: true
+  on_build_failure: false
+  on_build_status_changed: true
+
+deploy:
+- provider: GitHub
+  auth_token:
+    secure: QDHrqei4LL5ihC0nST2nAf3uCpjvNyKHH11V53o/lpnX5JZLq/gY41iJm9FIQ+Vr
+  artifact: openMalaria-windows.zip
+  draft: true
+  on:
+    APPVEYOR_REPO_TAG: true

doc/changelog.txt

@@ -2,6 +2,20 @@ This file lists significant changes in OpenMalaria from the point of view of
 users. It is however far from complete. The more complete changelog is on the
 wiki: https://github.com/SwissTPH/openmalaria/wiki/Changelog
 
+— 2015-06-19 — Schema 34 —
+
+## Vivax changes
+
+<primaquine> has been renamed to <liverStageDrug>
+Monitoring option nPQTreatments has been renamed to nLiverStageTreatments
+
+## Backwards-compatible schema changes
+
+Intervention usage:
+
+<GVI> and <IRS> now have an optional <usage> element.
+ITN's <usage> child element  is now optional too.
+It is assumed, that when no <usage> child is given, the usage modifier is 100% (proportion of use for a given intervention, which modifies the protectional effect).
 
 — 2014-11-?? — Schema 33 —
 

model/CMakeLists.txt

@@ -2,6 +2,16 @@
 # Copyright © 2005-2009 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
+# Configure this file
+file(STRINGS ${CMAKE_SOURCE_DIR}/version.txt OM_VERSION)
+# make sure version.h gets rebuilt everytime cmake is run
+unset(${CMAKE_CURRENT_BINARY_DIR}/util/version.h CACHE)
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/util/version.h.in
+    ${CMAKE_CURRENT_BINARY_DIR}/util/version.h
+    @ONLY
+)
+
 # Don't use aux_source_directory on . because we don't want to compile openMalaria.cpp in to the lib.
 set (Model_CPP
   Simulator.cpp
@@ -27,6 +37,9 @@ set (Model_CPP
 
   PkPd/LSTMModel.cpp
   PkPd/Drug/LSTMDrug.cpp
+  PkPd/Drug/LSTMDrugOneComp.cpp
+  PkPd/Drug/LSTMDrugThreeComp.cpp
+  PkPd/Drug/LSTMDrugConversion.cpp
   PkPd/Drug/LSTMDrugType.cpp
   PkPd/Drug/LSTMDrugAllele.cpp
   PkPd/LSTMTreatments.cpp
@@ -74,7 +87,6 @@ set (Model_CPP
   util/ModelOptions.cpp
   util/CommandLine.cpp
   util/random.cpp
-  util/StreamValidator.cpp
   util/AgeGroupInterpolation.cpp
   util/sampler.cpp
   util/SpeciesIndexChecker.cpp
@@ -90,6 +102,9 @@ set (Model_CPP
   interventions/Vaccine.cpp
 )
 
+if (${OM_STREAM_VALIDATOR})
+  list(APPEND Model_CPP util/StreamValidator.cpp)
+endif (${OM_STREAM_VALIDATOR})
 # Headers - only included so they show up in IDEs:
 # This misses loads of headers. Fix if you care.
 file (GLOB_RECURSE Model_H "${CMAKE_SOURCE_DIR}/model/*.h")
@@ -103,7 +118,8 @@ include_directories (SYSTEM
   ${Boost_INCLUDE_DIRS}
   ${SPIRIT_INCLUDE_DIRS}
   ${BOINC_INCLUDE_DIRS}
-
+
+  ${CMAKE_BINARY_DIR}/model
   ${CMAKE_SOURCE_DIR}/contrib
   ${CMAKE_SOURCE_DIR}/contrib/FastDelegate_src
   ${CMAKE_SOURCE_DIR}/contrib/floating_point_utilities_v3
@@ -115,6 +131,7 @@ include_directories (
 add_library (model
   ${Model_CPP}
   ${Model_H}
+  ${CMAKE_CURRENT_BINARY_DIR}/util/version.h
 )
 
 if (MSVC)

model/Clinical/CMDecisionTree.cpp

@@ -24,7 +24,7 @@
 #include "PkPd/LSTMTreatments.h"
 #include "util/random.h"
 #include "util/errors.h"
-#include "util/ModelOptions.h"
+#include "util/timeConversions.h"
 #include "interventions/Interfaces.hpp"
 
 #include <limits>
@@ -344,11 +344,6 @@ class CMDTTreatSimple : public CMDecisionTree {
             if( durL < neg1 || durB < neg1 ){
                 throw util::xml_scenario_error( "treatSimple: cannot have durationBlood or durationLiver less than -1" );
             }
-            if( util::ModelOptions::option( util::VIVAX_SIMPLE_MODEL ) ){
-                if( durL != sim::zero() || durB != neg1 )
-                    throw util::unimplemented_exception( "vivax model only supports timestepsLiver=0, timestepsBlood=-1" );
-                // Actually, the model ignores these parameters; we just don't want somebody thinking it doesn't.
-            }
             timeLiver = durL;
             timeBlood = durB;
         }catch( const util::format_error& e ){
@@ -367,8 +362,8 @@ class CMDTTreatSimple : public CMDecisionTree {
     }
 
     virtual CMDTOut exec( CMHostData hostData ) const{
-        hostData.withinHost().treatSimple( timeLiver, timeBlood );
-        return CMDTOut(true);
+        bool bsTreatment = hostData.withinHost().treatSimple( hostData.human, timeLiver, timeBlood );
+        return CMDTOut(bsTreatment);
     }
 
 private: