Merge pull request #1068 from sys-bio/develop

Merge for new release
sys-bio · Jan 23, 2023 · 8fa22f4 · 8fa22f4
2 parents 59c6f39 + 1d1e166
commit 8fa22f4
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,17 +8,17 @@ cmake_minimum_required(VERSION 3.16)
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 2)
-set(ROADRUNNER_VERSION_PATCH 2)
+set(ROADRUNNER_VERSION_MINOR 3)
+set(ROADRUNNER_VERSION_PATCH 1)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 
 if (APPLE AND NOT CMAKE_OSX_ARCHITECTURES)
     # Some CMake features like object libraries get confused if you don't
     # explicitly specify an architecture setting with the Xcode generator.
     #    set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64")
-    set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE INTERNAL "Compile for intel and M1 chips on apple" FORCE)
-    message(STATUS "building on mac with universal binaries")
+    set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE INTERNAL "Compile for intel chips on apple" FORCE)
+    message(STATUS "building on mac for intel chips only.")
 endif()
 
 project(
@@ -104,7 +104,7 @@ set(RR_DEPENDENCIES_INSTALL_PREFIX "${CMAKE_CURRENT_SOURCE_DIR}/dependencies"
 set(LLVM_INSTALL_PREFIX ${RR_DEPENDENCIES_INSTALL_PREFIX} CACHE PATH "Location of LLVM Root directory, which contains bin, lib, include and share directories")
 set(LLVM_ROOT_DIR "${LLVM_ROOT_DIR}")
 
-set(USE_UNIVERSAL_BINARIES "ON" CACHE BOOL "Build llvm with universal binaries on MacOS")
+#set(USE_UNIVERSAL_BINARIES "ON" CACHE BOOL "Build with universal binaries on MacOS")
 
 # todo difference between build tests and build test tools option? (cw)
 option(BUILD_TEST_TOOLS "Build and install test tools" OFF)
@@ -444,6 +444,19 @@ set(ZLIB_INCLUDE_DIR "${RR_DEPENDENCIES_INSTALL_PREFIX}/include/")
 message(STATUS "ZLIB_LIBRARY: ${ZLIB_LIBRARY}")
 message(STATUS "ZLIB_INCLUDE_DIR: ${ZLIB_INCLUDE_DIR}")
 
+#For some reason, something in the bowels of the dependencies needs ZLIB::ZLIB, and won't accept zlib::zlib.
+# I stole this from libsbml's CMakeLists.txt file, since they apparently also suffer the same problem
+# (and are the probable cause, at that.)  I've only seen this needed on Ubuntu, and even there, it's
+# not needed for the azure ubuntu build, just when actually running Ubuntu.
+if(NOT TARGET ZLIB::ZLIB)
+  add_library(ZLIB::ZLIB UNKNOWN IMPORTED)
+  set_target_properties(ZLIB::ZLIB PROPERTIES
+    IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+    IMPORTED_LOCATION "${ZLIB_LIBRARY}"
+    INTERFACE_INCLUDE_DIRECTORIES "${ZLIB_INCLUDE_DIR}")
+endif()
+
+
 find_package(${SBML_TARGET_NAME} CONFIG REQUIRED)
 find_package(rr-libstruct CONFIG REQUIRED)
 find_package(clapack CONFIG REQUIRED)

diff --git a/README.md b/README.md
@@ -20,50 +20,62 @@
 
 # Summary
 
-libroadrunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM to generate extremely high performace code and is the fastest SBML based simulator currently avaialable. Its main purpose is for use as a resuable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. 
+libRoadRunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM) to generate extremely high performance code and is the fastest SBML-based simulator currently available (ref). Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of python bindings that allow it to be easily used from python. 
 
 We provide C/C++, Python and Julia bindings.
 
-Sometimes the link to the C API docs goes bad in the readthedocs. If this happens, here is a permanent link that should remain whatever happens:
+# Documentation
+
+[Full Documentation](https://libroadrunner.readthedocs.io)
+
+[Local Documentation](http://sys-bio.github.io/roadrunner/)  (May be used if above link is failing.)
+
+[C API Documention](https://sys-bio.github.io/roadrunner/OriginalDoxygenStyleDocs/html/index.html)
 
 # Installation
-Python front end (stable):
+
+[Binaries](https://github.com/sys-bio/roadrunner/releases) for Windows, MacOS (including universal binaries for the M1 processor), and Linux
+
+Python wheels are available at the above binaries link, and can also be installed via pip:
 
 `pip install libroadrunner`
 
-Binaries:
+# Example Python usage
 
-Head over to the [Releases](https://github.com/sys-bio/roadrunner/releases) page to download binaries. 
+Once installed in Python (using pip or using the wheels directly), the following simple example script should demonstrate the basics of a roadrunner simulation:
 
-Experimental front end: 
+```python
+import roadrunner
+rr = roadrunner.RoadRunner("https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000010.2?filename=BIOMD0000000010_url.xml")
+results = rr.simulate(0, 2000, 200)
+rr.plot()
+print(results)
+```
 
-`pip install libroadrunner-experimental`
+This simple script downloads [BioModels 10](https://www.ebi.ac.uk/biomodels/BIOMD0000000010) (the Kholodenko model of MAPK oscillation) and runs a simulation for 2000 seconds, storing the results in `results`.  If your system is set up to display figures, it will display a plot of the simulation, then print the numerical values obtained.
 
-# Documentation
+# Dependencies
 
-[Python API Documentation](http://sys-bio.github.io/roadrunner/)
+All libRoadRunner binaries are self-contained, and should include all libraries it depends on.  When building libRoadRunner from source, its dependencies may either be downloaded *en masse* from the [libroadrunner-deps](https://github.com/sys-bio/libroadrunner-deps) repository, may be obtained directly from their [respective sources](https://github.com/sys-bio/libroadrunner-deps/tree/release/third_party), or the libraries may be installed directly on your operating system.  Compilation requires a C++17 compiler.
+
+The one exception to the above is that the libRoadRunner binaries depend on the 'ncurses' library on linux.
 
-[C API Documention](https://sys-bio.github.io/roadrunner/OriginalDoxygenStyleDocs/html/index.html)
 
 # Copyright
 
-Copyright 2013-2021
+Copyright 2013-2022
 
 E. T. Somogyi <sup>1</sup>, J. K. Medley <sup>3</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <sup>3</sup>, K. Choi <sup>3</sup>, W. Copeland <sup>3</sup>, L. Smith <sup>3</sup>, C. Welsh <sup>3</sup> and H. M. Sauro <sup>3</sup>
 
 1. Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405
 2. Dune Scientific, 10522 Lake City Way NE, #302 Seattle WA
 3. Department of Bioengineering, University of Washington, Seattle, WA, 98195
 
-The current (2021) developers are Lucian Smith and Ciaran Welsh.
-
-## Introduction
-
-libRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology.
+The current (2021-present) developer is Lucian Smith.
 
 ## Contributing
 
-**IMPORTANT!** Contributors **must** follow the [contribution guidelines](https://github.com/sys-bio/roadrunner/wiki). Contibuters are responsible for complying with the guidelines, including (but not limited to) making commits to the correct branch. Maintainers are not responsible for changes made to the wrong branch. Contributors take full responsibility for ensuring that their changes get merged into the develop branch.
+Contributors may submit pull requests at any time, and are asked to follow some general [contribution guidelines](https://github.com/sys-bio/roadrunner/wiki).  Bug requests and feature suggestions are also welcomed on the [issues page](https://github.com/sys-bio/roadrunner/issues).
 
 ## libRoadRunner supports the following features:
 
@@ -87,45 +99,44 @@ libRoadRunner is a high-performance and portable simulation engine for systems a
 RoadRunner is licensed for free as an open source programmatic library for use in other 
 applications and as a standalone command line driven application. Its C++ API, C API, and 
 Python APIs have comprehensive documentation. On Windows, OS X, and Linux binary files can be 
+downloaded from the [Releases](https://github.com/sys-bio/roadrunner/releases) page, and the 
+Python bindings can additionally be downloaded via pip. 
 
-downloaded from http://sourceforge.net/projects/libroadrunner/files and can be installed 
-ready for use.
 
 ## Docker images
-Currently we have a manylinux2014 [build](https://hub.docker.com/repository/docker/ciaranwelsh/roadrunner-manylinux2014-base) docker image. The 
-base provides the environment you need to be able to build roadrunner 
-yourself on manylinux2014 (centos 8).  
-
-There are two docker tags associated with roadrunner depending on which 
-version of llvm you want to build with. The options are llvm-13.x for newer 
-roadrunner versions (> v2.2.0) and llvm-6.x for older.
+Currently we have a manylinux2014 [build](https://hub.docker.com/repository/docker/sysbiouw/roadrunner-manylinux2014-base) docker image. The 
+base provides the environment you need to be able to build roadrunner yourself on manylinux2014 (centos 8).  
 
 To get the base image: 
 
-`docker pull ciaranwelsh/roadrunner-manylinux2014-base:llvm-13.x`
-
-and the build image:
-
-`docker pull ciaranwelsh/roadrunner-manylinux2014-build:llvm-13.x`
+`docker pull sysbiouw/roadrunner-manylinux2014-base:llvm-13.x`
 
 Docker build scripts can be found under the `docker` directory from the roadrunner
 root directory. 
 
 We can also build roadrunner in alternative docker environments (ubuntu etc.) on request. 
 
+## Citing
+
+If you use RoadRunner in your research, we would appreciate following citations in any works you publish:
+
+Ciaran Welsh, Jin Xu, Lucian Smith, Matthias König, Kiri Choi, Herbert M Sauro, libRoadRunner 2.0: a high performance SBML simulation and analysis library, *Bioinformatics*, Volume 39, Issue 1, January 2023, btac770, https://doi.org/10.1093/bioinformatics/btac770
+
+Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro, libRoadRunner: a high performance SBML simulation and analysis library, *Bioinformatics*, Volume 31, Issue 20, 15 October 2015, Pages 3315–3321, https://doi.org/10.1093/bioinformatics/btv363
+
 ## Acknowledgements
 
 This work is funded by NIGMS grant: GM081070
 
-Licence
+## Licence
 
 Licensed under the Apache License, Version 2.0 (the License); you may not use this 
 file except in compliance with the License. You may obtain a copy of the License at
 
 http://www.apache.org/licenses/LICENSE-2.0
 
 Unless required by applicable law or agreed to in writing, software distributed 
-under the License is distributed on an ÎAS IS BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+under the License is distributed on an AS-IS BASIS, WITHOUT WARRANTIES OR CONDITIONS 
 OF ANY KIND, either express or implied. See the License for the specific language 
 governing permissions and limitations under the License.
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -33,7 +33,7 @@ stages:
         displayName: MacBuildRoadrunnerCpp
         continueOnError: "false"
         pool:
-          vmImage: 'macOS-10.15'
+          vmImage: 'macOS-11'
         strategy:
           matrix:
             64-bit Mac Release:
@@ -114,7 +114,7 @@ stages:
               cd $(MinicondaRoot)
               echo "ls"
               ls
-              $(CondaExecutable) create --quiet --yes --name $(PythonName) python=$(PythonVersion)
+              $(CondaExecutable) create --quiet --yes --name $(PythonName) python=$(PythonVersion) -c conda-forge
             displayName: InstallCondaEnv
 
           - script: |
@@ -182,7 +182,7 @@ stages:
               targetFolder: $(Build.ArtifactStagingDirectory)
             displayName: Copy to Staging Area
           - publish: $(Build.ArtifactStagingDirectory)
-            artifact: roadrunner-MacOS10.15-$(BuildType)
+            artifact: roadrunner-MacOS11-$(BuildType)
             displayName: Publish
 
   - stage: MacBuildRoadrunnerPython
@@ -193,7 +193,7 @@ stages:
         displayName: MacBuildRoadrunnerPython
         continueOnError: "false"
         pool:
-          vmImage: 'macOS-10.15'
+          vmImage: 'macOS-11'
         strategy:
           matrix:
             py38:
@@ -205,6 +205,9 @@ stages:
             py310:
               PythonVersion: 3.10
               PythonName: py310
+            py311:
+              PythonVersion: 3.11
+              PythonName: py311
         variables:
           MinicondaRoot : '/usr/local/miniconda'
           PythonRoot: '$(MinicondaRoot)/envs/$(PythonName)'
@@ -237,7 +240,7 @@ stages:
               cd $(MinicondaRoot)
               echo "ls"
               ls
-              $(CondaExecutable) create --quiet --yes --name $(PythonName) python=$(PythonVersion)
+              $(CondaExecutable) create --quiet --yes --name $(PythonName) python=$(PythonVersion) -c conda-forge
               echo "running: $(PipExecutable) install -r $(SOURCE_DIR)/test-requirements.txt"
               $(PipExecutable) install -r $(SOURCE_DIR)/test-requirements.txt
             displayName: InstallCondaEnv
@@ -285,15 +288,15 @@ stages:
               rm -r $(DEPS_INSTALL_PREFIX)/install-azure
               ls
             displayName: Move Dependencies
-          - task: Cache@2
-            inputs:
-              key: "Swig | $(Agent.OS)"
-              path: $(SWIG_INSTALL_PREFIX)
-              cacheHitVar: SWIG_CACHE
-            displayName: Cache Swig-4.0.2
+#          - task: Cache@2
+#            inputs:
+#              key: "Swig | $(Agent.OS)"
+#              path: $(SWIG_INSTALL_PREFIX)
+#              cacheHitVar: SWIG_CACHE
+#            displayName: Cache Swig-4.0.2
           - script: |
               echo "installing pcre"
-              sudo apt install -y libpcre3 libpcre3-dev
+              brew install pcre pcre2
               mkdir -p $(SWIG_SOURCE_DIR)
               echo "cd to swig source dir: $(SWIG_SOURCE_DIR)"
               cd $(SWIG_SOURCE_DIR)
@@ -376,15 +379,15 @@ stages:
           - task: CopyFiles@2
             inputs:
               contents: '$(INSTALL_DIR)/**'
-              targetFolder: $(Build.ArtifactStagingDirectory)/roadrunner-MacOS10.15-$(PythonName)
+              targetFolder: $(Build.ArtifactStagingDirectory)/roadrunner-MacOS11-$(PythonName)
             displayName: Copy Install Tree to Staging Area
           - task: CopyFiles@2
             inputs:
               contents: '$(INSTALL_DIR)/dist/**'
               targetFolder: $(Build.ArtifactStagingDirectory)/pip-wheels
             displayName: Copy Pip Wheels to Staging Area
           - publish: $(Build.ArtifactStagingDirectory)
-            artifact: roadrunner-MacOS10.15-$(PythonName)
+            artifact: roadrunner-MacOS11-$(PythonName)
             displayName: Publish Pip Wheels Artifacts
 
 ########################################################################
@@ -566,6 +569,9 @@ stages:
             py310:
               PythonVersion: 3.10
               PythonName: py310
+            py311:
+              PythonVersion: 3.11
+              PythonName: py311
         variables:
           MinicondaRoot : 'C:\Miniconda'
           PythonRoot: '$(MinicondaRoot)\envs\$(PythonName)'
@@ -588,8 +594,9 @@ stages:
           - powershell: |
               where.exe conda
               where.exe python
-              conda update conda -y
+              conda update conda -y -c conda-forge
               conda install numpy
+              conda install python=3.11 -c conda-forge
               conda --version
               echo "PythonVersion $(PythonVersion)"
               echo "PythonName $(PythonName)"
@@ -611,7 +618,7 @@ stages:
               cacheHitVar: LLVM_CACHE
           - script: |
               echo "Creating new conda environment"
-              conda create --quiet --yes --name $(PythonName) python=$(PythonVersion)
+              conda create --quiet --yes --name $(PythonName) python=$(PythonVersion) -c conda-forge
               echo "pip help:"
               $(PipExecutable) install --help
 
@@ -696,7 +703,7 @@ stages:
               echo "ls"
               ls
               echo "Creating new conda environment"
-              conda create --quiet --yes --name $(PythonName) python=$(PythonVersion)
+              conda create --quiet --yes --name $(PythonName) python=$(PythonVersion) -c conda-forge
               echo "pip help:"
               $(PipExecutable) install --help
               echo "$(PipExecutable) install -q -r $(SOURCE_DIR)/test-requirements.txt and requirements.txt"
@@ -758,7 +765,7 @@ stages:
         displayName: UbuntuBuildRoadrunnerCpp
         continueOnError: "false"
         pool:
-          vmImage: 'Ubuntu-18.04'
+          vmImage: 'Ubuntu-20.04'
         strategy:
           matrix:
             64-bit Linux Release:
@@ -961,8 +968,11 @@ stages:
             py310:
               PythonVersion: 3.10
               PythonName: py310
+            py311:
+              PythonVersion: 3.11
+              PythonName: py311
         pool:
-          vmImage: 'ubuntu-18.04'
+          vmImage: 'ubuntu-20.04'
         container: sysbiouw/roadrunner-manylinux2014-base:latest
         variables:
           CCACHE_DIR: '$(Pipeline.Workspace)/ccache'

diff --git a/docs/docs-build/.buildinfo b/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: 6fe8ded2a92374737db879ef72778739
+config: 4fdea462f19561a75feef109d8a885cd
 tags: 645f666f9bcd5a90fca523b33c5a78b7