Merge pull request #1169 from sys-bio/develop

Release 2.5.0

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: docs/requirements.txt

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)

README.md

@@ -1,20 +1,15 @@
 # libRoadRunner
 [![GitHub version](https://badge.fury.io/gh/sys-bio%2Froadrunner.svg)](http://badge.fury.io/gh/sys-bio%2Froadrunner)
 [![Build Status](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_apis/build/status/sys-bio.roadrunner?branchName=develop)](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_build/latest?definitionId=8&branchName=develop)
-
-<table style="width:100%">
-  <tr>
-    <td><img alt="Read the Docs" src="https://img.shields.io/readthedocs/roadrunner"></td>
-    <td><a href="https://badge.fury.io/gh/sys-bio%2Froadrunner"><img src="https://badge.fury.io/gh/sys-bio%2Froadrunner.svg" alt="GitHub version" height="18"></a></td>
-  </tr>
-</table> 
+[![Documentation Status](https://readthedocs.org/projects/libroadrunner/badge/?version=latest)](https://libroadrunner.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/libroadrunner.svg)](https://badge.fury.io/py/libroadrunner)
 
  <table style="width:100%">
   <tr>
     <td><img alt="Licence", src="https://img.shields.io/badge/License-Apache%202.0-yellowgreen"</td>
     <td><img alt="PyPI - Downloads", src="https://img.shields.io/pypi/dm/roadrunner"></td>
     <td><img alt="Funding", src="https://img.shields.io/badge/Funding-NIH%20(GM123032)-blue"></td>
-    <td><a href="https://badge.fury.io/py/tellurium"><img src="https://badge.fury.io/py/roadrunner.svg" alt="PyPI version" height="18"></a> </td>
+    <td><img alt="Funding", src="https://img.shields.io/badge/Funding-NIBIB%20(EB028887)-blue"></td>    
    </tr>
 </table> 
 
@@ -40,6 +35,16 @@ Python wheels are available at the above binaries link, and can also be installe
 
 `pip install libroadrunner`
 
+### Google Colab
+libroadrunner can be used entirely in a browser using [Google Colab](https://colab.research.google.com/).  Ideally, it will work with the following steps (updated May 2023)
+
+1. run a cell with ```!apt-get install libncurses5```
+2. run a cell with ```!pip install libroadrunner```
+3. (Vert important) Restart the runtime (From the menu: 'Runtime / Restart runtime')
+4. Test by running ```import roadrunner```
+
+The Python version behind Colab is reasonably stable but can change. This issue to changes in how colab handles packages. we try to keep abreast of changes at colab.
+
 # Example Python usage
 
 Once installed in Python (using pip or using the wheels directly), the following simple example script should demonstrate the basics of a roadrunner simulation:

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
@@ -792,6 +788,8 @@ stages:
           - script: |
               echo "SOURCE_DIR $(SOURCE_DIR)"
               echo "BUILD_DIR $(BUILD_DIR)"
+              echo "BuildType $(BuildType)"
+              echo "BuildDocs $(BuildDocs)"
               echo "INSTALL_DIR $(INSTALL_DIR)"
               echo "LLVM_INSTALL_PREFIX $(LLVM_INSTALL_PREFIX)"
               echo "DEPS_INSTALL_PREFIX $(DEPS_INSTALL_PREFIX)"
@@ -842,14 +840,18 @@ stages:
               echo "g++ $(g++ --version)"
               sudo add-apt-repository ppa:ubuntu-toolchain-r/test
               sudo apt-get update
-              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra
+              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra graphviz
               sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 1
             displayName: Install g++10 and doxygen
           - script: |
               eval "$(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: |
+              echo "pip install dependencies"
+              $(PipExecutable) install -r $(SOURCE_DIR)/docs/requirements.txt
+            displayName: "Install doc requirements"
           - script: |
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
               echo "give execute permissions to llvm-config using chmod 777"
@@ -861,8 +863,7 @@ stages:
               source: 'specific'
               project: 'libroadrunner-deps'
               pipeline: 9
-              runVersion: 'latestFromBranch'
-              runBranch: 'refs/heads/release'
+              runVersion: 'latest'
               artifact: libroadrunner-deps-$(Agent.OS)-$(BuildType)
               path: $(DEPS_INSTALL_PREFIX)
             displayName: Download libroadrunner-deps install artifacts
@@ -886,8 +887,22 @@ stages:
               mkdir $(BUILD_DIR)
               echo "CD to build dir: $(BUILD_DIR)"
               cd $(BUILD_DIR)
-              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=$(BuildType) -DBUILD_DOCS=${BuildDocs} ..
+              echo "cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DBUILD_DOCS=$(BuildDocs) -DCMAKE_BUILD_TYPE=$(BuildType) -DSPHINX_EXECUTABLE=$(SphinxExecutable) .."
+              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DBUILD_DOCS=$(BuildDocs) -DCMAKE_BUILD_TYPE=$(BuildType) -DSPHINX_EXECUTABLE=$(SphinxExecutable) ..
             displayName: Run CMake Configure Command
+          - script: |
+              echo "cd to docs dir"
+              cd $(SOURCE_DIR)/docs/
+              rm -r -f docs-build doxygen-output
+            displayName: Remove roadrunner docs before re-building
+            condition: eq(variables.BuildType, 'Release')
+          - script: |
+              echo "cd to build dir"
+              cd $(BUILD_DIR)
+              make roadrunner-docs-doxygen
+              make roadrunner-docs-sphinx
+            displayName: Build roadrunner docs
+            condition: eq(variables.BuildType, 'Release')
           - script: |
               export CC=/usr/bin/gcc-10
               export CXX=/usr/bin/g++-10
@@ -920,20 +935,9 @@ stages:
             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 $(SOURCE_DIR)/docs/docs-build '$(INSTALL_DIR)/docs/docs-build'
               mv $(SOURCE_DIR)/docs/doxygen-output '$(INSTALL_DIR)/docs/doxygen-output'
               ls '$(INSTALL_DIR)/docs'
             displayName: Make Docs

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.

docs/CMakeLists.txt

@@ -1,7 +1,7 @@
 ##################################################################
 # Usage
 # -----
-# Build the roadrunner-docs-sphinx target
+# Build the roadrunner-docs-doxygen and roadrunner-docs-sphinx targets
 #
 
 ##################################################################
@@ -17,15 +17,14 @@
 # when you configure the cmake project. This defines two cmake targets
 #    1) roadrunner-docs-doxygen
 #    2) roadrunner-docs-sphinx
-# Building the roadrunner-docs-sphinx target will execute all commands necessary, since it depends
-# on roadruner-docs-doxygen target.
+# You need to build the first and then build the second.  At one point, the second was dependent on the first, but that seems to have broken at some point, but building them both explicitly does work.
 #
 
 ##################################################################
 # Dependencies
 # ------------
-# You will need Sphinx and some python packages
-#   - pip install sphinx breathe sphinxcontrib-bibtex sphinx-tabs sphinx_rtd_theme
+# You will need Sphinx and some python packages, all listed in docs/requirements.txt
+#   - pip install -r docs/requirements.txt
 # and doxygen. Make sure you either install doxygen in a default location, so that
 # cmake can find it or add the path to the doxygen executable to the PATH environment
 # variable so cmake can find it.