5.0.3 Release (#45)

Version 5.0.3 (2024-11)
==========================

Python API
----------
1. Added `HDF5MultiFileReader` to read simulation data from several HDF5 files at once.
2. `Simulation.toDB` can now be called without a `uid`.
3. Random number generators (`RNG` class) now have default constructor arguments

Bugfixes
--------
1. Improve behavior of stochastic paths (added in 5.0.1). Vesicles test more available sites on path, which reduces chance of vesicle becoming blocked if furthest site is unavailable.
2. Fix rare vesicle surface diffusion crash for boost versions < 1.73 (issue was introduced in 5.0.2)
3. Fix vesicles erroneously diffusing to different compartment (issue was introduced in 5.0.1)
5. Fix compilation issues with mpi4py >= 4.0.0 and Open MPI < 5.0.0
6. Fix `DistMesh.intersect` method computations failing under some conditions

Dependencies
------------

1. Updated the [overlap](https://github.com/severinstrobl/overlap) library to [d2a165e](https://github.com/severinstrobl/overlap/commits/d2a165e1e3ac3519fc18b9c260811f15ffe3aa5b) (development version)

.github/workflows/sdist.yml

@@ -0,0 +1,70 @@
+---
+name: Create and test source distribution
+on:
+  pull_request: null
+  push:
+    branches:
+      - main
+env:
+  apt_option: -o Acquire::Retries=3
+  apt_pkgs: >
+    build-essential git libgl1 libglu1 libopenblas-dev libopenmpi-dev
+    librdmacm-dev libxcursor1 libxft2 libxinerama1 libxrender1 pkg-config
+    zlib1g-dev
+jobs:
+  build-sdist:
+    name: build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.11
+      - name: Setup MPI
+        uses: mpi4py/setup-mpi@v1
+        with:
+          mpi: openmpi
+      - name: Install system packages for MPI
+        run: |
+          sudo apt-get ${{ env.apt_options }} update -y
+          sudo apt-get ${{ env.apt_options }} install ${{ env.apt_pkgs }}
+      - name: install Python build packages
+        run: |
+          python -m pip install build "pip<23.1"
+          python --version
+          pip --version
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Create source distribution
+        run: python -m build --sdist .
+      - name: upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: |
+            dist/*.tar.gz
+            requirements.txt
+      - name: Install source distribution
+        run: |
+          cd dist
+          tar zxf *.tar.gz
+          rm -f *.tar.gz
+          cd steps-*
+          python -m pip install ".[bundle]"
+      - name: Check installation by importing the steps module
+        uses: jannekem/run-python-script-action@v1
+        with:
+          script: |
+            import steps
+            steps._greet()
+      - name: Checkout STEPS example repository
+        uses: actions/checkout@v4
+        with:
+          repository: CNS-OIST/STEPS_Example
+          path: example
+      - name: Run a few simulations
+        run: |
+          python3 example/python_scripts/API_2/well_mixed/well_mixed.py
+          python3 example/python_scripts/API_2/diffusion/diffusion.py

.gitignore

@@ -66,7 +66,10 @@ Pipfile.lock
 .pre-commit-config.yaml
 .bbp-project-venv/
 
+# spack build files
 spconfig.*
+spack*
+.spack*
 
 # ignore checkpoints created by UT
 test/unit/py/*.cp

CMake/BundleOmega_h.cmake

@@ -22,6 +22,9 @@ ExternalProject_Add(
   CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=../omega_h-install -DOmega_h_USE_MPI:BOOL=ON
              -DCMAKE_CXX_COMPILER:FILEPATH=mpicxx -DOmega_h_USE_Gmsh_DEFAULT:BOOL=ON
              -DOmega_h_USE_Gmsh:BOOL=ON -DCMAKE_CXX_FLAGS=-O3
+             -DGmsh_INCLUDE_DIRS=${Gmsh_INCLUDE_DIRS}
+             -DGmsh_EXECUTABLE=${Gmsh_EXECUTABLE}
+             -DGmsh_LIBRARIES=${Gmsh_LIBRARIES}
   EXCLUDE_FROM_ALL True)
 ExternalProject_Add_StepTargets(omega_h install)
 

CMake/FindEigen3.cmake

@@ -0,0 +1,97 @@
+# ~~~
+# - Try to find Eigen3 lib
+#
+# This module supports requiring a minimum version, e.g. you can do
+#   find_package(Eigen3 3.1.2)
+# to require version 3.1.2 or newer of Eigen3.
+#
+# Once done this will define
+#
+#  EIGEN3_FOUND - system has eigen lib with correct version
+#  EIGEN3_INCLUDE_DIR - the eigen include directory
+#  EIGEN3_VERSION - eigen version
+#
+# This module reads hints about search locations from
+# the following enviroment variables:
+#
+# EIGEN3_ROOT
+# EIGEN3_ROOT_DIR
+
+# Copyright (c) 2006, 2007 Montel Laurent, <[email protected]> Copyright (c) 2008, 2009 Gael
+# Guennebaud, <[email protected]> Copyright (c) 2009 Benoit Jacob <[email protected]>
+# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
+# ~~~
+
+if(NOT Eigen3_FIND_VERSION)
+  if(NOT Eigen3_FIND_VERSION_MAJOR)
+    set(Eigen3_FIND_VERSION_MAJOR 2)
+  endif(NOT Eigen3_FIND_VERSION_MAJOR)
+  if(NOT Eigen3_FIND_VERSION_MINOR)
+    set(Eigen3_FIND_VERSION_MINOR 91)
+  endif(NOT Eigen3_FIND_VERSION_MINOR)
+  if(NOT Eigen3_FIND_VERSION_PATCH)
+    set(Eigen3_FIND_VERSION_PATCH 0)
+  endif(NOT Eigen3_FIND_VERSION_PATCH)
+
+  set(Eigen3_FIND_VERSION
+      "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}")
+endif(NOT Eigen3_FIND_VERSION)
+
+macro(_eigen3_check_version)
+  file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
+
+  string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match
+               "${_eigen3_version_header}")
+  set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match
+               "${_eigen3_version_header}")
+  set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match
+               "${_eigen3_version_header}")
+  set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}")
+
+  set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION})
+  if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+    set(EIGEN3_VERSION_OK FALSE)
+  else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+    set(EIGEN3_VERSION_OK TRUE)
+  endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+
+  if(NOT EIGEN3_VERSION_OK)
+
+    message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, "
+                   "but at least version ${Eigen3_FIND_VERSION} is required")
+  endif(NOT EIGEN3_VERSION_OK)
+endmacro(_eigen3_check_version)
+
+if(EIGEN3_INCLUDE_DIR)
+
+  # in cache already
+  _eigen3_check_version()
+  set(EIGEN3_FOUND ${EIGEN3_VERSION_OK})
+
+else(EIGEN3_INCLUDE_DIR)
+
+  # search first if an Eigen3Config.cmake is available in the system, if successful this would set
+  # EIGEN3_INCLUDE_DIR and the rest of the script will work as usual
+  find_package(Eigen3 ${Eigen3_FIND_VERSION} NO_MODULE QUIET)
+
+  if(NOT EIGEN3_INCLUDE_DIR)
+    find_path(
+      EIGEN3_INCLUDE_DIR
+      NAMES signature_of_eigen3_matrix_library
+      HINTS ENV EIGEN3_ROOT ENV EIGEN3_ROOT_DIR
+      PATHS ${CMAKE_INSTALL_PREFIX}/include ${KDE4_INCLUDE_DIR}
+      PATH_SUFFIXES eigen3 eigen)
+  endif(NOT EIGEN3_INCLUDE_DIR)
+
+  if(EIGEN3_INCLUDE_DIR)
+    _eigen3_check_version()
+  endif(EIGEN3_INCLUDE_DIR)
+
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
+
+  mark_as_advanced(EIGEN3_INCLUDE_DIR)
+
+endif(EIGEN3_INCLUDE_DIR)

CMake/FindGmsh.cmake

@@ -51,7 +51,8 @@ if(Gmsh_EXECUTABLE)
 endif()
 
 find_path(Gmsh_INCLUDE_DIRS NAMES gmsh.h)
-find_library(Gmsh_LIBRARIES NAMES gmsh)
+find_library(Gmsh_LIBRARIES NAMES gmsh gmsh.${Gmsh_VERSION_MAJOR}.${Gmsh_VERSION_MINOR}
+                                  libgmsh.so.${Gmsh_VERSION_MAJOR}.${Gmsh_VERSION_MINOR})
 
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(