5.0.4 Release (#47)

Version 5.0.4 (2025-05)
==========================

Dependencies
------------
1. Bump bundled SUNDIALS to 6.0.0 for compatibility with CMake 4.0

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)

5.0.2 Release (#44)

Version 5.0.2 (2024-06)
==========================

Python API
----------
1. The minimum python version was bumped from 3.6 to 3.8.

Bugfixes
--------
1. Fixed compilation issue when PETSc is not installed.
2. Fixed installation issue in Conda environments.

Internal code base
------------------
1. Use Boost instead of GSL for computing qtable for vesicle surface diffusion.
2. Remove GSL as a minimum prerequisite.

stepsblender python package
---------------------------
1. Fixed issues caused by changes in Blender 4.1 python API.

5.0.1 Release (#37)

Version 5.0.1 (2024-03)
==========================

New Features
------------
1. Added a new mode of kiss-and-run release allowing for partial release of vesicle content.
2. Added a variety of automatic checks to vesicle-based models.
3. Added support for network-free simulation of multi-state complexes with `Wmdirect`.

Python API
----------
1. Added a new `CustomResults` result selector to save arbitrary data to STEPS HDF5 files.
1. Added a `.description` property to `ResultSelector`s.
2. Added a `.patchTriNeighbs` property to `TriReference`s to get neighboring triangles in the same patch.

Version 5.0.0 (2023-06)
==========================

New Features
------------
1. Introduce a new solver named `TetVesicle` that simulates vesicles, lipid rafts and related phenomena such as endocytosis, exocytosis and active transport on virtual actin filaments. 
   The solver is built on top of the `TetOpSplit` routines for parallel simulation of SSA reaction and diffusion events. 
2. Add a new `stepsblender` python module that allows visualisation of STEPS simulation data recorded with `XDMFHandler` using the Blender 3D computer graphics software (https://www.blender.org/).
3. Checkpointing added or updated for solvers `TetVesicle`, `TetOpSplit`, `Tetexact`, `TetODE`, `Wmdirect`, `Wmrk4`,  `Wmrssa`.

beta release of 5.0.0

Remove older cmake files (#31)

Version 4.1.1 (2023-04)
==========================
Build and Packaging
-------------------
1. Fix older cmake files causing installation issues
2. Fix `-DSTEPS_USE_DIST_MESH=False` cmake flag not preventing `Omega_h` installation

Release 4.1.0 (#30)

Version 4.1.0 (2023-04)
==========================
License update
------------------
1. Project license changed to GPL3.0.

Python API
----------
1. Added automatic saving to HDF5 files (HDF5Handler) and XDMF files (XDMFHandler). Data saved
   with XDMFHandler can be visualized with scientific visualization software like Paraview.

Internal code base
------------------
1. Performance improvement: Identify the tetrahedra with molecule changes via diffusion 
(changes caused by reaction are updated by the ssa operator) and update the associated propensities.

this tag applies the necessary fixes on efield while maintaining the …

…same performance as 4.0.0 for publication reference.

4.0.0 Release (#26)

Python API
----------

Introduce a new parallel stochastic reaction-diffusion solver and a deterministic
membrane potential solver named `DistTetOpSplit`. The solver is based on a 
distributed mesh named `DistMesh`.

Build and Packaging
-------------------
1. STEPS requires a C++ compiler compatible with C++ 17.
2. New CMake variables to enable profiling of the simulation:
   `STEPS_USE_LIWKID_PROFLING`, `STEPS_USE_CALIPER_PROFILING`, and `STEPS_USE_NATIVE_PROFILING`
   see [doc/dev/README.md] for more details on how to use it.
3. Add support to Apple M1
4. Add support to compilers GCC 11, LLVM 13, and Apple Clang 13

3.6.0 Release (#21)