From 7fb4d8fd8c501fca96d03a29d2832d1c3357c4a7 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Mon, 7 Mar 2022 17:29:14 -0800 Subject: [PATCH 1/3] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3eac99cc..2cf28137 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@

- +

SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems embedded in Lagrangian reference frame particle based fluid dynamics domain @@ -7,7 +7,7 @@ SpatialPy is a Python 3 package for simulation of spatial deterministic/stochast This package is intended to replace the PyURDME software https://github.com/pyurdme/pyurdme and will feature both a NSM solver for RDME simulation on static domains and a sSSA-SDPD particle based fluid dynamics solver as described in the publication "A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems" by Drawert, Jacob, Li, Yi, Petzold https://www.sciencedirect.com/science/article/pii/S0021999118307101
- + PLEASE REGISTER AS A USER, so that we can prove SpatialPy has many users when we seek funding to support development. SpatialPy is part of the StochSS project.
From 9b71836faa06e254e8399744e0a852115e303676 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Wed, 9 Mar 2022 10:20:22 -0800 Subject: [PATCH 2/3] more readme cleanup --- README.md | 7 +++++-- RELEASE_NOTES | 17 ----------------- 2 files changed, 5 insertions(+), 19 deletions(-) delete mode 100644 RELEASE_NOTES diff --git a/README.md b/README.md index 2cf28137..2e6a4d93 100644 --- a/README.md +++ b/README.md @@ -25,9 +25,11 @@ Table of contents - [_Using the source code repository_](#using-the-source-code-repository) - [Usage](#usage) - [_Simple example to illustrate the use of SpatialPy_](#simple-example-to-illustrate-the-use-of-spatialpy) + - [Getting help](#getting-help) - [Contributing](#contributing) - [License](#license) @@ -72,8 +74,8 @@ SpatialPy provides simple object-oriented abstractions for defining a model of a The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more. For more detailed examples on how to use SpatialPy, please see the Jupyter notebooks contained in the [examples](https://github.com/StochSS/SpatialPy/tree/main/examples) subdirectory. - -### Docker environment + Getting help ------------ diff --git a/RELEASE_NOTES b/RELEASE_NOTES deleted file mode 100644 index 718c22b1..00000000 --- a/RELEASE_NOTES +++ /dev/null @@ -1,17 +0,0 @@ - RELEASE NOTES - SpatialPy - -These are release notes for SpatialPy. ----------------------------------------- -Date: 2/25/2021 -Version: 0.5.0+beta ----------------------------------------- -- Initial beta release ----------------------------------------- -Date: 3/9/2021 -Version: 0.5.1+beta ----------------------------------------- -- Added pickling Results -- Added add_mesh() function -- timespan() now includes option to set timestep size -- Added ability to read StochSS domains From af6d642fc54e137676ebbf7817ab91a6189ef662 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Wed, 9 Mar 2022 11:17:12 -0800 Subject: [PATCH 3/3] Bumped version 1.0.1 --- spatialpy/__version__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py index 22fc6782..9ebc0fc0 100644 --- a/spatialpy/__version__.py +++ b/spatialpy/__version__.py @@ -23,7 +23,7 @@ # @website https://github.com/StochSS/SpatialPy # ============================================================================= -__version__ = '1.0' +__version__ = '1.0.1' __title__ = 'SpatialPy' __description__ = 'Python Interface for Spatial Stochastic Biochemical Simulations' __url__ = 'https://spatialpy.github.io/SpatialPy/'