From c9952d9a7b988da4804100c8f589d875043fc63f Mon Sep 17 00:00:00 2001 From: James Marshall Date: Mon, 30 Sep 2019 15:40:49 +0100 Subject: [PATCH 1/5] Update version number and contributors for first release patch --- DemoNotebooks/EpidemicsDemo_SIRI.ipynb | 4 ++-- mumot/__init__.py | 5 ++++- mumot/_version.py | 2 +- mumot/utils.py | 1 + 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/DemoNotebooks/EpidemicsDemo_SIRI.ipynb b/DemoNotebooks/EpidemicsDemo_SIRI.ipynb index ea86ebc..0c6e67c 100644 --- a/DemoNotebooks/EpidemicsDemo_SIRI.ipynb +++ b/DemoNotebooks/EpidemicsDemo_SIRI.ipynb @@ -423,7 +423,7 @@ "source": [ "MuMoT also enables more sophisticated stochastic simulations of your model. The `multiagent` command allows you to run simulations either with static agents interacting over a static communication network, or mobile agents communicating to neighbours within a local range of communication. Here we will focus on the network setting.\n", "\n", - "Each agent represents an individual, and exchanges messages to interact with other agents and change its internal state (described as a *probabilistic finite state machine*). The conversion of transition rates into the probabilities is done following the methodology proposed in Reinal et al. ([2005](#references)).\n", + "Each agent represents an individual, and exchanges messages to interact with other agents and change its internal state (described as a *probabilistic finite state machine*). The conversion of transition rates into the probabilities is done following the methodology proposed in Reina et al. ([2005](#references)).\n", "\n", "Similarly to the well-mixed SIRI model, the network SIRI model also has different dynamical regimes which are distinguished by the values of $r_0$ and $r_1$. However, while in the well-mixed case the threshold value for $r_0$ and $r_1$ was 1, in the network setting the threshold value can be shown to be $1/\\lambda_{max}(A)$ , where $\\lambda_{max}(A)$ is the largest eigenvalue of the adjacency matrix for the network. For example, for a fully connected network $\\lambda_{max}(A) = N-1$ where $N$ is the number of nodes in the graph. \n", "\n", @@ -474,7 +474,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.4" + "version": "3.7.4" }, "toc": { "base_numbering": 1, diff --git a/mumot/__init__.py b/mumot/__init__.py index f55cbc1..f32502f 100644 --- a/mumot/__init__.py +++ b/mumot/__init__.py @@ -2,9 +2,12 @@ For documentation and version information use about() -Contributors: +Authors: James A. R. Marshall, Andreagiovanni Reina, Thomas Bose +Contributors: +Robert Dennison + Packaging, Documentation and Deployment: Will Furnass diff --git a/mumot/_version.py b/mumot/_version.py index 816ee07..d9233f1 100644 --- a/mumot/_version.py +++ b/mumot/_version.py @@ -1,2 +1,2 @@ -version_info = (1, 0, 0) +version_info = (1, 1, 0) __version__ = "{}.{}.{}".format(*version_info) diff --git a/mumot/utils.py b/mumot/utils.py index 2e5f45a..f075941 100644 --- a/mumot/utils.py +++ b/mumot/utils.py @@ -19,6 +19,7 @@ def about() -> None: """Print version, author and documentation information.""" print("Multiscale Modelling Tool (MuMoT): Version " + _version.__version__) print("Authors: James A. R. Marshall, Andreagiovanni Reina, Thomas Bose") + print("Contributors: Robert Dennison, Will Furnass") print("Documentation: https://mumot.readthedocs.io/") From 1a610dabc6aed8f9f3848e4df78bb3f156799384 Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Mon, 30 Sep 2019 16:54:17 +0100 Subject: [PATCH 2/5] Update mybinder.org links so latest stable release (1.1.0) is built by default) --- README.md | 2 +- docs/source/development.rst | 2 +- docs/source/getting_started.rst | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index f148030..e42e991 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![Build Status](https://api.travis-ci.org/DiODeProject/MuMoT.svg?branch=master)](https://travis-ci.org/DiODeProject/MuMoT/branches) [![Documentation Status](https://readthedocs.org/projects/mumot/badge/?version=latest)](https://mumot.readthedocs.io/en/latest/?badge=latest) [![Coverage Status](https://codecov.io/github/DiODeProject/MuMoT/coverage.svg?branch=master)](https://codecov.io/gh/DiODeProject/MuMoT) -[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/DiODeProject/MuMoT/master?filepath=docs%2FMuMoTuserManual.ipynb) +[![Binder (latest stable release)](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/DiODeProject/MuMoT/v1.1.0?filepath=docs%2FMuMoTuserManual.ipynb) ## Introduction / overview diff --git a/docs/source/development.rst b/docs/source/development.rst index 3098998..7f5a099 100644 --- a/docs/source/development.rst +++ b/docs/source/development.rst @@ -282,7 +282,7 @@ The repo2docker build process takes ~15 mins for MuMoT; therefore note that any pushes to the master branch will invalidate any cached image for the tip of the master branch, which will increase mybinder.org startup times from seconds to ~15 mins. -**Button**: A mybinder.org session for the User Manual as of the tip of the master branch can be started by +**Button**: A mybinder.org session for the User Manual as of the latest stable release of MuMoT can be started by following the link in the instructions for :ref:`getting started online `. Branch, tag and version policy, inc. how to create a new release diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 1e2310e..cee934e 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -21,7 +21,7 @@ View and interact with the user manual online: .. image:: https://mybinder.org/badge.svg :alt: Start running MuMoT user manual on mybinder.org - :target: https://mybinder.org/v2/gh/DiODeProject/MuMoT/master?filepath=docs%2FMuMoTuserManual.ipynb + :target: https://mybinder.org/v2/gh/DiODeProject/MuMoT/v1.1.0?filepath=docs%2FMuMoTuserManual.ipynb Note that this uses the excellent and free `mybinder.org `__ service, funded by the `Gordon and Betty Moore Foundation `__, @@ -36,8 +36,8 @@ Demo notebooks -------------- The following demo notebooks are also available online: -* `Paper `_: (*MuMoT authors, University of Sheffield*) -* `Epidemics `_: (*Renato Pagliara, Princeton University*) +* `Paper `_: (*MuMoT authors, University of Sheffield*) +* `Epidemics `_: (*Renato Pagliara, Princeton University*) On your own machine ------------------- From 7b4c40ede2d4b9bc3fd3ebb75ebe0514fcedc1bb Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Tue, 1 Oct 2019 10:11:18 +0100 Subject: [PATCH 3/5] Add version and Python version badge to README --- README.md | 5 ++++- setup.py | 3 ++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e42e991..3867eb2 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,12 @@ # MuMoT: Multiscale Modelling Tool +[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/DiODeProject/MuMoT/v1.1.0?filepath=docs%2FMuMoTuserManual.ipynb) +[![PyPI version](https://badge.fury.io/py/mumot.svg)](https://badge.fury.io/py/mumot) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mumot) + [![Build Status](https://api.travis-ci.org/DiODeProject/MuMoT.svg?branch=master)](https://travis-ci.org/DiODeProject/MuMoT/branches) [![Documentation Status](https://readthedocs.org/projects/mumot/badge/?version=latest)](https://mumot.readthedocs.io/en/latest/?badge=latest) [![Coverage Status](https://codecov.io/github/DiODeProject/MuMoT/coverage.svg?branch=master)](https://codecov.io/gh/DiODeProject/MuMoT) -[![Binder (latest stable release)](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/DiODeProject/MuMoT/v1.1.0?filepath=docs%2FMuMoTuserManual.ipynb) ## Introduction / overview diff --git a/setup.py b/setup.py index c876415..07b13da 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,8 @@ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: OS Independent", "Programming Language :: Python", - "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Mathematics", From b2af896e8a988e145a655d19e654f4cc26f6099a Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Tue, 1 Oct 2019 14:27:14 +0100 Subject: [PATCH 4/5] Add Robert Dennison to Sphinx "about" page --- docs/source/about.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/source/about.rst b/docs/source/about.rst index 6a80972..8925492 100644 --- a/docs/source/about.rst +++ b/docs/source/about.rst @@ -10,6 +10,10 @@ Core Development Team: * `Andreagiovanni Reina`_ * `Thomas Bose`_ +Contributors: + +* `Robert Dennison`_ + Packaging, Documentation and Deployment: * `Will Furnass`_ From 8b0ef67283a997b633ec8e00d24d246645bbc16f Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Tue, 1 Oct 2019 17:04:00 +0100 Subject: [PATCH 5/5] v1.1.0: add (reserved) DOI --- docs/source/about.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/about.rst b/docs/source/about.rst index 8925492..616b4df 100644 --- a/docs/source/about.rst +++ b/docs/source/about.rst @@ -12,7 +12,7 @@ Core Development Team: Contributors: -* `Robert Dennison`_ +* Robert Dennison (rtdennison1@sheffield.ac.uk) Packaging, Documentation and Deployment: @@ -28,6 +28,7 @@ Citation If you use MuMoT in your own work please cite the original paper describing MuMoT, as well as the DOI for the version of MuMoT you used (to credit developers involved in that version): * Marshall, J. A. R., Reina, A., Bose, T. (2019) Multiscale Modelling Tool: Mathematical modelling of collective behaviour without the maths. *Under submission* +* Marshall, J. A. R., Reina, A., Bose, T., Dennison, R., Furnass, W., Pagliara Vasquez, R. (2019) MuMoT release 1.1.0 doi: https://doi.org/10.15131/shef.data.9925010 * Marshall, J. A. R., Reina, A., Bose, T. (2019) MuMoT release 1.0.0 doi: https://doi.org/10.15131/shef.data.7951298.v1 .. todo:: Add formatted citation and BibTeX entry inc ORDA_ (FigShare) / Zenodo_ DOI.