From 8e2b55583d27bc0f8ed7bc9b476f67ff700fdadd Mon Sep 17 00:00:00 2001 From: yannikschaelte Date: Wed, 21 Mar 2018 10:35:34 +0100 Subject: [PATCH] improve readme --- README.md | 26 +++++++++----------------- 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 12f54ec..901bde8 100644 --- a/README.md +++ b/README.md @@ -21,14 +21,13 @@ the original source code found [here](https://github.com/ICB-DCM/pABC-SMC) from ### Installation ### -It is required, +It is required that -* that SWIG is installed, +* SWIG is installed, * either use your system package manager, or ``conda install swig`` if running anaconda * BLAS is installed - * use your system package manager, if not installed. It should be already installed - if you're running anaconda (e.g. the MKL or OpenBLAS) + * use your system package manager, if not installed. It should be already installed if you're running anaconda (e.g. the MKL or OpenBLAS) Python requirements are: @@ -39,16 +38,16 @@ Python requirements are: Then, * clone the repository ``git clone https://github.com/ICB-DCM/tumor2d`` -* chane into the repository directory ``cd tumor2d`` +* change into the repository directory ``cd tumor2d`` * and run ``python setup.py build_ext --inplace`` from within the repository * if the repo is in your ``PYTHONPATH``, you should be able to use it now -* if you want to install the package run ``pip install .`` +* if you want to install the package, run ``pip install .`` ### Usage ### The function ``tumor2d.simulate`` is the main entry point. -To run it with the default parameters do +To run it with the default parameters, do ``` from tumor2d import simulate @@ -73,20 +72,13 @@ The function returns a dictionary containing the * ``proliferation_profile`` which can be used as summary statistics for ABC-SMC inference -with [pyABC](http://pyabc.readthedocs.io/en/latest/). +with [pyABC](http://pyabc.readthedocs.io/en/latest/). In the documentation of pyABC, there is an [example](http://pyabc.readthedocs.io/en/latest/examples/multiscale_agent_based.html) included, showing how to perform analysis for this model. ### Distribution ### -Currently not possible to make a package via ``python setup.py bdist_wheel`` -reliably. -The reason is, that ``build_ext`` has to be run before the other installation steps -so that the SWIG generated ``.py`` is properly included. -There are indications online on how to achieve running SWIG first. -However, these did not work so far. -However, it works to run ``python setup.py build_ext --inplace``, possibly followed -by ``python setup.py bdist_wheel``, as the SWIG generated ``.py`` file is -then already there. +Currently, it is not possible to make a package via ``python setup.py bdist_wheel`` reliably. The reason i, that ``build_ext`` has to be run before the other installation steps, so that the SWIG generated ``.py`` is properly included. +There are indications online on how to achieve running SWIG first. However, these did not work so far. Meanwhile, it works to run ``python setup.py build_ext --inplace``, possibly followed by ``python setup.py bdist_wheel``, as the SWIG generated ``.py`` file is then already there.