@@ -23,23 +23,33 @@ The following software is required before installing StochPy (see user guide for
2323- [ libxml2] ( http://xmlsoft.org ) (optional)
2424- [ mpmath] ( http://mpmath.org ) (optional)
2525
26- Install the StochPy dependencies with PIP using the following command (in your StochPy Python virtual environment):
26+ Install StochPy and dependencies with PIP using the following command (in your StochPy Python virtual environment):
2727``` bash
28- pip install numpy scipy matplotlib python-libsbml mpmath lxml jedi==0.17.2 ipython
28+ pip install scipy matplotlib python-libsbml jedi==0.17.2 ipython stochpy
2929```
3030
31- #### Linux/MAC OS/Cygwin
31+ If you are using Anaconda, create a custom conda environment for StochPy, for example:
32+ ``` bash
33+ conda create -n " stochpy39" -c sbmlteam python=3.9 pip scipy matplotlib sympy ipython
34+ ```
35+ activate your new environment, install StochPy (only required once per environment) and start ipython.
36+ ``` bash
37+ conda activate stochpy39
38+ pip install stochpy
39+ ipython
3240
41+ ```
3342
34- In the directory where you downloaded StochPy, go to the directory _ StochPy-2.1.0 _ and exec the next command:
43+ #### Linux/MAC OS/Cygwin from source.
3544
45+ In the directory where you downloaded/cloned the StochPy source, for example, the git main branch:
3646``` bash
3747sudo python setup.py install
3848```
3949
4050### Windows
4151
42- Use the available windows installer or the setup file
52+ Use the available windows installer or use PyPI (described above).
4353
4454## Getting Started
4555
@@ -192,4 +202,4 @@ http://dx.doi.org/10.1371/journal.pone.0079345
192202Copyright (c) 2011-2021, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
193203Vrije Universiteit Amsterdam. All rights reserved.
194204
195- StochPy is open source software distributed under the BSD 3-Clause License see LICENSE file for more details.
205+ StochPy is open source software distributed under the BSD 3-Clause License see LICENSE file for more details.
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