From e16b537a854c6e584f33029469f03773947b0a9b Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Wed, 31 Oct 2018 09:19:54 +0530
Subject: [PATCH] Update install.rst
---
docs/source/install/install.rst | 53 +++++++++++++++++----------------
1 file changed, 28 insertions(+), 25 deletions(-)
diff --git a/docs/source/install/install.rst b/docs/source/install/install.rst
index 82265fb5..cd0fe1f6 100644
--- a/docs/source/install/install.rst
+++ b/docs/source/install/install.rst
@@ -4,12 +4,16 @@ Use pre-built packages
pip
^^^^
-If you only need `python` interface, use `pip`. This is the easiest way to install Python interface.
-This solution has been tested for Linux and MacOSX.
+If you only need `python` interface, the recommended way is via `pip`.
::
- pip install pymoose
+ pip install pymoose --user
+
+To install nightly version
+::
+ pip install pymoose --pre --upgrade --user
+
-We also build moose package with additional components such as gui and `moogli`.
+We also have moose package with additional components such as gui and `moogli`.
Linux
^^^^^^
@@ -28,7 +32,9 @@ to pick your distribution and follow instructions.
Mac OSX
^^^^^^^^
-MacOSX support for moose-gui is not complete yet. However, the python-scripting interface can be installed on OSX using ``homebrew``
+MacOSX support for moose-gui is not complete yet because moose-gui depends on PyQt4 but that
+world has moved onto PyQt5 (See the status here: https://github.com/BhallaLab/moose-gui/issues/16).
+However, the python-scripting interface can be installed on OSX using ``homebrew``
::
$ brew tap BhallaLab/moose
$ brew install moose
@@ -83,36 +89,33 @@ Core MOOSE
""""""""""
- Required:
- cmake (version 2.8 or higher)
- - g++ (>= 4.6.x) For building the C++ MOOSE core.
+ - g++ or clang (with `c++11` support).
- gsl-1.16 or higher.
- Optional
- - HDF5 (>=1.8.x) For reading and writing data into HDF5 based formats
+ - HDF5 (>=1.8.x) For reading and writing data into HDF5 based formats. Disabled by default.
Python interface for core MOOSE API (pymoose)
"""""""""""""""""""""""""""""""""""""""""""""
- Required
- - Python2 ( >= 2.7.x) For building the MOOSE Python bindings
- - Python-dev ( >= 2.7.x) Python development headers and libraries, e.g. `python-dev` or `python-devel`
+ - python (Both 2.7 and 3.x versions are supported).
+ - python-dev. Python development headers and libraries, e.g. `python-dev` or `python-devel`
- NumPy ( >= 1.6.x) For array interface, e.g. `python-numpy` or `numpy`
- Optional
- - NetworkX (1.x) For automatical layout
- - pygraphviz For automatic layout for chemical models
- - Matplotlib (>=1.1.x) For plotting simulation results
- - python-libsbml For reading and writing chemical models from and into SBML format
+ - networkx (>=1.x) For automatical layout
+ - pygraphviz. For automatic layout for chemical models
+ - matplotlib (>=2.x). For plotting simulation results
+ - python-libsbml. For reading and writing chemical models from and into SBML format
+ - pylibsbml
-Most of the dependencies can be installed using package manager.
+All of these dependencies can be installed using `pip` or your package manager.
On ``Debian/Ubuntu``
::
$ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
-.. note::
-
- Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
- higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
On ``CentOS/Fedora/RHEL/Scientific Linux``
::
@@ -124,7 +127,7 @@ On ``OpenSUSE``
$ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
-build moose
+Build moose
^^^^^^^^^^^
.. code-block:: bash
@@ -183,12 +186,12 @@ Alternatively the moose-gui folder exists within the moose folder downloaded and
Below are packages which you may want to install to use MOOSE Graphical User Interface.
- Required:
- - PyQt4 (4.8.x) For Python GUI
- - Matplotlib ( >= 1.1.x) For plotting simulation results
- - NetworkX (1.x) For automatical layout
- - suds/suds-jurko (0.4) For accessing models hosted on biomodels database.
+ - PyQt4 (4.8.x). For Python GUI
+ - Matplotlib ( >= 2.x). For plotting simulation results
+ - NetworkX (1.x). For automatical layout
+
- Optional:
- - python-libsbml For reading and writing signalling models from and into SBML format
+ - python-libsbml. For reading and writing signalling models from and into SBML format
On ``Ubuntu/Debian``, these can be installed with
::
@@ -258,7 +261,7 @@ After this, building and installing ``moogli`` should be as simple as
$ mkdir _build
$ cd _build
$ cmake ..
- $ make
+ $ make -j3
$ sudo make install
If you run into troubles, please report it on our `github repository
--
GitLab