Commit f1bbb90c authored by JoseGuzman's avatar JoseGuzman

updated Linux install document

parent c0947af3
...@@ -5,7 +5,7 @@ Building Stimfit ...@@ -5,7 +5,7 @@ Building Stimfit
:Author: Jose Guzman, Christoph Schmidt-Hieber :Author: Jose Guzman, Christoph Schmidt-Hieber
:Date: |today| :Date: |today|
This document describes how to install `Stimfit <http://www.stimfit.org>`_ |version| under GNU/Linux. The installation was tested on a GNU/Debian testing/unstable system, with a 2.6-based kernel and with support for Python 2.5. and Python 2.6. It should work on other Debian-based systems (e.g Ubuntu) aswith newer version of Stimfit as well. I assume that you have the GNU C compiler (gcc) and the GNU C++ compiler (g++) already installed in your system. Please, check that both versions match. For our installation we will use gcc-4.2.4 and the same version of g++. This document describes how to install `Stimfit <http://www.stimfit.org>`_ |version| under GNU/Linux. The installation was tested on a GNU/Debian testing/unstable with support for Python 2.*. It should work on other Debian-based systems (e.g. Ubuntu) as with newer version of Stimfit as well. I assume that you have the GNU C compiler (gcc) and the GNU C++ compiler (g++) and that both versions match. For this installation, we tested 4.2.4versions.
============================ ============================
What we need before we start What we need before we start
...@@ -36,19 +36,22 @@ For the impatient, here are all `Stimfit <http://www.stimfit.org>`_ build depend ...@@ -36,19 +36,22 @@ For the impatient, here are all `Stimfit <http://www.stimfit.org>`_ build depend
This will get you, amongst others: This will get you, amongst others:
* [wxWidgets]_: C++ library that contains the user interface (version 2.8 is only recommended!)
* [wxPython]_: GUI toolkit for the Python language.
* [boost]_: C++ library that is mainly used for its shared pointers. * [boost]_: C++ library that is mainly used for its shared pointers.
* [Lapack]_: A linear algebra library. * [Lapack]_: A linear algebra library.
* [fftw]_: Library for computing Fourier transformations. * [fftw]_: Library for computing Fourier transformations.
* [NumPy]_: To handle multidimensional arrays and perform more complex numerical computations with Python. * [NumPy]_: To handle numerical computations with Python (use version >=1.7.1).
* [HDF5]_: This is the hierarchical Data Format 5 (HDF5) to manage large amount of data. * [HDF5]_: Hierarchical Data Format 5 (HDF5) to manage large amount of data.
* [Matplotlib]_: Plotting library for Python (use version >= 1.5.1)
In addition, you can install doxygen, python-sphinx and graphviz if you want to build the documentation. In addition, you can install doxygen, python-sphinx (with graphviz and Latex) if you want to build the documentation.
======================= =======================
Optional: PyEMF Optional: PyEMF
======================= =======================
[PyEMF]_ is needed to export figures to the windows meta file format (WMF/EMF). EMF is a vector graphics format and can be imported in different Office software including LibreOffice. In order to install it, do: [PyEMF]_ is needed to export figures to the windows meta fileformat (WMF/EMF). EMF is a vector graphics format and can be imported in different Office software including LibreOffice. To install it, do:
:: ::
...@@ -91,8 +94,7 @@ to generate the configure script. Remember that we need Autoconf, Automake and L ...@@ -91,8 +94,7 @@ to generate the configure script. Remember that we need Autoconf, Automake and L
$ ./configure --enable-python $ ./configure --enable-python
The **--enable-python** option is absolutely necessary to install `Stimfit <http://www.stimfit.org>`_ since some of the functionality depends on Python. The configure script has some additional options. For example, we may want to use `IPython <http://www.scipy.org>`_ instead of the default embedded python shell with the option **---enable-ipython** (note that the `IPython <http://www.scipy.org>`_ shell is only available under GNU/Linux and it is still very experimental). The **--enable-python** option is absolutely necessary to install `Stimfit <http://www.stimfit.org>`_ since some of the functionality depends on Python. The configure script has some additional options.
Finally, after running configure, you can type Finally, after running configure, you can type
...@@ -141,7 +143,7 @@ We recommend to build `Stimfit <http://www.stimfit.org>`_ with the `BioSig libr ...@@ -141,7 +143,7 @@ We recommend to build `Stimfit <http://www.stimfit.org>`_ with the `BioSig libr
:: ::
cd biosig-code/biosig4c+ cd biosig-code/biosig4c++
autoconf # needed first time after getting repository autoconf # needed first time after getting repository
./configure ./configure
make make
...@@ -153,7 +155,7 @@ After that you can enter the option --with-biosig in the configure script of `St ...@@ -153,7 +155,7 @@ After that you can enter the option --with-biosig in the configure script of `St
Building documentation Building documentation
====================== ======================
The manual of `Stimfit <http://www.stimfit.org>`_ including the documentation is accessible on-line in http://www.stimfit.org/doc/sphix/. To have your local copy, you will need to install sphinx: The manual of `Stimfit <http://www.stimfit.org>`_ including the documentation is accessible on-line in http://www.stimfit.org/doc/sphix/. To have your local copy, you will need to install sphinx version 1.7 or older:
:: ::
...@@ -188,6 +190,7 @@ The local documentation of the source code will be in $HOME/stimfit/doc/doxygen/ ...@@ -188,6 +190,7 @@ The local documentation of the source code will be in $HOME/stimfit/doc/doxygen/
.. [Lapack] http://www.netlib.org/lapack/ .. [Lapack] http://www.netlib.org/lapack/
.. [HDF5] http://www.hdfgroup.org/HDF5/ .. [HDF5] http://www.hdfgroup.org/HDF5/
.. [NumPy] http://www.numpy.org .. [NumPy] http://www.numpy.org
.. [PyEMF] http://http://pyemf.sourceforge.net .. [PyEMF] http://pyemf.sourceforge.net
.. [fftw] http://www.fftw.org .. [fftw] http://www.fftw.org
.. [Doxygen] http://www.doxygen.org .. [Doxygen] http://www.doxygen.org
.. [Matplotlib] https://matplotlib.org
...@@ -158,7 +158,7 @@ You can pass a 2D-NumPy array to :func:`stf.new_window_matrix()`. The first dime ...@@ -158,7 +158,7 @@ You can pass a 2D-NumPy array to :func:`stf.new_window_matrix()`. The first dime
>>> numpy_matrix[1] = np.sqrt( np.abs(get_trace()) ) >>> numpy_matrix[1] = np.sqrt( np.abs(get_trace()) )
>>> new_window_matrix(numpy_matrix) >>> new_window_matrix(numpy_matrix)
In this example, np is the NumPy namespace. Typing np. at the command prompt will show you all available NumPy functions. :func:`stf.get_size_trace()` will be explained later on. In this example, np is the [NumPy]_ namespace. Typing np. at the command prompt will show you all available [NumPy]_ functions. :func:`stf.get_size_trace()` will be explained later on.
* **new_window_list()** * **new_window_list()**
...@@ -394,7 +394,7 @@ Cutting traces is best done using the squared braked operators ([]) to slice a [ ...@@ -394,7 +394,7 @@ Cutting traces is best done using the squared braked operators ([]) to slice a [
>>> new_window(a[:100]) >>> new_window(a[:100])
>>> new_window(a[100:]) >>> new_window(a[100:])
In this example, a[:100] refers to a sliced NumPy array that comprises all sampling points from index 0 to index 99, and a[100:] refers to an array from index 100 to the last sampling point. In this example, a[:100] refers to a sliced [NumPy]_ array that comprises all sampling points from index 0 to index 99, and a[100:] refers to an array from index 100 to the last sampling point.
* **cut_traces(pt)** and **cut_traces_multi(pt_list)** * **cut_traces(pt)** and **cut_traces_multi(pt_list)**
...@@ -452,5 +452,4 @@ will cut the selected traces at every 100th sampling point, starting with the 10 ...@@ -452,5 +452,4 @@ will cut the selected traces at every 100th sampling point, starting with the 10
.. [Python-tutorial] http://docs.python.org/tut/ .. [Python-tutorial] http://docs.python.org/tut/
.. [Python-website] http://www.python.org/doc/ .. [Python-website] http://www.python.org/doc/
.. [NumPy] http://numpy.scipy.org/
.. [SciPy] http://www.scipy.org/ .. [SciPy] http://www.scipy.org/
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