Unverified Commit ee7f38d3 authored by Christoph Schmidt-Hieber's avatar Christoph Schmidt-Hieber Committed by GitHub

Merge pull request #69 from JoseGuzman/master

update documentation
parents e8cc8faa c4e3a37f
......@@ -18,7 +18,7 @@ Then, you need the `Stimfit <http://www.stimfit.org>`_ source code:
$ cd $HOME
$ git clone https://github.com/neurodroid/stimfit.git
This will download the code to a directory called *stimfit*.
It will download the code to a directory called *stimfit*.
Next, you need to generate the build system:
......@@ -38,10 +38,17 @@ Now you can configure. I strongly recommend building in a separate directory.
$ cd module
$ ../../configure --enable-module
Remember to add the argument *--with-biosig* to the configure script
if you want to have extra biomedical fileformats for stfio.
We recommend to use BioSig to read extra biomedical fileformats (see :ref:`BioSigBuild`) :
If you want to install the *stfio* module for a non-default Python distribution, such as **Anaconda Python**, use the argument *--prefix=* to specify the installation path as where your favorite Python distribution is installed. The following example will install *stfio* for Anaconda Python 2.7:
::
$ ../../configure --enable-module --with-biosig
===================================================
Building stfio for non-default Python distributions
===================================================
To install the *stfio* module in distributions such as **Anaconda Python**, use the argument *--prefix=* to specify the path where the Python distribution is installed. For example, to install *stfio* for Anaconda Python 2.7 use:
::
......@@ -53,6 +60,11 @@ If using virtual environment, try something like this:
$ ../../configure --enable-module --prefix=$HOME/anaconda/envs/py36
Other Python versions are also possible. For example, to install the module in your local Python version, you could use:
::
$ ../../configure --enable-module --prefix=$HOME/.local/lib/python2.7
Then, build and install:
......
......@@ -42,7 +42,7 @@ This will get you, amongst others:
* [NumPy]_: To handle multidimensional arrays and perform more complex numerical computations with Python.
* [HDF5]_: This is the hierarchical Data Format 5 (HDF5) to manage large amount of data.
In addition, you can install doxygen, python-sphinx and graphviz if you want to build yourself the documentation.
In addition, you can install doxygen, python-sphinx and graphviz if you want to build the documentation.
=======================
Optional: PyEMF
......@@ -82,6 +82,7 @@ Go to the stimfit directory (in our example $HOME/stimfit) and type:
::
$ cd $HOME/stimfit
$ ./autogen.sh
to generate the configure script. Remember that we need Autoconf, Automake and LibTool to use autogen. After that, you can call it with
......@@ -116,28 +117,33 @@ where [N] is the number of parallel builds you want to start. And finally:
and after that call **make** and **make install** as normal user. The Stimfit executable will be now in $HOME/.local
.. _BioSigBuild:
==========================================
Building Stimfit with BioSig import filter
==========================================
It is recommended to build `Stimfit <http://www.stimfit.org>`_ with the `BioSig <http://biosig.sourceforge.net>`_ import the file filters to read HEKA files or to have the possibility import some other file formats used biomedical signal processing. To do it, follow this instructions:
We recommend to build `Stimfit <http://www.stimfit.org>`_ with the `BioSig library <http://biosig.sourceforge.net>`_ to import files in from different biomedical disciplines. It is necessary to read files acquired with `HEKA amplifiers <http://www.heka.com>`_ or with `Signal <http://ced.co.uk/products/sigovin>`_ from CED. To do it, follow this instructions:
1. It is first recommended to install libsuitesparse and libz libraries:
1. Install libsuitesparse and libz libraries:
::
sudo apt-get install libsuitesparse-dev libz-dev gawk
2. Download BioSig sources: you can obtain the latest BioSig version in `BioSig downloads <http://biosig.sourceforge.net/download.html>`_ . Choose BioSig for C/C++, libbiosig (v1.5.6 or higher is recommended). Alternatively, you can obtain the latest developmental version from the git repository:
2. Download the BioSig sources: you can obtain the latest BioSig version in `BioSig downloads <http://biosig.sourceforge.net/download.html>`_ . Choose BioSig for C/C++, libbiosig (v1.5.6 or higher is recommended). Alternatively, you can obtain the latest developmental version from the git repository:
::
git clone git://git.code.sf.net/p/biosig/code biosig-code
git clone https://git.code.sf.net/p/biosig/code biosig-code
3. Compile and install the sources: enter the directory **biosig4c++** and type:
3. Enter the directory **biosig4c++** and compile and install the sources:
::
cd biosig-code/biosig4c+
autoconf # needed first time after getting repository
./configure
make
sudo make install
......@@ -147,17 +153,17 @@ After that you can enter the option --with-biosig in the configure script of `St
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 own local copy of the documentation, 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:
::
sudo apt-get install python-sphinx
It is possible to build a local copy of the documentation there by calling:
To build a local copy call:
::
sphinx-build $HOME/Stimfit/doc/sphinx/ <destinyFolder>
sphinx-build $HOME/Stimfit/doc/sphinx/ <destinyFolder> # destiny folder could be $HOME/tmp/stf/doc/
The html documentation will be located in <destinyFolder>/index.html
......@@ -171,6 +177,7 @@ Enter a directory called **doc** inside Stimfit (e.g $HOME/stimfit/doc) and type
::
cd $HOME/stimfit/doc
doxygen DoxyFile
The local documentation of the source code will be in $HOME/stimfit/doc/doxygen/html
......
......@@ -11,6 +11,16 @@ References
`Stimfit <http://www.stimfit.org>`_ has been used for data analysis in the following publications. If you miss a reference to your publication, please let us know `here <https://groups.google.com/forum/#!forum/stimfit>`_.
====
2018
====
* `Hua Hu, Fabian C. Roth, David Vandael, Peter Jonas (2018) https://www.sciencedirect.com/science/article/pii/S0896627318301454?via%3Dihub>`_ Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons. *Neuron* 10.1016/j.neuron.2018.02.024.
* `Sooyun Kim, Yoonsub Kim, Suk-Ho Lee, Won-Kyung Ho (2018) https://elifesciences.org/articles/35269>`_ Dendritic spikes in hippocampal granule cells are necessary for long-term potentiation at the perforant path synapse. *eLife* 2018:Mar 26:7.
* `John J Marshall, Jian Xu, Anis Contractor (2018) <http://www.jneurosci.org/content/early/2018/03/14/JNEUROSCI.1788-17.2018>`_ Kainate receptors inhibit glutamate release via mobilization of endocannabinoids in striatal direct pathway Spiny Projection Neurons (dSPNs). *J Neurosci* 38(16):1788-17.
====
2017
====
......
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