Differences between revisions 21 and 46 (spanning 25 versions)

Python

We provide as many modules as possible that come with the current Debian GNU/Linux stable release. Nevertheless, that might not be enough for your needs since you may want to use the newest version of some module or one that is not part of Debian. Furthermore you might want to use a different version of Python.

The recommended way to install additional python modules is through pip. Unfortunately, pip does not allow users to install modules in the user context. That means that you will first have to install your own version of python in your home. From that moment on, you can install modules through pip.

Installing your own python versions with pyenv

Pyenv is a collection of tools that allow users to manage different versions of python. In the simplest case you will need it to simply get an installation of python in your user space. Using that custom python installation, you will then be able to install additional modules in a very comfortable way, since you can install them in the "system path" (which is then somewhere within your home).

Here is a small howto for installing python 2.7.13 in your home:

Install pyenv:

curl https://raw.githubusercontent.com/yyuu/pyenv-installer/master/bin/pyenv-installer -o pyenv-installer

Check what the script is doing and then execute it:

bash ./pyenv-installer

You can remove the installer file afterwards.

Add the following three lines to your ~/.bash_profile:

export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init -)" 
eval "$(pyenv virtualenv-init -)"

Restart your shell so the path changes take effect:
```
exec $SHELL
```
Install some python version, e.g. for python 2.7.13:
```
env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 2.7.13
pyenv rehash
```
Note, that settting of PYTHON_CONFIGURE_OPTS="--enable-shared" is needed if you need to link against the libpython shared library.
Make sure that this new python version will be used when you run python. You only need to run this command once:
```
pyenv global 2.7.13
```
In order to update pyenv run:
```
pyenv update
```

Documentation of pyenv

Website of pyenv

https://github.com/yyuu/pyenv/

Website of pyenv installer

https://github.com/yyuu/pyenv-installer

Installation of additional or newer modules with pip

Once you installed your custom python with the explanations given above, you are ready to install additional or newer modules the easy way. The usage of pip is very easy. The following command installs the module numpy

pip install numpy

while the next command would upgrade an existing installation of numpy

pip install --upgrade numpy

For advanced usage of pip, please consult the manuals: http://pip.readthedocs.org/en/latest/

Installation of Python modules that are not available in the archives of pip

Here we provide some shell script snippets for installing frequently asked modules which cannot be installed through pip. These scripts just provide an example installation. You might have to adapt some paths in order to make the module work correctly with the version of python you are using (e.g. if you run your custom python provided through pyenv).

nlopt

   1 #!/bin/bash
   2 
   3 # Installation script for nlopt library
   4 
   5 VERSION=2.3
   6 INSTALLDIR=$HOME/.local
   7 BUILDDIR=/scratch/$USER/nlopt
   8 
   9 mkdir -p $BUILDDIR
  10 cd $BUILDDIR
  11 
  12 wget "http://ab-initio.mit.edu/nlopt/nlopt-${VERSION}.tar.gz"
  13 tar -xvvzkf nlopt-${VERSION}.tar.gz
  14 cd nlopt-${VERSION}
  15 
  16 ./configure \
  17         --enable-shared \
  18         --prefix=$INSTALLDIR \
  19         OCT_INSTALL_DIR=$INSTALLDIR/octave/oct \
  20         M_INSTALL_DIR=$INSTALLDIR/octave/m/ \
  21         MEX_INSTALL_DIR=$INSTALLDIR/mex \
  22         GUILE_INSTALL_DIR=$INSTALLDIR/guile
  23 
  24 make
  25 make install

CategoryLXSW

-  ⇤ ← Revision 21 as of 2014-05-12 08:34:56 → 
  Size: 4311
  Editor: bonaccos
  Comment:
+   ← Revision 46 as of 2018-08-28 08:41:49 → ⇥
  Size: 4032
  Editor: davidsch
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#rev 2018-08-28 davidsch
-Line 3:
+Line 5:
-We provide as many modules as possible that come with the current Debian GNU/Linux stable release. Nevertheless, that might not be enough for your needs since you may want to use the newest version of some module or one that is not part of Debian.
+We provide as many modules as possible that come with the current Debian GNU/Linux stable release. Nevertheless, that might not be enough for your needs since you may want to use the newest version of some module or one that is not part of Debian. Furthermore you might want to use a different version of Python.
-Line 5:
+Line 7:
-Since Python 2.6 there is an easy way to install missing or outdated modules in your home through `easy_install`.
+The recommended way to install additional python modules is through {{{pip}}}. Unfortunately, {{{pip}}} does not allow users to install modules in the user context. That means that you will first have to install your own version of python in your home. From that moment on, you can install modules through {{{pip}}}.
-Line 7:
+Line 9:
-== How to use easy_install ==
-Line 9:
+Line 10:
- || Command line help:         || `easy_install --help` ||
 || Online documentation:      || http://packages.python.org/distribute/easy_install.html ||
 || Install a new module:      || `easy_install --user MODULENAME` ||
 || Update an existing module: || `easy_install --user -U MODULENAME` ||
+== Installing your own python versions with pyenv ==
-Line 14:
+Line 12:
-Modules will be installed in your home within `~/.local/`. You do not need to adapt the `PYTHONPATH` environment variable since python will look for modules in this directory automatically.
+{{{Pyenv}}} is a collection of tools that allow users to manage different versions of python. In the simplest case you will need it to simply get an installation of python in your user space. Using that custom python installation, you will then be able to install additional modules in a very comfortable way, since you can install them in the "system path" (which is then somewhere within your home).
-Line 16:
+Line 14:
-== Installing other versions of Python ==
+Here is a small howto for installing python 2.7.13 in your home:
-Line 18:
+Line 16:
-You can of course install other versions of Python in your home. A very comfortable way of doing that is by using [[https://github.com/yyuu/pyenv|pyenv]]. You will find a howto on that website with detailled instructions how to use it.
+ * Install pyenv:
 {{{
curl https://raw.githubusercontent.com/yyuu/pyenv-installer/master/bin/pyenv-installer -o pyenv-installer}}}
 Check what the script is doing and then execute it:
 {{{
bash ./pyenv-installer
}}}
 You can remove the installer file afterwards.
 * Add the following three lines to your ~/.bash_profile:
 {{{
export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init -)" 
eval "$(pyenv virtualenv-init -)"}}}
-Line 20:
+Line 30:
-With pyenv you can also install additional Python modules like the whole scipy stack in the home directory.
+ * Restart your shell so the path changes take effect:
 {{{
exec $SHELL}}}
-Line 22:
+Line 34:
-== Installation of custom (non easy_install-able) Python modules in the home directory of a user ==
+ * Install some python version, e.g. for python 2.7.13:
 {{{
env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 2.7.13
pyenv rehash}}}
 Note, that settting of `PYTHON_CONFIGURE_OPTS="--enable-shared"` is needed if you need to link against the libpython shared library.
-Line 24:
+Line 40:
-We are sometimes asked for newer version of Python modules. We do no longer build Python modules in SEPP as the requests for modules and their versions is too widespread to keep these modules maintainable.
+ * Make sure that this new python version will be used when you run python. You only need to run this command once:
 {{{
pyenv global 2.7.13}}}
-Line 26:
+Line 44:
-On this page we will list some bash-snippets that install some often requested modules in a users home.
+ * In order to update {{{pyenv}}} run:
 {{{
pyenv update}}}
-Line 28:
+Line 48:
-== numpy ==
+=== Documentation of pyenv ===
 || Website of pyenv || https://github.com/yyuu/pyenv/ ||
 || Website of pyenv installer || https://github.com/yyuu/pyenv-installer ||
-Line 30:
+Line 52:
-{{{#!highlight bash
#!/bin/bash
-Line 33:
+Line 53:
-VERSION_NUMPY=1.7.1
builddir="/scratch/${USER}/build/numpy"
+== Installation of additional or newer modules with pip ==
-Line 36:
+Line 55:
-mkdir -p ${builddir}
+Once you installed your custom python with the explanations given above, you are ready to install additional or newer modules the easy way. The usage of {{{pip}}} is very easy. The following command installs the module {{{numpy}}}
{{{
pip install numpy}}}
while the next command would upgrade an existing installation of {{{numpy}}}
{{{
pip install --upgrade numpy}}}
-Line 38:
+Line 62:
-cd ${builddir}
wget --output-document=numpy-${VERSION_NUMPY}.tar.gz \
    http://sourceforge.net/projects/numpy/files/NumPy/${VERSION_NUMPY}/numpy-${VERSION_NUMPY}.tar.gz/download
tar -xvvzkf numpy-${VERSION_NUMPY}.tar.gz
cd numpy-${VERSION_NUMPY}
python setup.py build --fcompiler=gnu95
python setup.py install --user
}}}
+For advanced usage of {{{pip}}}, please consult the manuals: http://pip.readthedocs.org/en/latest/
-Line 47:
+Line 64:
-== scipy ==
-Line 49:
+Line 65:
-|| '''Depends on''' ||
|| numpy ||
+== Installation of Python modules that are not available in the archives of pip ==
-Line 52:
+Line 67:
-{{{#!highlight bash
#!/bin/bash

VERSION_SCIPY=0.13.0b1
builddir="/scratch/${USER}/build/scipy"

mkdir -p ${builddir}

cd ${builddir}
wget --output-document=scipy-${VERSION_SCIPY}.tar.gz \
    http://downloads.sourceforge.net/project/scipy/scipy/${VERSION_SCIPY}/scipy-${VERSION_SCIPY}.tar.gz
tar -xvvzkf scipy-${VERSION_SCIPY}.tar.gz
cd scipy-${VERSION_SCIPY}
python setup.py build
python setup.py install --user
}}}

== matplotlib ==

|| '''Depends on''' ||
|| numpy ||

{{{#!highlight bash
#!/bin/bash

VERSION_MATPLOTLIB=1.3.0
builddir="/scratch/${USER}/build/matplotlib"

mkdir -p ${builddir}

cd ${builddir}
wget --output-document=matplotlib-${VERSION_MATPLOTLIB}.tar.gz \
    http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-${VERSION_MATPLOTLIB}/matplotlib-${VERSION_MATPLOTLIB}.tar.gz/download
tar -xvvzkf matplotlib-${VERSION_MATPLOTLIB}.tar.gz
cd matplotlib-${VERSION_MATPLOTLIB}
python setup.py build
python setup.py install --user
}}}

== nose ==

|| '''Depends on''' ||
|| numpy ||
|| scipy ||

{{{#!highlight bash
#!/bin/bash

VERSION_NOSE=1.0.0
builddir="/scratch/${USER}/build/nose"

mkdir -p ${builddir}

cd ${builddir}
wget http://somethingaboutorange.com/mrl/projects/nose/nose-${VERSION_NOSE}.tar.gz
tar -xvvzkf nose-${VERSION_NOSE}.tar.gz
cd nose-${VERSION_NOSE}
python setup.py build
python setup.py install --user
}}}
+Here we provide some shell script snippets for installing frequently asked modules which cannot be installed through {{{pip}}}. These scripts just provide an example installation. You might have to adapt some paths in order to make the module work correctly with the version of python you are using (e.g. if you run your custom python provided through {{{pyenv}}}).

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