Differences between revisions 25 and 49 (spanning 24 versions)

Python

We provide some modules that come with the current Debian GNU/Linux stable release, but usually this is because they are dependencies of an installed software. For python we strongly recommend to build own python environments with the desired python versions and modules.

Our recommended way to install such environments is trough Conda, alternatively via building an environment via pyenv is as well possible. Additional module can then either be installed by conda itself or trough pip.

Installing your own python environment with Conda

For a detailed overview for conda please follow to the Conda documentation.

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 2.7.15 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 2.7.15:
```
env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 2.7.15
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 2.7.15
```
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 25 as of 2014-06-20 14:06:30 → 
  Size: 5006
  Editor: alders
  Comment:
+   ← Revision 49 as of 2020-09-10 09:28:50 → ⇥
  Size: 4059
  Editor: bonaccos
  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 some modules that come with the current Debian GNU/Linux stable release, but usually this is because they are dependencies of an installed software. For python we strongly recommend to build own python environments with the desired python versions and modules.
-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`.
+Our recommended way to install such environments is trough Conda, alternatively via building an environment via `pyenv` is as well possible. Additional module can then either be installed by conda itself or trough `pip`.
-Line 7:
+Line 9:
-== How to use easy_install ==
+== Installing your own python environment with Conda ==
-Line 9:
+Line 11:
- || 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` ||
+For a detailed overview for conda please follow to the [[Programming/Languages/Conda|Conda documentation]].
-Line 14:
+Line 13:
-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.
+== Installing your own python versions with pyenv ==
-Line 16:
+Line 15:
-== Installing other versions of Python 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).
-Line 18:
+Line 17:
-You can of course install other versions of Python in your home. A very comfortable way of doing that is by using {{{pyenv}}}. Here is a short install howto. Further down you find links to documentation etc.
+Here is a small howto for installing python 2.7.15 in your home:
-Line 22:
+Line 21:
-curl -L https://raw.githubusercontent.com/yyuu/pyenv-installer/master/bin/pyenv-installer | bash}}}

 * Add the following three lines to your ~/.bashrc:
+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:
-Line 34:
+Line 37:
- * Install some python version, e.g. for python 2.7.7:
+ * Install some python version, e.g. for python 2.7.15:
-Line 36:
+Line 39:
-pyenv install 2.7.7
+env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 2.7.15
-Line 38:
+Line 41:
+ Note, that settting of `PYTHON_CONFIGURE_OPTS="--enable-shared"` is needed if you need to link against the libpython shared library.
-Line 41:
+Line 45:
-pyenv global 2.7.7}}}
+pyenv global 2.7.15}}}
-Line 47:
+Line 51:
+=== Documentation of pyenv ===
-Line 50:
+Line 55:
-== Installation of custom (non easy_install-able) Python modules in the home directory of a user ==
-Line 52:
+Line 56:
-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.
+== Installation of additional or newer modules with pip ==
-Line 54:
+Line 58:
-On this page we will list some bash-snippets that install some often requested modules in a users home.
+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 56:
+Line 65:
-== numpy ==
+For advanced usage of {{{pip}}}, please consult the manuals: http://pip.readthedocs.org/en/latest/
-Line 58:
+Line 67:
-{{{#!highlight bash
#!/bin/bash
-Line 61:
+Line 68:
-VERSION_NUMPY=1.7.1
builddir="/scratch/${USER}/build/numpy"
+== Installation of Python modules that are not available in the archives of pip ==
-Line 64:
+Line 70:
-mkdir -p ${builddir}

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
}}}

== scipy ==

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

{{{#!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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