Scientific setup on fresh Fedora 23 installation

su -
dnf update

RPM Fusion repository
http://rpmfusion.org/Configuration

Install the missing software:

dnf install gnome-tweak-tool gimp inkscape thunderbird bluefish filezilla vlc python-openoffice epiphany
dnf install VirtualBox
dnf install dconf-editor

Software for development

dnf groupinstall "Development Tools"

Scientific software

dnf install numpy scipy python-matplotlib python-pandas python-ipython

Upgrade SciPy

dnf install python-pip blas-devel lapack-devel gcc-c++ rpm-build
dnf groupinstall "Development Tools"
pip install --upgrade scipy

How to upgrade SciPy on Fedora 23

As it was with Fedora 22, the Fedora 23 still ships with SciPy version 0.14.1. To upgrade SciPy please run the following commands as root:

dnf install python-pip
dnf install blas-devel
dnf install lapack-devel
dnf install gcc-c++
dnf groupinstall "Development Tools"

If you now try to upgrade scipy you will get the following error
g++: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory

On Fedora 23 one has also to install rpm-build to avoid errors during compilation of scipy:
dnf search rpm-build

Finally uninstall scipy 0.14.1, download 0.16.0, compile it and install. All with the following command:
pip install --upgrade scipy

Things to do after fresh Fedora 22 installation

After fresh Fedora 22 install, first update the preinstalled software.
The prerequisite to all af the following commands is root access.
su -
dnf update

Add Fusion repository (found this on fosspedro.wordpress.com)
dnf install --nogpgcheck http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-22.noarch.rpm http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-22.noarch.rpm

Run the update again
dnf update

Install the missing software:

dnf install gnome-tweak-tool gimp inkscape thunderbird bluefish filezilla vlc python-openoffice
dnf install VirtualBox
dnf install dconf-editor
dnf install epiphany

Software for development
dnf groupinstall "Development Tools"

Scientific software
dnf install numpy scipy
dnf install python-matplotlib
dnf install python-pandas
dnf install python-ipython

Fedora 22 ships with SciPy version 0.14. To upgrade to 0.15.1 follow these instructions: How to upgrade SciPy on Fedora
To check SciPy version, in python console type:
import scipy
scipy.__version__

Working with asciidoc on Fedora

Install Asciidoc and DocBook
yum install asciidoc
yum install docbook-dtds
yum install publican
yum install dblatex
yum install libxml2-devel
yum install libxslt docbook5-style-xsl docbook-utils

To generate PDF files LaTeX is required. See here how to install LaTeX and XeLaTeX on Fedora.

Generate html file from asciidoc file
asciidoc myfile.txt
Use ‘-n’ to have numbered sections
asciidoc -n myfile.txt

Generate PDF file
Although it is possible to directly create PDF files using a2x utility, I prefer to convert my file to docbook format and then to PDF.
asciidoc -n --doctype=article --backend=docbook45 myfile.txt
or
asciidoc --doctype=book --backend=docbook45 myfile.txt
Then
dblatex gramata.xml
or
dblatex --backend=xetex gramata.xml

Things to do after fresh Fedora 20 install

Open a terminal and become root
su -

Add RPM fusion repository

yum localinstall --nogpgcheck http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-$(rpm -E %fedora).noarch.rpm http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-$(rpm -E %fedora).noarch.rpm

Install Flash plugin for 64bit systems
yum install http://linuxdownload.adobe.com/adobe-release/adobe-release-x86_64-1.0-1.noarch.rpm -y
yum install flash-plugin nspluginwrapper alsa-plugins-pulseaudio libcurl

Read more about playing flash here.

Install applications according to your needs

yum install gnome-tweak-tool
yum install dconf-editor
yum install gimp
yum install inkscape
yum install thunderbird
yum install bluefish
yum install filezilla
yum install vlc
yum install python-openoffice
yum install VirtualBox

Gnome Weather and Gnome Maps in Fedora 20
Gnome Weather and Gnome Maps in Fedora 20

Install Gnome weather and Gnome maps
yum install gnome-weather
yum install gnome-maps

Fix AltTab behavior so it switches windows only on the active workspace
https://extensions.gnome.org/extension/15/alternatetab/ (does not group windows by application)

Install Chromium browser

Place the repo file and save it as /etc/yum.repos.d/churchyard-chromium-russianfedora.repo

yum install chromium

Enable mp3 and DVD playback
rpm -Uvh http://rpm.livna.org/livna-release.rpm

yum install gstreamer-plugins-bad gstreamer-plugins-bad-free-extras gstreamer-plugins-bad-nonfree gstreamer-plugins-ugly gstreamer-ffmpeg ffmpeg mencoder ffmpeg2theora mplayer libdvdcss

yum install gstreamer1-libav gstreamer1-plugins-bad-free-extras gstreamer1-plugins-bad-freeworld gstreamer1-plugins-base-tools gstreamer1-plugins-good-extras gstreamer1-plugins-ugly gstreamer1-plugins-bad-free gstreamer1-plugins-good gstreamer1-plugins-base gstreamer1

yum install libdvdread libdvdnav lsdvd libdvdcss libdvdcss2

See also: How to install LaTeX and XeLaTeX in Fedora

libSBML 5.8.0 in Fedora 19 with Python bindings

How to install libSBML 5.8.0 in Fedora 19 with Python bindings

Install compiler
yum install gcc-c++
yum groupinstall "Development Tools"

Install some additional packages if needed
yum install python-devel
yum install libxml2-devel
yum install swig

Compile and install libSBML
Go to the directory where you have exctracted libsbml source and run these 3 commands
./configure --with-python
make
make install

Make libsbml accessible to Python
In Fedora 18 you would export full path to libsbml:
export PYTHONPATH=/usr/local/lib64/python2.7/site-packages/libsbmlIn Fedora 18 you would import _libsbml not just import libsbml.

In Fedora 19 you have to export path like this:
export PYTHONPATH=/usr/local/lib64/python2.7/site-packages/

The export command expires when user leaves his/her session.

Use the libSBML in your code
import libsbml

Things to do after fresh Fedora 19 install

Add RPM fusion repository
Download RPM fusion package from http://rpmfusion.org/Configuration
Add it
yum localinstall –nogpgcheck rpmfusion-free-release-19.noarch.rpm
yum localinstall –nogpgcheck rpmfusion-nonfree-release-19.noarch.rpm

Install Flash plugin for 64bit systems
yum install http://linuxdownload.adobe.com/adobe-release/adobe-release-x86_64-1.0-1.noarch.rpm -y
Read more about playing flash here.

Install applications according to your needs
yum install gnome-tweak-tool
yum install gimp
yum install inkscape
yum install thunderbird

yum install vlc
yum install VirtualBox
yum install filezilla
yum install bluefish
yum install python-openoffice

Fix AltTab behavior so it switches windows only on the active workspace
https://extensions.gnome.org/extension/15/alternatetab/ (does not group windows by application)
https://extensions.gnome.org/extension/310/alt-tab-workspace/ (groups windows by application)

Fix keyboard shortcuts for static workspaces
yum install dconf-editor
In dconf-editor go to org → gnome → desktop → wm → keybindings
fix_keyboard_shortcuts
You have to disable dynamic workspaces prior to this.

Enable DVD playback
rpm -Uvh http://rpm.livna.org/livna-release.rpm
yum -y install gstreamer-plugins-bad gstreamer-plugins-bad-free-extras gstreamer-plugins-bad-nonfree gstreamer-plugins-ugly gstreamer-ffmpeg ffmpeg mencoder ffmpeg2theora mplayer libdvdcss
yum -y install gstreamer1-libav gstreamer1-plugins-bad-free-extras gstreamer1-plugins-bad-freeworld gstreamer1-plugins-base-tools gstreamer1-plugins-good-extras gstreamer1-plugins-ugly gstreamer1-plugins-bad-free gstreamer1-plugins-good gstreamer1-plugins-base gstreamer1
yum -y install libdvdread libdvdnav lsdvd libdvdcss libdvdcss2

Chromium web browser
yum-config-manager --add-repo=http://repos.fedorapeople.org/repos/spot/chromium-stable/fedora-chromium-stable.repo
yum install chromium -y

Read more about Chromium web browser here.

See also: How to install LaTeX and XeLaTeX in Fedora

How to download a complete website

If you ever need to download an entire Web site, wget can do the job:
wget \
--recursive \
--no-clobber \
--page-requisites \
--adjust-extension \
--convert-links \
--restrict-file-names=windows \
--domains example.com \
--no-parent http://example.com.lv/thefolder/

The options are:
--recursivedownload the entire Web site.

--domains example.com don’t follow links outside example.com.

--no-parent don’t follow links outside the directory thefolder/.

--page-requisites get all the elements that compose the page (images, CSS and so on).

--html-extension save files with the .html extension.

--convert-links convert links so that they work locally, off-line.

--restrict-file-names=windows modify filenames so that they will work in Windows as well.

--no-clobber don’t overwrite any existing files (used in case the download is interrupted and resumed).

Also note that in wget 1.12, –html-extension is renamed to –adjust-extension

The orignal resource: http://www.linuxjournal.com/…