Software Carpentry Boot Camp Python V 0 1

Software Carpentry Boot Camp Python V 0. 1 dd 07 -04 -2015

Boot Camp Introduction Introductory session • Install necessary software http: //www. strw. leidenuniv. nl/python/1 ejaar/ Python. Boot. Camp. ppt • Get you at a basic level http: //www. strw. leidenuniv. nl/python/1 ejaar/ or more in depth http: //www. strw. leidenuniv. nl/python/1 ejaar/

Boot Camp What Software Required software • Python (2 or 3) https: //www. python. org/downloads/ – – – Numpy http: //www. scipy. org/scipylib/download. html Scipy http: //www. scipy. org/scipylib/download. html Matplotlib http: //matplotlib. org/users/installing. html Astro. Py (FITS) http: //www. astropy. org/ h 5 py (HDF) http: //docs. h 5 py. org/en/latest/build. html • Cython http: //docs. cython. org/src/quickstart/install. html • f 2 py (part of numpy) • Git http: //git-scm. com/book/en/v 2/Getting-Started-Installing-Git Optional: • ipython http: //ipython. org/install. html

Boot Camp Install Different Operating systems This document will help you out installing the required software for the Python Software Carpentry Boot Camp on the following operating systems: §Mac. OS §Linux § FC § Ubuntu §Windows

Boot Camp Install Python 2 or Python 3 python 2 is legacy, python 3 is the present and future, but… §Reason http: //docs. python. org/py 3 k/whatsnew/3. 0. html • • Language cleanup Better unicode support strings Several core aspects made more consistent Class new-style §Why still use Python 2 • Legacy • All required packages are python 2 and 3 compatible • Many astronomical packages are python 2 ony • Many OS-es still use version 2

Boot Camp Install Mac. OS § Mac. OS https: //www. python. org/downloads/mac-osx/ • If you have Yosemite (10. x): $ python --version Python 2. 7. 6 • Need Python 2. 7. 9 (latest version) • install this next to the official OS related python • Prerequisites: • gcc compiler (for Cython) • gfortran compiler (for f 2 py) • Go to the App. Store, search Xcode and ‘Install App’, may take some time as size is 1 Gb – use activity monitor to track progress…

Boot Camp Install on Mac. OS • Go to the App. Store, search Xcode and ‘Install App’, may take some time as size is 1 Gb – use activity monitor to track progress… – will install gcc, but we need a more recent version and $ which gcc /usr/bin/gcc $ gcc –v Configured with: --prefix=/Applications/Xcode. app/Contents/Developer/usr --with-gxx-includedir=/Applications/Xcode. app/Contents/Developer/Platforms/Mac. OSX. platform/Developer/SDKs/Mac. OSX 10. sdk/usr/include/c++/4. 2. 1 Apple LLVM version 6. 0 (clang-600. 0. 57) (based on LLVM 3. 5 svn) Target: x 86_64 -apple-darwin 14. 1. 0 Thread model: posix – still need to install gfortran $ which gfortran

Boot Camp Install on Mac. OS • Go to http: //hpc. sourceforge. net/ and download the appropriate version gcc-5. 0 -bin. tar. gz, gcc-4. 9 -bin. tar. gz, gcc-4. 8 -bin. tar. gz, gcc-4. 7 -bin. tar. gz, gfortran-5. 0 -bin. tar. gz gfortran-4. 9 -bin. tar. gz gfortran-4. 8 -bin. tar. gz gfortran-4. 7 -bin. tar. gz (gfortran only), updated Nov 2014 (Yosemite). Nov 2014 (Mavericks & Yosemite). Oct 2013 (M. Lion & Mavericks). July 2012 (Lion & M. Lion). • and install the newest version of gcc and gfortran $ $ cd cd Downloads sudo tar –zxvf gcc-5. 0 -bin. tar. gz –C / sudo tar –zxvf gfortran-5. 0 -bin. tar. gz –C / • which should now be in your path $ which gcc /usr/local/bin/gcc $ which gfortran /usr/local/bin/gfortran

Boot Camp Install Mac. OS § Mac. OS https: //www. python. org/downloads/mac-osx/ • If you have Yosemite (10. x): $ python --version Python 2. 7. 6 • Need Python 2. 7. 9 (latest version) • install this next to the official OS related python • Download the appropriate install package • and run the installer $ which python /usr/local/bin/python $ python –version Python 2. 7. 9

Boot Camp Install Mac. OS § Additional packages • use the pip utility for this $ which pip /usr/local/bin/pip • load numpy $ sudo pip install numpy. . . • load scipy $ sudo pip install scipy. . . • load matplotlib $ sudo pip install matplotlib. . .

Boot Camp Install Mac. OS • load astropy $ sudo pip install astropy. . . • load h 5 py, as you can seen, this automatically installs Cython as well $ sudo pip install h 5 py Downloading/unpacking h 5 py Downloading h 5 py-2. 4. 0 -cp 27 -nonemacosx_10_6_intel. macosx_10_9_x 86_64. macosx_10_10_intel. macosx_10_10_ x 86_64. whl (4. 3 MB): 4. 3 MB downloaded Downloading/unpacking Cython>=0. 17 (from h 5 py) Downloading Cython-0. 22 -cp 27 -nonemacosx_10_6_intel. macosx_10_9_x 86_64. macosx_10_10_intel. macosx_10_10_ x 86_64. whl (3. 7 MB): 3. 7 MB downloaded Requirement already satisfied (use --upgrade to upgrade): numpy>=1. 6. 1 in /Library/Frameworks/Python. framework/Versions/2. 7/lib/python 2. 7/site-packages/numpy$ pip matplotlib 1. 9. 2 -py 2. 7 -macosx-10. 6 -intel. egg (from h 5 py). . . Installing collected packages: h 5 py, Cython Successfully installed h 5 py Cython Cleaning up. . .

Boot Camp Install Mac. OS § GIT http: //git-scm. com/download/mac • download of the. dmg should start automatically • Double click the package and then double click the installer $ which git /usr/bin/git • i. Python install $ sudo pip install “ipython[notebook]”. . . $ cd /usr/local/bin $ sudo ln –s. . /Library/Frameworks/Python. framework/Versions/2. 7/bin/ipython $ which ipython /usr/local/bin/ipython

Boot Camp Install Linux § Linux https: //www. python. org/downloads/source/ • You can install a fresh version of python: $ python --version Python 2. 7. 8 • Need Python 2. 7. 9 (latest version) • install this next to the official OS related python • Prerequisites: • gcc compiler (for Cython) • gfortran compiler (for f 2 py)

Boot Camp Install on Linux • Check version of gcc and gfortran in OS $ which gcc $ which gfortran /usr/bin/gcc /usr/bin/gfortran $ gcc –v $ Using built-in specs. COLLECT_GCC=gfortran COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x 86_64 -redhat-linux/4. 9. 2/lto-wrapper Target: x 86_64 -redhat-linux Configured with: . . /configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http: //bugzilla. redhat. com/bugzilla --enable-bootstrap --enable-shared --enablethreads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-buildid id --with-linker-hash-style=gnu --enable-languages=c, c++, objc, obj-c++, fortran, ada, go, lto -enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc 4. 9. 2 -20150212/obj-x 86_64 -redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc 4. 9. 2 -20150212/obj-x 86_64 -redhat-linux/cloog-install --enable-gnu-indirect-function --withtune=generic --with-arch_32=i 686 --build=x 86_64 -redhat-linux Thread model: posix gcc version 4. 9. 2 20150212 (Red Hat 4. 9. 2 -6) (GCC) – still need to install gfortran

Boot Camp Install on Linux • Install gcc and gfortran in OS $ which gcc $ sudo yum groupinstall "Development Tools and Libraries". . . # Fedora Core $ sudo apt-get install buildessentials. . . # Ubuntu $ which gfortran $ sudo yum install gcc-gfortran. . . # Fedora Core $ sudo apt-get install gfortran # Ubuntu

Boot Camp Install Linux • Need Python 2. 7. 9 (latest version) • install this next to the official OS related python $ python --version Python 2. 7. 6 • Download the source code $ cd /data 2 $ wget https: //www. python. org/ftp/python/2. 7. 9/Python-2. 7. 9. tgz Connecting to www. python. org (www. python. org)|23. 235. 43. 223|: 443. . . connected. HTTP request sent, awaiting response. . . 200 OK Length: 16657930 (16 M) [application/octet-stream] Saving to: âPython-2. 7. 9. tgzâ Python-2. 7. 9. tgz 100%[==============================>] in 0. 3 s 15. 89 M 2015 -04 -06 15: 08: 19 (46. 5 MB/s) - Python-2. 7. 9. tgz saved [16657930/16657930] 46. 5 MB/s

Boot Camp Install on Linux • unpack and install in alternative directory $ tar xzvf Python-2. 7. 9. tgz. . . $ cd Python-2. 7. 9 $. /configure --prefix=/net/bree/data 2/mypython/. . . $ make install. . . and set your environment to use this version: $ vi mypython. csh setenv PYTHONPATH /net/bree/data 2/mypython/site-packages setenv PATH "/net/bree/data 2/mypython/bin/": "$PATH" $ source mypython. csh $ which python /net/bree/data 2/mypython/bin/python

Boot Camp Install on Linux • add python tools # Let's download the installation file using wget: wget --no-check-certificate https: //pypi. python. org/packages/source/s/setuptools 1. 4. 2. tar. gz # Extract the files from the archive: tar -xvf setuptools-1. 4. 2. tar. gz # Enter the extracted directory: cd setuptools-1. 4. 2 # Install setuptools using the Python we've installed (2. 7. 9) python setup. py install and also install pip: $ curl https: //raw. githubusercontent. com/pypa/pip/master/contrib/get-pip. py |python. . .

Boot Camp Install Linux § Additional packages • use the pip utility for this, note to get your personal one! $ which pip /net/bree/data 2/mypython/bin/pip • load numpy $ pip install numpy. . . • load scipy $ pip install scipy. . . • load matplotlib $ pip install matplotlib. . .

Boot Camp Install Linux • load astropy $ pip install astropy. . . • load h 5 py, as you can seen, this automatically installs Cython as well $ sudo pip install h 5 py Downloading/unpacking h 5 py Downloading h 5 py-2. 4. 0 -cp 27 -nonemacosx_10_6_intel. macosx_10_9_x 86_64. macosx_10_10_intel. macosx_10_10_ x 86_64. whl (4. 3 MB): 4. 3 MB downloaded Downloading/unpacking Cython>=0. 17 (from h 5 py) Downloading Cython-0. 22 -cp 27 -nonemacosx_10_6_intel. macosx_10_9_x 86_64. macosx_10_10_intel. macosx_10_10_ x 86_64. whl (3. 7 MB): 3. 7 MB downloaded Requirement already satisfied (use --upgrade to upgrade): numpy>=1. 6. 1 in /Library/Frameworks/Python. framework/Versions/2. 7/lib/python 2. 7/site-packages/numpy$ pip matplotlib 1. 9. 2 -py 2. 7 -macosx-10. 6 -intel. egg (from h 5 py). . . Installing collected packages: h 5 py, Cython Successfully installed h 5 py Cython Cleaning up. . .

Boot Camp Install Linux § GIT, with root access install $ sudo yum install git $ sudo apt-get install git # Fedora Core # Ubuntu $ whcih git /usr/bin/git § Download http: //git-scm. com/download/ $ wget https: //www. kernel. org/pub/software/scm/git-2. 3. 5. tar. gz. . . $ tar zxvf git-2. 3. 5. tar. gz. . . $cd git-2. 3. 5 $. /configure –prefix=/nen/bree/data 2/mypython. . . $ make install. . .

Boot Camp Install Linux • i. Python install $ pip install “ipython[notebook]”. . . $ cd /usr/local/bin $ sudo ln –s. . /Library/Frameworks/Python. framework/Versions/2. 7/bin/ipython $ which ipython /usr/local/bin/ipython

Boot Camp Install Windows § Windows – By default Windows does not have python installed – so get the Windows x 86 -64 MSI installer • Prerequisites: – Also windows does not have any compilers installed either – gcc compiler (for Cython) – gfortran compiler (for f 2 py)

Boot Camp Install Windows § We wil make use of Anaconda installer as this allows easy installation pypi based packages § Go to http: //continuum. io/downloads – and download the Windos 4 -Bit Python 2. 7 Graphical Installer

Boot Camp Install Windows Featured Packages Num. Py pip $ which Sci. Py /usr/local/bin/pip Pandas Py. Tables $ sudo pip install h 5 py. . . Matplotlib IPython Spyder Qt/Py. Side numpy VTK Numexpr Astropy Cython LLVM, LLVMpy Numba Scikit-learn Scikit-image NLTK Network. X Maya. Vi

Boot Camp Install Windows § GIT http: //git-scm. com/download/win • download of the. exe should start automatically • Double click the installer and follow the instructions (allow use from Windows command line)

Data processing example End