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  • From an internet-accessible machine, download the latest Python 2.7.x source tarball (https://www.python.org/downloads/source/)

  • Create the Python installation directory structure in LCLS production: $PACKAGE_TOP/python/python<version> (e.g., $PACKAGE_TOP/python/python2.7.13),
    which should look as follows:

    Code Block
    languagebash
    themeMidnight
    $ ls /usr/local/lcls/package/python/python2.7.13/linux-x86_64
bin include lib man share src

  • Transfer the Python source tarball to $PACKAGE_TOP/python/python<version>/src:

    Code Block
    languagebash
    themeMidnight
    $ ls /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src
Python-2.7.13.tgz

  • Configure the build with the following options:

    Anchor
    bootstrap_pip
    bootstrap_pip

    Info

    --prefix=$PACKAGE_TOP/python/python2.7.13/linux-x86_64 (To create all build directories under the current structure)
    --enable-shared (To allow building of shared libraries [.so files], required for packages such as PyQt)
    --with-ensurepip=upgrade (To bootstrap the latest pip installer for Python 2.7.x >= 2.7.9)

    Code Block
    languagebash
    themeMidnight
    $ ./configure --prefix=$PACKAGE_TOP/python/python2.7.13/linux-x86_64 --enable-shared --with-ensurepip=upgrade
$ make
$ make install

  • Set the environment to use the newly-installed Python instance (example uses a script):

    Code Block
    languagebash
    themeMidnight
    $ cat init_python2.7.13.bash
#!/bin/bash
# Sets the user environment to use Python2.7.13

if [ -d /afs/slac/g/lcls ]; then
    export LCLS_ROOT=/afs/slac/g/lcls
else
    export LCLS_ROOT=/usr/local/lcls
fi

export ORACLE_HOME=${LCLS_ROOT}/package/oracle/product/11.2.0.4/linux-x86_64
export QT_HOME=${LCLS_ROOT}/package/Qt/Qt-5.9.1/linux-x86_64
export PYTHON_ROOT=${LCLS_ROOT}/package/python/python2.7.13/linux-x86_64
export PATH=${QT_HOME}/bin:${ORACLE_HOME}/bin:${PYTHON_ROOT}/bin:${PATH}
export LD_LIBRARY_PATH=${EPICS_BASE_RELEASE}/lib/linux-x86_64:${EPICS_EXTENSIONS}/lib/linux-x86_64:${EPICS_BASE_TOP}/base-cpp-R4-6-0/lib/linux-x86_64:${QT_HOME}/lib:${ORACLE_HOME}/lib:${PYTHON_ROOT}/lib:${PYTHON_ROOT}/build/Python2.7.13/Lib:${LD_LIBRARY_PATH}

$ source init_python2.7.13.bash


  • Check that the core installation includes pip and setuptools (required for building Python modules from source):

    Code Block
    languagebash
    themeMidnight
    $ pip list
pip (9.0.1)
setuptools (28.8.0)

...

Python packages installed in LCLS controls production are obtained from various sources. When possible, it is preferable to build the packages from source in the production environment to ensure compatibility.

...

satisfy dependencies, but this is by no means guaranteed. The --find-links argument can be specified more than once to look for files in multiple locations. Barring this, the --no-deps argument can be used to ignore dependencies):

...

Core packages are required in order to install and build other Python packages from source. The pip and setuptools packages should be bootstrapped via the base Python installation process (see above). The wheels package is required to install packages from wheels (.whl), which is necessary if the source tarball cannot be obtained.

...

Site packages are available on the official Python Package Index (PyPI) repository. When possible, packages should be obtained from this repo for maintainability and consistency. Python packages with complex dependencies have their own requirements files that are referenced by the top-level site-requirements.txt file. Note that redundant packages are ignored in later requirements files if the dependency is already satisfied:

  • Flask

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/Flask-requirements.txt
Flask
Werkzeug
Jinja2
itsdangerous
click
MarkupSafe

  • IPython

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/ipython-requirements.txt
appdirs
backports.shutil-get-terminal-size
decorator
enum34
ipython
ipython-genutils
packaging
pathlib2
pexpect
pickleshare
prompt-toolkit
ptyprocess
pygments
pyparsing
scandir
setuptools
simplegeneric
six
traitlets
wcwidth

  • Jupyter

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/jupyter-requirements.txt
alabaster
appdirs
Babel
backports-abc
backports.shutil-get-terminal-size
backports.ssl-match-hostname
bleach
certifi
Cheetah
click
configparser
cx-Oracle
cycler
decorator
docutils
dpkt
entrypoints
enum34
first
Flask
functools32
html5lib
imagesize
ipykernel
ipython
ipython-genutils
ipywidgets
itsdangerous
Jinja2
jsonschema
jupyter
jupyter-client
jupyter-console
jupyter-core
Markdown
MarkupSafe
matplotlib
mistune
mpmath
nbconvert
nbformat
nose
notebook
numpy
packaging
pandas
pandocfilters
pathlib2
pexpect
pickleshare
PIL
pip
pip-tools
plex
prompt-toolkit
ptyprocess
Pygments
pyparsing
pyqtgraph
PyQwt
python-dateutil
pytz
pyzmq
qtconsole
requests
roman
scandir
scikit-learn
scipy
setuptools
setuptools-scm
simplegeneric
singledispatch
six
snowballstemmer
Sphinx
subprocess32
sympy
terminado
testpath
tornado
traitlets
virtualenv
wcwidth
webencodings
Werkzeug
wheel
widgetsnbextension

  • pip-tools

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/pip-tools-requirements.txt
pip-tools
click
first
setuptools-scm
six

  • Scikit-learn

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/scikit-learn-requirements.txt
numpy
scipy
scikit-learn

  • Matplotlib

    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/matplotlib-requirements.txt
cycler
functools32
matplotlib
numpy
pyparsing
python-dateutil
pytz
six
subprocess32

  • Top-level requirements*:
    * - cx_Oracle >= 5.3.0 requires 64-bit Oracle 11.2 client or later. The proper ORACLE_HOME and related environment settings must be configured before
    attempting to install the package via pip:

    Code Block
    languagebash
    themeMidnight
    $ source /usr/local/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
    Code Block
    languagebash
    themeMidnight
    $ cat /usr/local/lcls/package/python/python2.7.13/linux-x86_64/src/site-packages/site-requirements.txt
# package-specific requirements

-r ./Flask-requirements.txt
-r ./ipython-requirements.txt

# global package requirements
alembic
Babel
Cheetah
Jinja2
Markdown
MarkupSafe
Pygments
alabaster
backports.ssl_match_hostname
backports_abc
certifi
click
cothread
colorama
cx_Oracle
cycler
decorator
docutils
dpkt
first
functools32
imagesize
ipython
ipython_genutils
Mako
mpmath
nose
numpy
pandas
pathlib2
pexpect
pickleshare
plex
pydm
pyepics == 3.2.7
pyqtgraph
python-dateutil
python-editor
pytz
PyYAML
QtPy
requests
roman
scipy
scikit-learn
simplegeneric
singledispatch
sip
six
snakefood
snowballstemmer
SQLAlchemy
subprocess32
sympy
tabulate
tornado
traitlets
vcversioner
virtualenv
wsgiref

-r ./jupyter-requirements.txt
-r ./pip-tools-requirements.txt
-r ./scikit-learn-requirements.txt
-r ./matplotlib-requirements.txt

...