Simple command line utility for getting a Python virtual environment to work with CVMFS LCG views. This is done by adding additional hooks to the Python virtual environment's bin/activate script.
Either clone the repo to your directory or simply download the relevant files and place on PATH
$ mkdir -p ~/.local/bin
$ export PATH=~/.local/bin:"${PATH}" # If ~/.local/bin not on PATH already
$ curl -sL https://raw.githubusercontent.com/matthewfeickert/cvmfs-venv/main/cvmfs-venv.sh -o ~/.local/bin/cvmfs-venv
$ chmod +x ~/.local/bin/cvmfs-venvSource the script to create a Python 3 virtual environment that can coexist with a CVMFS LCG view. The default name is venv.
$ cvmfs-venv --help
Usage: cvmfs-venv [-s|--setup] [--no-system-site-packages] [--no-update] [--no-uv] <virtual environment name>
Options:
-h --help Print this help message
-s --setup String of setup options to be parsed
--no-system-site-packages
The venv module '--system-site-packages' option is used by
default. While it is not recommended, this behavior can be
disabled through use of this flag.
--no-update After venv creation don't update pip, setuptools, and wheel
to the latest releases. Use of this option is not recommended,
but is faster.
--no-uv After venv creation don't install uv and use it to update pip,
setuptools, and wheel. By default, uv is installed.
Note: cvmfs-venv extends the Python venv module and so requires Python 3.3+.
Examples:
* Create a Python 3 virtual environment named 'lcg-example' with the Python
runtime provided by LCG view 104 on CentOS7.
setupATLAS -3
lsetup 'views LCG_104 x86_64-centos7-gcc12-opt'
cvmfs-venv lcg-example
. lcg-example/bin/activate
* Create a Python 3 virtual environment named 'atlas-ab-example' with the
Python runtime provided by ATLAS AnalysisBase release v24.2.30.
setupATLAS -3
asetup AnalysisBase,24.2.30
cvmfs-venv atlas-ab-example
. atlas-ab-example/bin/activate
* Create a Python 3 virtual environment named 'venv' with whatever Python
runtime "\$(command -v python3)" evaluates to.
cvmfs-venv
. venv/bin/activate
* Setup LCG view 104 on CentOS7 and create a Python virtual environment
named 'lcg-example' using the Python 3.9 runtime it provides.
. cvmfs-venv --setup "lsetup 'views LCG_104 x86_64-centos7-gcc12-opt'" lcg-example
* Setup ATLAS AnalysisBase release v24.2.30 and create a Python virtual
environment named 'atlas-ab-example' using the Python 3.9 runtime it
provides.
. cvmfs-venv --setup 'asetup AnalysisBase,24.2.30' atlas-ab-example$ ssh lxplus
[feickert@lxplus924 ~]$ mkdir -p ~/.local/bin
[feickert@lxplus924 ~]$ export PATH=~/.local/bin:"${PATH}"
[feickert@lxplus924 ~]$ curl -sL https://raw.githubusercontent.com/matthewfeickert/cvmfs-venv/main/cvmfs-venv.sh -o ~/.local/bin/cvmfs-venv
[feickert@lxplus924 ~]$ chmod +x ~/.local/bin/cvmfs-venv
[feickert@lxplus924 ~]$ setupATLAS -3 --quiet
[feickert@lxplus924 ~]$ lsetup 'views LCG_105 x86_64-el9-gcc12-opt'
************************************************************************
Requested: views ...
Setting up views LCG_104:x86_64-centos7-gcc12-opt ...
>>>>>>>>>>>>>>>>>>>>>>>>> Information for user <<<<<<<<<<<<<<<<<<<<<<<<<
************************************************************************
[feickert@lxplus924 ~]$ cvmfs-venv lcg-example
# Creating new Python virtual environment 'lcg-example'
[feickert@lxplus924 ~]$ . lcg-example/bin/activate
(lcg-example) [feickert@lxplus924 ~]$ python -m pip list --local # Show installed defaults
Package Version
---------- -------
pip 24.0
setuptools 69.5.1
uv 0.1.42
wheel 0.43.0
(lcg-example) [feickert@lxplus924 ~]$ python -m pip show hepdata-lib # Still have full LCG view
Name: hepdata-lib
Version: 0.12.0
Summary: Library for getting your data into HEPData
Home-page: https://github.com/HEPData/hepdata_lib
Author: Andreas Albert, Clemens Lange
Author-email: [email protected]
License: UNKNOWN
Location: /cvmfs/sft.cern.ch/lcg/views/LCG_105/x86_64-el9-gcc12-opt/lib/python3.9/site-packages
Requires: future, hepdata-validator, numpy, PyYAML
Required-by:
(lcg-example) [feickert@lxplus924 ~]$ uv pip install --upgrade awkward
(lcg-example) [feickert@lxplus924 ~]$ python
Python 3.9.12 (main, Jul 11 2023, 14:44:04)
[GCC 12.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ROOT
>>> import XRootD
>>> import awkward
>>> exit()
(lcg-example) [feickert@lxplus924 ~]$ python -m pip show awkward # Get version installed in venv
Name: awkward
Version: 2.6.4
Summary: Manipulate JSON-like data with NumPy-like idioms.
Home-page:
Author:
Author-email: Jim Pivarski <[email protected]>
License: BSD-3-Clause
Location: /afs/cern.ch/user/f/feickert/lcg-example/lib/python3.9/site-packages
Requires: awkward-cpp, fsspec, importlib-metadata, numpy, packaging, typing-extensions
Required-by: cabinetry, coffea, servicex, uproot_browser
(lcg-example) [feickert@lxplus924 ~]$ python -m pip list --local # View of virtual environment controlled packages
Package Version
------------------ --------
awkward 2.6.4
awkward-cpp 33
fsspec 2024.3.1
importlib_metadata 7.1.0
numpy 1.26.4
packaging 24.0
pip 24.0
setuptools 69.5.1
typing_extensions 4.11.0
uv 0.1.42
wheel 0.43.0
zipp 3.18.1
(lcg-example) [feickert@lxplus924 ~]$ uv pip list # uv will show the same view
Package Version
------------------ --------
awkward 2.6.4
awkward-cpp 33
fsspec 2024.3.1
importlib-metadata 7.1.0
numpy 1.26.4
packaging 24.0
pip 24.0
setuptools 69.5.1
typing-extensions 4.11.0
uv 0.1.42
wheel 0.43.0
zipp 3.18.1
(lcg-example) [feickert@lxplus924 ~]$ deactivate # Resets PYTHONPATH given added hooks
[feickert@lxplus924 ~]$ python -m pip show awkward # Get CVMFS's old version
Name: awkward
Version: 1.10.3
Summary: Manipulate JSON-like data with NumPy-like idioms.
Home-page: https://github.com/scikit-hep/awkward-1.0
Author: Jim Pivarski
Author-email: [email protected]
License: BSD-3-Clause
Location: /cvmfs/sft.cern.ch/lcg/views/LCG_105/x86_64-el9-gcc12-opt/lib/python3.9/site-packages
Requires: numpy, packaging
Required-by: cabinetry, coffea, servicex, uproot_browsercvmfs-venv has no dependencies beyond the ones it aims to extend: A Linux operating system that has CVMFS installed on it with a Python 3.3+ runtime with a functioning venv module.
A full listing of all programs used outside of Bash shell builtins are:
catedfindreadlinksed- Python 3.3+ with
pip
When an LCG view or an ATLAS computing environment that uses software from CVFMS is setup, it manipulates and alters the PYTHONPATH environment variable.
By placing the contents of all the installed software of an LCG view or ATLAS release onto PYTHONPATH for the rest of the shell session, the protections and isolation of a Python virtual environment are broken.
It is not possible to fix this in a reliable and robust way that will not break the access of other software in the LCG view or ATLAS environment dependent on the Python packages in them.
The best that can be done is to control the directory tree at the head of PYTHONPATH in a stable manner that allows for most of the benefits of a Python virtual environment (control of install and versions of packages, isolation of directory tree).
While lcgenv allows for package specific environment building, it still lacks the control to specify arbitrary versions of Python packages and will load additional libraries beyond what is strictly required by the target package dependency requirements.
That being said, if you are able to use an LCG view or lcgenv without any additional setup, you may not have need of specifying a Python virtual environment.
While Python's venv module does have the --system-site-packages option to
Give the virtual environment access to the system site-packages dir.
this unfortunately isn't quite enough.
It does allow for isolation to work, but the manipulation of PYTHONPATH makes it so that while packages can be installed properly in the local virtual environment and will show up with python -m pip list if there is another version of that package provided by the already setup environment that package version's location on PYTHONPATH will take precedence.
Using --system-site-packages without cvmfs-venv is arguably even worse as it provides confusing differences in information between what pip has purported to install in the user's virtual environment and the user pip list view and the runtime environment.
Caveat: This is an LCG view specific issue mostly. If nothing from LCG is used (like a pure ATLAS AnalysisBase environment, or an environment in a Linux container) then --system-site-packages by itself should be sufficient.
cvmfs-venv provides a shim layer to manage activation and use of a Python virtual environment created with LCG view resources.
It does this by copying the structure of the activate scripts generated by Python's venv module.
When venv creates a virtual environment it generates a shell script under the virtual environment's directory tree at bin/activate.
This activate script controls and edits the shell environmental variables PATH and PYTHONHOME — placing the virtual environment's bin/ directory onto PATH and unsetting PYTHONHOME upon activation, and restoring their original values when deactivate is run.
cvmfs-venv simply extends this existing behavior to also place the virtual environment's site-packages/ directory onto PYTHONPATH during activation and to remove it on deactivation.
This is done by injecting Bash snippets directly into the bin/activate script generated by venv at positions found relative to the manipulation of PYTHONHOME.
-
As
cvmfs-venvis just altering the contents of thevenvvirtual environment'sbin/activatescript it is extending existing functionality and not trying to remake virtual environments. -
Once the virtual environment is setup and modified there is no additional dependency on the
cvmfs-venvscript that generated it.- While it saves time it is not needed. You can setup the environment again without it.
$ . cvmfs-venv --setup "lsetup 'views LCG_104 x86_64-centos7-gcc12-opt'" venvvs.
$ setupATLAS -3 $ lsetup "views LCG_104 x86_64-centos7-gcc12-opt" $ . venv/bin/activate
-
As the virtual environment is prepended to
PYTHONPATHall packages installed in the virtual environment are automatically given higher precedence over existing packages of the same name found in the LCG view.- If a package named
awkwardis found in thevenvvirtual environment and in the LCG view,import awkwardwith import it from the virtual environment.
- If a package named
-
Python packages not installed in the
venvvirtual environment but installed in the LCG view (e.g. ROOT, XRootD) can still be accessed inside of the virtual environment.- N.B.: This is considered a "advantage" loosely, as it is only happening as a side effect of the isolation of the virtual environment being broken by the LCG view's
PYTHONPATHmanipulation.
- N.B.: This is considered a "advantage" loosely, as it is only happening as a side effect of the isolation of the virtual environment being broken by the LCG view's
-
Through additional manipulation of
PYTHONPATHandPATHwith the addedcvmfs-venv-rebasefunctionality, any software added toPATHorPYTHONPATH(e.g., by CVMFS or ATLAS software) while the virtual environment is active will persist onPATHorPYTHONPATHwhen the virtual environment is deactivated, allowing for a smoother interactive experience.- Example: If you want to use
rucioboth inside and outside of the virtual environment you can set it up either before sourcing thebin/activatescript
$ setupATLAS -3 $ lsetup "views LCG_104 x86_64-centos7-gcc12-opt" $ lsetup "rucio -w" # PYTHONPATH is altered by lsetup $ command -v rucio # rucio is found $ . venv/bin/activate (venv) $ command -v rucio # rucio is found (venv) $ deactivate $ command -v rucio # rucio is found
or after, as
cvmfs-venv-rebasewill update path variables and keep the virtual environment's directory trees at the heads.$ setupATLAS -3 $ lsetup "views LCG_104 x86_64-centos7-gcc12-opt" $ . venv/bin/activate (venv) $ lsetup "rucio -w" # PYTHONPATH is altered by lsetup (venv) $ command -v rucio # rucio is found (venv) $ deactivate # deactivate calls cvmfs-venv-rebase to persist non-venv paths $ command -v rucio # rucio is found
- Example: If you want to use
- The isolation of a Python virtual environment is not recovered.
Python packages installed in the LCG view can still be accessed inside of the virtual environment.
This can result in packages from the LCG view meeting requirements of other dependencies during a package install or upgrade (depending on the upgrade strategy) and installing older versions then expected.
- Suggestion: When installing or upgrading with
pipuse the--ignore-installedflag. - Suggestion: When using
pip listto inspect installed packages, use the--localflag to not list packages from the LCG view.
(venv) $ python -m pip list --local - Suggestion: When installing or upgrading with
- As the Python version tied to the virtual environment is provided by LCG view, any changes to the LCG view version require setting up the Python virtual environment from scratch.
- It is highly advised that your environment be controlled with strict
requirements.txtand lock files (e.g. generated frompip-toolsusingpip-compile) making it reproducible and easy to setup again as a consequence. - Example:
(venv) $ python -m pip install --upgrade pip-tools (venv) $ echo "scipy==1.11.3" > requirements.txt # define high level requirements (venv) $ pip-compile --generate-hashes --output-file requirements.lock requirements.txt # Generate full environment lock file (venv) $ python -m pip install --no-deps --require-hashes --only-binary :all: --requirement requirements.lock # secure-install for reproducibility
- It is highly advised that your environment be controlled with strict
- Having all of the environment manipulation happen inside of the
venv'sbin/activatescript means that the virtual environment needs to be activated after any LCG view or ATLAS software (which makePYTHONPATHnot empty) to triggerPYTHONPATHmanipulation. This essentially means that the virtual environment must not be activated first in any setup script.
The preferred BibTeX entry for citation of cvmfs-venv is
@software{cvmfs-venv,
author = {Matthew Feickert},
title = "{cvmfs-venv: v0.0.6}",
version = {0.0.6},
doi = {10.5281/zenodo.7751033},
url = {https://doi.org/10.5281/zenodo.7751033},
note = {https://github.com/matthewfeickert/cvmfs-venv/releases/tag/v0.0.6}
}
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent