10 Nov 2022
We are happy to announce that MDAnalysis has been awarded a grant from the Chan Zuckerberg Initiative as part of the Essential Open Source Software for Science program: “EOSS5: Growing the MDAnalysis community sustainably: A dedicated project manager, teaching and outreach initiatives”.
The MDAnalysis organisation strongly believes that engaging in outreach, mentoring and teaching is key to its mission of being the leading software package for molecular simulation analysis in Python.
This 2-year grant will enable us to hire a full-time community, outreach, and project manager to extend our teaching and mentoring commitments and engage with the molecular simulation community across academia and industry.
Over the next two years, our key deliverables include:
- Increasing our participation in outreach activities
- Organising user group meetings (UGMs)
- Hosting a series of online teaching workshops (3 per year)
- Networking with other software projects within and outside the molecular simulation space
- Engaging with industrial partners towards opening additional funding streams for the project
A big thank you to all contributors, past and present, for making this possible.
See the job description and apply for the role of community, outreach and project manager
07 Nov 2022
This blog post outlines MDAnalysis’ proposal to change its license
to the GNU Lesser General Public License (LGPL v3+).
A summary of our reasons for proposing this license
change, alongside upcoming actions
for community members and library
contributors are provided.
⚠️ Disclaimer
The MDAnalysis core team members are not
lawyers. As such the information provided here does not, and is not
intended to, constitute legal advice. This blog post also does not
represent MDAnalysis’ full legal position on software licensing; it
simply aims to inform MDAnalysis developers and users on why
we believe the library should be relicensed.
Further information on open-source software licensing can be found
from sources such as the Open Source Initiative,
tl;drLegal and the Software Sustainability Insitute.
Should you have any concerns about licensing, we always strongly
recommend getting legal advice before making any decisions on how
licensing changes may affect you.
Overview
We want to change the license of MDAnalysis from the GNU General
Public License v2 (or any later versions) (GPL v2+) to the less
restrictive GNU Lesser General Public License v3 (or any later versions)
(LGPL v3+) license. Both are open source licenses but it is
our view that the LGPL v3+ will give developers more freedom
in how they license any of their own codes that make use of MDAnalysis.
As detailed by the Open Source Definition, licenses are core to
the definition of open source. “Open source doesn’t just mean access
to the source code”. The license defines how code can be used, copied,
changed, and incorporated into other code.
License changes will affect how people interact with the MDAnalysis code
base going forward. We need the agreement of our contributors and
community members to change from GPL v2+ to LGPL v3+.
In this post we want to share our motivation, outline the relicensing
process, and invite comments / questions from the community.
Rationale for license change
Why is GPL v2+ no longer the best choice?
Since its initial release in 2008, MDAnalysis has grown from a small
Python package used by a handful of enthusiastic graduate students and
postdocs to a mature library that is used by thousands of researchers
in the molecular sciences. The MDAnalysis library was published under
an open source license from the start so that anyone could freely use
it, contribute to it, and build on it. We chose the GNU General Public License
version 2+ (GPL v2+) for this purpose. The GPL v2+ has a “copy-left”
clause that requires anyone using MDAnalysis in their own code to
also adopt a compatible version of the GPL for their code. This means
that code contributors could feel that any time and work that they
invested into MDAnalysis would not end up contributing to software
without open-source licensing.
However, the GPL v2+ has also created barriers to adoption of MDAnalysis.
Under many interpretations, ours included, this prevents developers
who use MDAnalysis from making their own code available under non-GPL
licenses. It is the MDAnalysis core team’s view that we do not want
to dictate how our developers and users should license their code, but we
do wish that work on the MDAnalysis library remains open and free.
Changing to a less restrictive license would benefit the MDAnalysis
community, increasing the number of codes which can use MDAnalysis,
and enabling users in corporate environments to use the library with more
certainty. The reduced licensing complexity also paves the way for our
proposed MDAKit ecosystem.
Why now the LGPL v3+?
We therefore propose to undergo the process of relicensing MDAnalysis
under the GNU Lesser General Public License v3 (or any later versions).
This open source license fulfills a number of important requirements for us:
-
Downstream codes are able to freely import or link to MDAnalysis
library components without impacting the license choice of the
downstream code.
-
Downstream codes are able to use and subclass any MDAnalysis components
under its application programming interface (classes, methods, and
data objects), without impacting the license choice of the
downstream code.
-
Codes that either copy or extend the MDAnalysis library should
fall under the copyleft license requirements of the MDAnalysis
library license.
Thus, it is our view that the LGPL v3+ license gives people the freedom
to choose any license for their own code that makes use of the MDAnalysis
library as a whole (namely import MDAnalysis or subclassing). This
includes closed / commercial licenses (although we encourage the use of
open source licenses). However, one would not be able to just take parts of
the MDAnalysis code and add it into another codebase unless this
other code is then also licensed under a compatible copyleft license
(e.g. GPLv3+/LGPLv3+).
We considered other popular licenses but none fulfilled the requirements
listed above.
How will the relicensing process work?
As of writing, MDAnalysis has over 160 contributors,
all of whom have contributed code under the terms of the GPL v2+
license. We also have a large user community that uses the library
for many wonderful scientific applications, including several
downstream libraries.
Ultimately, the final decision on relicensing rests with code
authors. However, we fully recognise that
this is a big change for the MDAnalysis user base and the wider
molecular sciences community. As always, we are fully invested in
ensuring that our actions reflect the needs of our community. We
therefore want to give everyone an opportunity to ask questions about
or comment on the relicensing effort as part of
this process.
Consultation period (7th November until 5th December 2022)
We will start the process with an open consultation period lasting
28 days from 7th November to 5th December 2022.
During this period we encourage members of the community,
both developers and users, to comment on and ask questions about the
proposed relicensing efforts. The aim is to ensure that relicensing is
indeed in the interest of the community. We will do our best to account
for any concerns raised before attempting to continue with the long and
time-consuming process of relicensing.
We wish to open this conversation on our public forums (mailing lists, discord, twitter). As legal
matters such as licensing can sometimes be sensitive in nature we have
also set up an email address ([email protected]) monitored
solely by the MDAnalysis Core Developers for any private queries that
you may have.
A summary of open discussions and frequently asked questions will be
made available on the MDAnalysis wiki.
Note: Whilst the consultation will only last 28 days, we will continue
to engage with conversations on this topic for the entire length of the
relicensing process.
After the consultation period, we will contact every code contributor to
the core MDAnalysis library with a request to agree to changing their
contribution’s license from the current “GPL v2 or any later version”
to “LGPL v3 or any later version”.
It is important that we hear back from as many contributors as possible.
If you have contributed to MDAnalysis in the past but have since changed
your git-linked contact details, we would kindly ask if you could email
[email protected] to let us know how best to contact you.
License change
We do not know how long relicensing will take, especially as contacting
historical contributors will likely be a very slow process. Nevertheless,
our aim is to change the license as quickly as possible. We will keep the
community regularly updated on our progress.
Acknowledgments
We are very grateful for the administrative and legal support from our
fiscal sponsor, NumFOCUS.
– The MDAnalysis Core Developers
04 Sep 2022
We are happy to release the version 2.3.0 of MDAnalysis!
This relatively small update to MDAnalysis reflects our commitment
to doing more frequent (trimonthly) releases of the library.
In line with NEP 29, the minimum required NumPy version has been
raised to 1.20.0 (1.21.0 for macosx-arm64).
Supported Python versions: 3.8, 3.9, 3.10
Supported Operating Systems:
Upgrading to MDAnalysis version 2.3.0
To update with conda from the conda-forge channel run
conda update -c conda-forge mdanalysis
To update from PyPi with pip run
pip install --upgrade MDAnalysis
For more help with installation see the installation instructions in the User Guide.
Notable changes
For a full list of changes, bugfixes and deprecations see the CHANGELOG.
Fixes:
- Fixed reading error when dealing with corrupt PDB CONECT records, and an issue where MDAnalysis would write out unusable CONECT records with index>100000 (Issue #988).
Enhancements:
- Formal charges are now read from PDB files and stored in a
formalcharge attribute (PR #3755).
- A new normalizing
norm parameter for the InterRDF and InterRDF_s analysis methods (Issue #3687).
- Improved Universe serialization performance (Issue #3721, PR #3710).
Changes:
- To install optional packages for different file formats supported by MDAnalysis, use
pip install ./package[extra_formats] (Issue #3701, PR #3711).
Deprecations:
- The
extra_requires target AMBER for pip install ./package[AMBER] will be removed in 2.4.0. Use extra_formats (Issue #3701, PR #3711).
A series of performance improvements to the MDAnalysis library’s backend have been made as per planned work under MDAnalysis’ Chan Zuckerberg Initiative EOSS4 grant. Further details about these will be provided in a future blog post.
-
MDAnalysis.lib.distances now accepts AtomGroups as well as NumPy arrays (PR #3730).
- Timestep has been converted to a Cython Extension type (PR #3683).
Author statistics
This release was the work of 10 contributors, 3 of which are new contributors.
Our new contributors are:
@miss77jun
@rzhao271
@hsadia538
Acknowledgements
MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and the Chan Zuckerberg Initiative for supporting MDAnalysis under an EOSS4 award.
— The MDAnalysis Team