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* release 2.8.0 blog post * changelog 280 * Update _posts/2024-11-22-release-2.8.0.md Co-authored-by: Irfan Alibay <[email protected]> * added more recognition * links + fixes * finalized blog post - all deprecations - links to role list instead of role description - MDAKits with links * untabified * no cf package for py13 Co-authored-by: Irfan Alibay <[email protected]> --------- Co-authored-by: Irfan Alibay <[email protected]>
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| --- | ||
| layout: post | ||
| title: Release 2.8.0 of MDAnalysis | ||
| --- | ||
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| We are happy to release version 2.8.0 of MDAnalysis! | ||
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| This is a minor release of the MDAnalysis library, which means that it | ||
| contains enhancements, bug fixes, deprecations, and other | ||
| backwards-compatible changes. | ||
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| However, in this case *minor* does not quite do justice to what is | ||
| happening in this release, given that we have (at least) three big | ||
| changes/additions: | ||
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| 1. The [license was changed](#license-change-to-lgpl) to the **GNU | ||
| Lesser General Public License** so that MDAnalysis can be used by | ||
| packages under *any* license while keeping the source code itself | ||
| free and protected. | ||
| 2. We introduce the **[Guesser][guesser modules docs] API** for | ||
| guessing missing topology attributes such as element or mass in a | ||
| *context-dependent* manner. Until release 3.0, you should not | ||
| notice any differences but under the hood we are getting ready to | ||
| make it easier to work with simulations in a different *context* | ||
| (e.g., with the MARTINI force field or experimental PDB | ||
| files). With consistent attributes, such as elements, it becomes a | ||
| lot easier to interface with tools like the cheminformatics RDKit | ||
| (via the [converters][converter modules docs]). | ||
|
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| The guessers are the [GSoC 2022 project][] of @aya9aladdin with | ||
| help from @lilyminium, @IAlibay, and @jbarnoud.[^guesserPR] | ||
| 3. We are introducing **[parallel analysis][]** for tools in | ||
| [MDAnalysis.analysis][] following the simple | ||
| *split-apply-combine* paradigm that we originally prototyped in | ||
| [PMDA][] [^PMDApaper]. What's really exciting is that *any* analysis code | ||
| that is based on [MDAnalysis.analysis.base.AnalysisBase][] can | ||
| enable parallelization with a few lines of extra code---all the | ||
| hard work is done behind the scenes in the base class (in a way | ||
| that is fully backwards compatible!). | ||
|
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| This new feature is the work of @marinegor who brought his | ||
| [GSoC 2023 project][] to completion, with great contributions by | ||
| @p-j-smith, @yuxuanzhuang and @RMeli [^parallelizationPR]. | ||
|
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||
| Not all MDAnalysis analysis classes have parallelization enabled | ||
| yet but @talagayev has been working tirelessly on already updating | ||
| `GNMAnalysis`, `BAT`, `Dihedral`, `Ramachandran`, `Janin`, `DSSP` | ||
| (yes, MDAnalysis has _finally_ got DSSP, based on [pydssp][], also | ||
| thanks to @marinegor), `HydrogenBondAnalysis`, in addition to | ||
| `RMSD`. | ||
|
|
||
| Read on for more details on the license change and the usual | ||
| information on [supported environments](#supported-environments), | ||
| [upgrading](#upgrading-to-mdanalysis-version-280) your version of MDAnalysis, and a | ||
| [summary of the most important changes](#notable-changes). | ||
|
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| ## License change to LGPL | ||
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| <a href="https://www.gnu.org/licenses/lgpl-3.0.en.html"> | ||
| <img src="https://www.gnu.org/graphics/lgplv3-with-text-154x68.png" | ||
| title="LGPLv3" alt="LGPLv3 logo" style="float: right"/> | ||
| </a> | ||
|
|
||
| This is the first release of MDAnalysis under the **Lesser General | ||
| Public License**. We have been working towards this license change for | ||
| the last 3 years; this release (almost) concludes the process that we | ||
| described in our [licensing update blog post][licensing update]. | ||
|
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| * **All code** is now under [LGPLv2.1 | ||
| license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) | ||
| or any higher version. | ||
| * The package is under the [LGPLv3 | ||
| license](https://www.gnu.org/licenses/lgpl-3.0.html) or any higher | ||
| version. However, once we have removed dependencies that prevent | ||
| licensing under LGPLv2.1+ at the moment, we will also license the | ||
| package under the same **LGPLv2.1+** as the code itself. | ||
|
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||
| We would like to thank all our contributors who granted us permission to | ||
| change the license. We would also like to thank a number of | ||
| institutions who were especially supportive of our open source | ||
| efforts, namely Arizona State University, Australian National | ||
| University, Johns Hopkins University, and the Open Molecular Science | ||
| Foundation. We are also grateful to [NumFOCUS][] for legal | ||
| support. The [relicensing team][roles] was lead by @IAlibay and @orbeckst. | ||
|
|
||
| ## Supported environments | ||
|
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| The minimum required NumPy version is 1.23.3; MDAnalysis now builds | ||
| against NumPy 2.0. | ||
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| Supported Python versions: **3.10, 3.11, 3.12, 3.13**. Support for version | ||
| 3.13 has been added in this release and support for 3.9 has been | ||
| dropped (following [SPEC 0][]). | ||
|
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| Please note that Python 3.13 is limited to [PyPi][] for now, the [conda-forge channel][] installs only provide support for Python 3.10 to 3.12. | ||
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| Supported Operating Systems: | ||
| - **Linux** (on [x86-64][]) | ||
| - **Windows** (on [x86-64][]) | ||
| - **MacOS** (on [x86-64][] and [ARM64][]) | ||
|
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|
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| ## Upgrading to MDAnalysis version 2.8.0 | ||
|
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| To update with `mamba` (or `conda`) from the [conda-forge channel][] run | ||
|
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| ```bash | ||
| mamba update -c conda-forge mdanalysis | ||
| ``` | ||
|
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| To update from [PyPi][] with `pip` run | ||
|
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| ```bash | ||
| python -m pip install --upgrade MDAnalysis | ||
| ``` | ||
|
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| For more help with installation see the [installation instructions in the User Guide][]. | ||
| Make sure you are using a Python version compatible with MDAnalysis | ||
| before upgrading (Python >= 3.10). | ||
|
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|
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| ## Notable changes | ||
|
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| For a full list of changes, bugfixes and deprecations see the [CHANGELOG][]. | ||
|
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| #### Enhancements: | ||
|
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| * Added `guess_TopologyAttrs()` API to the Universe to handle attribute | ||
| guessing (PR #3753) | ||
| * Added the `DefaultGuesser` class, which is a general-purpose guesser with | ||
| the same functionalities as the existing guesser.py methods (PR #3753) | ||
| * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class | ||
| (Issue #4158, PR #4304) | ||
| * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP) | ||
| * Improved performance of PDBWriter (Issue #2785, PR #4472) | ||
| * Added parsing of arbitrary columns of the LAMMPS dump parser. (Issue #3504) | ||
| * Implement average structures with iterative algorithm from | ||
| DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524) | ||
| * Add support for TPR files produced by Gromacs 2024.1 (PR #4523) | ||
|
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| #### Fixes: | ||
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| * Fix Bohrium (Bh) atomic mass in tables.py (PR #3753) | ||
| * Catch higher dimensional indexing in GroupBase & ComponentBase (Issue #4647) | ||
| * Do not raise an Error reading H5MD files with datasets like | ||
| `observables/<particle>/<property>` (part of Issue #4598, PR #4615) | ||
| * Fix failure in double-serialization of TextIOPicklable file reader. | ||
| (Issue #3723, PR #3722) | ||
| * Fix failure to preserve modification of coordinates after serialization, | ||
| e.g. with transformations | ||
| (Issue #4633, PR #3722) | ||
| * Fix PSFParser error when encountering string-like resids | ||
| (Issue #2053, Issue #4189 PR #4582) | ||
| * Convert openmm Quantity to raw value for KE and PE in OpenMMSimulationReader. | ||
| * Atomname methods can handle empty groups (Issue #2879, PR #4529) | ||
| * Fix bug in PCA preventing use of `frames=...` syntax (PR #4423) | ||
| * Fix `analysis/diffusionmap.py` iteration through trajectory to iteration | ||
| over `self._sliced_trajectory`, hence supporting | ||
| `DistanceMatrix.run(frames=...)` (PR #4433) | ||
|
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||
|
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| #### Changes: | ||
|
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| * Relicense code contributions from GPLv2+ to LGPLv2.1+ | ||
| and the package from GPLv3+ to LGPLv3+ (PR #4794) | ||
| * only use distopia < 0.3.0 due to API changes (Issue #4739) | ||
| * The `fetch_mmtf` method has been removed as the REST API service | ||
| for MMTF files has ceased to exist (Issue #4634) | ||
| * MDAnalysis now builds against numpy 2.0 rather than the | ||
| minimum supported numpy version (PR #4620) | ||
|
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||
|
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||
|
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| #### Deprecations: | ||
|
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| * Deprecations of old guessing functionality (in favor of the new | ||
| Guesser API) | ||
| * `MDAnalysis.topology.guessers` is deprecated in favour of the new | ||
| Guessers API and will be removed in version 3.0 (PR #4752) | ||
| * The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` | ||
| kwargs are deprecated for bond guessing during Universe | ||
| creation. Instead, pass `("bonds", "angles", "dihedrals")` into | ||
| `to_guess` or `force_guess` during Universe creation, and the | ||
| associated `vdwradii`, `fudge_factor`, and `lower_bound` kwargs | ||
| into `Guesser` creation. Alternatively, if `vdwradii`, | ||
| `fudge_factor`, and `lower_bound` are passed into | ||
| `Universe.guess_TopologyAttrs`, they will override the previous | ||
| values of those kwargs. (Issue #4756, PR #4757) | ||
| * `MDAnalysis.topology.tables` is deprecated in favour of | ||
| `MDAnalysis.guesser.tables` and will be removed in version 3.0 (PR #4752) | ||
| * Element guessing in the `ITPParser` is deprecated and will be removed in version 3.0 | ||
| (Issue #4698) | ||
| * **Unknown masses are still set to 0.0 for current version**, this | ||
| will be changed **in version 3.0.0 and replaced by | ||
| `Masses` "no_value_label" attribute (`np.nan`)** (PR #3753) | ||
| * A number of analysis modules have been moved into their own | ||
| [MDAKits][], following the [3.0 roadmap towards a trimmed down core | ||
| library][roadmap]. Until release 3.0, these modules are still | ||
| available through `MDAnalysis.analysis` (either as an import of the | ||
| MDAKit as an automatically installed dependency of the MDAnalysis | ||
| package or as the original code) but from 3.0 onwards, users must | ||
| install the MDAKit explicitly and then import it by themselves. | ||
|
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||
| * The `MDAnalysis.analysis.encore` module has been deprecated in | ||
| favour of the [mdaencore]() MDAKit and will be removed in version | ||
| 3.0.0 (PR #4737) | ||
| * The `MDAnalysis.analysis.waterdynamics` module has been deprecated in favour | ||
| of the [waterdynamics][] MDAKit and will be removed in version 3.0.0 (PR #4404) | ||
| * The `MDAnalysis.analysis.psa` module has been deprecated in favour of | ||
| the [PathSimAnalysis][] MDAKit and will be removed in version 3.0.0 | ||
| (PR #4403) | ||
| * The MMTF Reader is deprecated and will be removed in version 3.0 as | ||
| the MMTF format is no longer supported (Issue #4634). | ||
|
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| ## Author statistics | ||
|
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| This release was the work of 22 contributors, **10** of which are **new contributors**. | ||
|
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| Our **new contributors** are: | ||
| - @aditya292002 | ||
| - @pstaerk | ||
| - @kainszs | ||
| - @SampurnaM | ||
| - @leonwehrhan | ||
| - @PythonFZ | ||
| - @kurtmckee | ||
| - @laksh-krishna-sharma | ||
| - @MattTDavies, | ||
| - @talagayev | ||
|
|
||
| ## Acknowledgements | ||
|
|
||
| MDAnalysis thanks [NumFOCUS][] for its continued support as our fiscal sponsor and | ||
| the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOSS5 awards. | ||
|
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| — @IAlibay ([release manager][roles]) on behalf of the [MDAnalysis Team][] | ||
|
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||
|
|
||
| ---- | ||
|
|
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|
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| [^guesserPR]: The Guesser API was a _big_ undertaking: Her merged [PR | ||
| #3753][] totalled 668 (!) comments. We look forward to the | ||
| community providing Guessers for specific context. | ||
|
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||
| [^PMDApaper]: Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard | ||
| J. Gowers, Michael Gecht, and Oliver Beckstein. *PMDA - Parallel | ||
| Molecular Dynamics Analysis.* In Chris Calloway, David Lippa, | ||
| Dillon Niederhut, and David Shupe, editors, *Proceedings of the | ||
| 18th Python in Science Conference*, 134 – 142. Austin, | ||
| TX, 2019. SciPy. doi:[10.25080/Majora-7ddc1dd1-013](https://doi.org/10.25080/Majora-7ddc1dd1-013). | ||
|
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||
| [^parallelizationPR]: Adding parallelization in a transparent manner | ||
| was quite a difficult undertaking that touched many parts of the | ||
| analysis code and required a lot of thought. Feedback is very | ||
| welcome! See [PR #4162][] with 713 (!) comments. | ||
|
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||
| [guesser modules docs]: https://docs.mdanalysis.org/stable/documentation_pages/guesser_modules.html | ||
| [converter modules docs]: https://docs.mdanalysis.org/stable/documentation_pages/converters.html | ||
|
|
||
| [GSoC 2022 project]: {{ site.baseurl }}{% post_url 2022-12-9-Aya-gsoc-final-report %} | ||
| [GSoC 2023 project]: {{ site.baseurl }}{% post_url 2024-01-18-gsoc2023_marinegor %} | ||
| [parallel analysis]: https://docs.mdanalysis.org/stable/documentation_pages/analysis/parallelization.html | ||
| [MDAnalysis.analysis.base.AnalysisBase]: https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase | ||
| [PR #3753]: https://github.com/MDAnalysis/mdanalysis/pull/3753 | ||
| [PR #4162]: https://github.com/MDAnalysis/mdanalysis/pull/4162 | ||
| [pydssp]: https://github.com/ShintaroMinami/PyDSSP | ||
| [MDAnalysis.analysis]: https://docs.mdanalysis.org/stable/documentation_pages/analysis_modules.html | ||
| [PMDA]: https://github.com/mdanalysis/pmda | ||
| [SPEC 0]: https://scientific-python.org/specs/spec-0000/ | ||
| [x86-64]: https://en.wikipedia.org/wiki/X86-64 | ||
| [ARM64]: https://en.wikipedia.org/wiki/Apple_M1 | ||
| [installation instructions in the User Guide]: https://userguide.mdanalysis.org/stable/installation.html | ||
| [conda-forge channel]: https://anaconda.org/conda-forge/mdanalysis | ||
| [PyPi]: https://pypi.org/project/MDAnalysis/ | ||
| [NumFOCUS]: https://www.numfocus.org | ||
| [CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/package/CHANGELOG | ||
| [Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ | ||
| [licensing update]: {{ site.baseurl }}{% post_url 2023-09-22-licensing-update %} | ||
| [roles]: {{ site.baseurl }}/pages/team/#roles | ||
| [MDAnalysis Team]: {{ site.baseurl }}/pages/team | ||
| [MDAKits]: https://mdakits.mdanalysis.org/ | ||
| [roadmap]: {{ site.baseurl }}{% post_url 2023-10-25-towards_3.0 %}#a-trimmed-down-core-library | ||
| [mdaencore]: https://mdakits.mdanalysis.org/mdaencore.html | ||
| [waterdynamics]: https://mdakits.mdanalysis.org/waterdynamics.html | ||
| [PathSimAnalysis]: https://mdakits.mdanalysis.org/PathSimAnalysis.html |