Published June 15, 2024 | Version release-0.9.0
Software Open

Becksteinlab/GromacsWrapper: release 0.9.0

Creators

  • 1. Arizona State University
  • 2. University of Rochester//FutureHouse
  • 3. Datryllic LLC
  • 4. Boston University
  • 5. CHARM-Tx
  • 6. QuantifiedCode
  • 7. Princeton
  • 8. Rutgers University
  • 9. Harvard, USA

Description

With this release, GromacsWrapper discontinues support for legacy versions of Python; if you need support for Python 2.7 (ye served us well, RIP) of Python ≤3.8 please use the 0.8.5 release.

Python 3.9 - 3.12 are officially supported and tested on Linux and macOS. (Windows probably works, too, but we can't test it without GROMACS conda packages for Windows.)

The package is now also tested with GROMACS 2024, so we know GW works with GROMACS 4.6.5 to 2024.2.

Summary

Contributors: @orbeckst, @jandom, @njzjz

  • officially support Python 3.12 (PR #271, issue #263)

  • supports GROMACS 2024.2 (PR #280)

  • removed support for legacy Python (<= 3.8) (#259)

  • fixed GROMACS TOP reader not reading angle parameters from topology file (#261)

  • fixed Python 3.12: No module named ('pkg_resources' #263)

  • fixed AttributeDict does not support hasattr (#214)

  • fixed handle KeyboardInterrupts when using MDRunner.run() (#255 )

  • internally switched to pyproject.toml (#278)

  • Pending Deprecation for the gw-*.py scripts:

    The gw-*.py scripts are NOT anymore installed (it's technically messy with the new system #278 and requires code refactoring). They will likely be DEPRECATED. See issue #279 for more details and voice your opinion if you really need these scripts.

What's Changed

  • updated RTD config by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/258
  • removed support for Python <= 3.7 by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/265
  • updated to versioneer 0.29 by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/266
  • fix #216: angle parameters are not being read from topology file by @jandom in https://github.com/Becksteinlab/GromacsWrapper/pull/264
  • updated CI environments by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/268
  • fix #214: AttributeDict does not support hasattr by @jandom in https://github.com/Becksteinlab/GromacsWrapper/pull/269
  • fix #263: No module named 'pkg_resources' by @jandom in https://github.com/Becksteinlab/GromacsWrapper/pull/271
  • fix #252: handle keyboard interrupts by @jandom in https://github.com/Becksteinlab/GromacsWrapper/pull/270
  • ci: try a simple ci.yaml (experiment) by @jandom in https://github.com/Becksteinlab/GromacsWrapper/pull/272
  • fix SyntaxWarning: invalid escape sequence by @njzjz in https://github.com/Becksteinlab/GromacsWrapper/pull/274
  • full pyproject.toml support by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/280

New Contributors

  • @njzjz made their first contribution in https://github.com/Becksteinlab/GromacsWrapper/pull/274

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.8.5...release-0.9.0

Files

Becksteinlab/GromacsWrapper-release-0.9.0.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/Becksteinlab/GromacsWrapper/tree/release-0.9.0 (URL)