gromacswrapper - release 0.9.2

Patch-level release that extends Python support to 3.13.

What's Changed

• support and test Python 3.13

Not relevant for users:

• updated CI/CD deployment workflow by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/305
• fix coverage reporting by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/294

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.9.1...release-0.9.2

- Python
Published by orbeckst 11 months ago

gromacswrapper - release 0.9.2 (release candidate 1)

What's Changed

• support Python 3.13
• updated CI/CD deployment workflow by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/305

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.9.1...release-0.9.2rc1

- Python
Published by orbeckst 11 months ago

gromacswrapper - release 0.9.1

Patch-level releases with fixes only.

What's Changed

• fix "DeprecationWarning: invalid escape sequence '\s'" by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/286
• use importlib.resources instead of pkg_resources by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/284
• replaced numpy.NAN,INF with numpy.nan,inf by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/292
• configure codecov by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/293
• some more regex string fixes; and: use numpy.nan instead of numpy.NAN by @hsk17 in https://github.com/Becksteinlab/GromacsWrapper/pull/288
• add automated deployment workflow by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/296

New Contributors

• @hsk17 made their first contribution in https://github.com/Becksteinlab/GromacsWrapper/pull/288

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.9.0...release-0.9.1

- Python
Published by orbeckst over 1 year ago

gromacswrapper - Release 0.9.1 rc2 (testing deployment)

What's Changed

• fix "DeprecationWarning: invalid escape sequence '\s'" by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/286
• use importlib.resources instead of pkg_resources by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/284
• replaced numpy.NAN,INF with numpy.nan,inf by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/292
• configure codecov by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/293
• some more regex string fixes; and: use numpy.nan instead of numpy.NAN by @hsk17 in https://github.com/Becksteinlab/GromacsWrapper/pull/288
• add automated deployment workflow by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/296

New Contributors

• @hsk17 made their first contribution in https://github.com/Becksteinlab/GromacsWrapper/pull/288

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.9.0...release-0.9.1-rc2

- Python
Published by orbeckst over 1 year ago

gromacswrapper - release 0.9.0

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

- Python
Published by orbeckst almost 2 years ago

gromacswrapper - release 0.8.5

Patch-level release with no functional changes (only minor bug fixes and house-keeping, see below).

This is the last release to support very old Python versions (2.7, <3.7) — see #259 .

What's Changed

• use pandas.testing.assertframeequal by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/250
• modernized CI workflow by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/254
• Blacken by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/247
• test GROMACS 2023.1 (and use Py 3.11 for the all version test) by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/255

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.8.4...release-0.8.5

- Python
Published by orbeckst over 2 years ago

gromacswrapper - release 0.8.4

patch release to fix supported Python version metadata (no functional changes compared to 0.8.3)

What's Changed

• fix setup.py metadata by @orbeckst in https://github.com/Becksteinlab/GromacsWrapper/pull/239

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.8.3...release-0.8.4

- Python
Published by orbeckst about 3 years ago

gromacswrapper - release 0.8.3

Minor bugfix and compatibility enhancement release.

What's Changed

• now tested with GROMACS 2022
• now tested with Python 3.10 & 3.11
• confirmed support for GROMACS 4.6.5, 2018, 2019, 2020, 2021, 2022 on Python 2.7 and 3.6--3.11 on Linux and macOS
  
• replaced deprecated logger.warn() with logger.warning() (#229)

Full Changelog: https://github.com/Becksteinlab/GromacsWrapper/compare/release-0.8.2...release-0.8.3

- Python
Published by orbeckst about 3 years ago

gromacswrapper - Release 0.8.2

Minor fix, doc updates, and installation from conda packages is now possible.

- Python
Published by orbeckst over 4 years ago

gromacswrapper - Release 0.8.1

Bug fixes and improved testing - see CHANGES for fixes (mostly to make it work under Python 3) - tested with Gromacs 2021.1, 2020.6, 2019.1, 2018.6, 4.6.5 (and Gromacs 5 and 2016.x should als work) - tested with Python 2.7 and 3.6 – 3.9 - tested on Linux and macOS (Windows should work but we don't have Gromacs builds for testing) - updated style of the online docs

- Python
Published by orbeckst almost 5 years ago

gromacswrapper - Release 0.8.0

Major release of GromacsWrapper (see CHANGES for details).

Highlights: * tested with Gromacs 2019.1, 2018.4, 4.6.5 (and Gromacs 2016.x also works) * supported on Python 2.7 and 3.4+ (tested on 2.7 and 3.6/3.7) * better handling of _mpi and _d suffixes for Gromacs executables * new gromacs.release() command to show the Gromacs version string (such as "4.6.5" or "2019.1") * bug fixes

- Python
Published by orbeckst about 7 years ago

gromacswrapper - Release 0.7.0

Major release of GromacsWrapper (see CHANGES for details).

Highlights: * supports Python 2.7.x and Python 3.5+ (Python 3.4 probably also works) * supports Gromacs 4.6.x, 5.x, 2016, 2018 * obsolete code removed (fileformats.itp, fileformats.preprocessor, gromacs.analysis, gromacs.manager, vmd, staging) * numkit was moved to its own package https://github.com/Becksteinlab/numkit

- Python
Published by orbeckst almost 8 years ago

gromacswrapper - Release 0.6.2

Bug fixes.

Note that this is the last release that contains the bundled packages vmd (for remote execution of scripts in the vmd server), staging (obsolete), and numkit as well as gromacs.analysis. numkit is now available as a separate package at Becksteinlab/numkit.

- Python
Published by orbeckst about 9 years ago

gromacswrapper - Release 0.6.1

Bug fixes

- Python
Published by orbeckst over 9 years ago

gromacswrapper - Release 0.6.0

Major release with usability improvements but also backwards-incompatible configuration file changes

Performance improvements

• GromacsWrapper does not execute all tools on start up anymore but instead loads documentation lazily. This means that import gromacs is now instantaneous (instead of taking a few seconds)

Configuration

• The configuration file (.gromacswrapper.cfg) is not strictly necessary anymore and can be omitted when used with the new automatic tool loading feature.
• automatic tool loading from the environment (manually source GMXRC and either Gromacs 4 or 5 tools are picked up)
• automatic tool loading with GMXRC keyword in the Gromacs section of the config file (GromacsWrapper loads the GMXRC file and automatically loads the environment and all tools)
• Backwards-incompatible change: The Gromacs 5 syntax for tools ("gmx:toolname") is not supported any more in the config file (and an error will be raised). Instead, just provide the driver in the tools keyword, e.g. tools = gmx and all tools are automatically set up).

For more details see the new docs on configuring GromacsWrapper.

- Python
Published by orbeckst over 9 years ago

gromacswrapper - Release 0.5.1

This patch release contains bug fixes and one small change in the internals of core.Command (new use_shell keyword).

- Python
Published by orbeckst almost 10 years ago

gromacswrapper - Release 0.5.0

• Python 2.7 is required (earlier versions are not supported anymore)
• Support for Gromacs 5.x is now the default
  • You can use custom driver prefixes such as gmx or gmx_mpi in your gromacswrapper.cfg file to customize the tools that are being made available.
  • Gromacs 4.6.x still works. typically, GromacsWrapper scripts ought to be able to either use Gromacs 4 or Gromacs 5 because a number of compatibility hacks are included that make Gromacs 5 tools also appear under Gromacs 4 names.
• Removed GridMAT-MD and gridmatmd plugin (no demand and thus no longer supported)

- Python
Published by orbeckst about 10 years ago

gromacswrapper - v0.4.0

Primitive support for Gromacs 5.x and we are now on RTD: gromacswrapper.readthedocs.org

- Python
Published by orbeckst over 10 years ago

gromacswrapper - v0.3.3

Small improvements and updated all links to the new repository and site.

- Python
Published by orbeckst about 11 years ago