release 0.9.1

Patch-level releases with fixes only.

What's Changed

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

New Contributors

• @hsk17 made their first contribution in #288

Full Changelog: release-0.9.0...release-0.9.1

Release 0.9.1 rc2 (testing deployment)

What's Changed

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

New Contributors

• @hsk17 made their first contribution in #288

Full Changelog: release-0.9.0...release-0.9.1-rc2

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

New Contributors

• @njzjz made their first contribution in #274

Full Changelog: release-0.8.5...release-0.9.0

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.assert_frame_equal by @orbeckst in #250
• modernized CI workflow by @orbeckst in #254
• Blacken by @orbeckst in #247
• test GROMACS 2023.1 (and use Py 3.11 for the all version test) by @orbeckst in #255

Full Changelog: release-0.8.4...release-0.8.5

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 #239

Full Changelog: release-0.8.3...release-0.8.4

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: release-0.8.2...release-0.8.3

Release 0.8.2

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

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

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

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