From 301ef52c2b55be7ed78acd61b196a8dcf5af3eea Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 30 Jun 2023 16:12:59 -0700 Subject: [PATCH] test on GROMACS 2022 and 2023 - add conda-forge GROMACS 2022 and 2023 to CI - update README and INSTALL - update docs (supported versions of GROMACS) - update CHANGES --- .github/workflows/ci.yaml | 8 ++++---- CHANGES | 9 +++++---- INSTALL.rst | 2 +- README.rst | 6 ++++-- doc/sphinx/source/index.txt | 17 ++++++++++------- 5 files changed, 24 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 46157f06..0e24dcfd 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -32,17 +32,17 @@ jobs: os: [ubuntu-latest] python-version: ["3.10"] - gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1"] + gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1"] include: - os: ubuntu-latest python-version: "3.8" - gromacs-version: "2021.1" + gromacs-version: "2023.1" - os: ubuntu-latest python-version: "3.9" - gromacs-version: "2021.1" + gromacs-version: "2023.1" - os: macos-latest python-version: "3.10" - gromacs-version: "2021.1" + gromacs-version: "2023.1" env: MPLBACKEND: agg diff --git a/CHANGES b/CHANGES index 8eb2d017..c0bc0208 100644 --- a/CHANGES +++ b/CHANGES @@ -10,6 +10,11 @@ cadeduckworth, orbeckst, VOD555 Changes +* added support for Python 3.10 (#202) +* dropped testing on Python 3.6 (PR #220, #202) +* dropped testing on Python 3.7 (minimally supported Python >= 3.8, #248) +* support Gromacs 2022.4 and 2023.1 (#256) +* use pymbar >= 4 and alchemlyb >= 2 (#246) * for ensemble.EnsembleAnalysis._single_frame() changed 'pass' to 'raise NotImplementedError' (#216) * for ensemble.EnsembleAnalysis._single_universe() @@ -18,10 +23,6 @@ Changes and use _single_frame OR _single_universe (#216) * _prepare_universe and _conclude_universe removed from EnsembleAnalysis.run() method, no longer needed (per comments, #199) -* added support for Python 3.10 (#202) -* dropped testing on Python 3.6 (PR #220, #202) -* dropped testing on Python 3.7 (minimally supported Python >= 3.8, #248) -* use pymbar >= 4 and alchemlyb >= 2 (#246) * internal log_banner() now uses logger as argument (PR #247) Enhancements diff --git a/INSTALL.rst b/INSTALL.rst index 63ead9e1..093a4740 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -32,7 +32,7 @@ Make a conda environment with the latest packages for Python 3.8 or higher with the name *mdpow*; this installs the larger dependencies that are pre-requisites for MDPOW:: - conda create -c conda-forge -n mdpow numpy scipy matplotlib mdanalysis pyyaml alchemlyb pandas gromacswrapper + conda create -c conda-forge -n mdpow numpy scipy matplotlib seaborn mdanalysis pyyaml alchemlyb pandas gromacswrapper rdkit conda activate mdpow Install MDPOW with ``pip``:: diff --git a/README.rst b/README.rst index c1c89d34..de85b25b 100644 --- a/README.rst +++ b/README.rst @@ -6,6 +6,7 @@ .. |P_ow| replace:: *P*\ :sub:`OW` .. |P_cw| replace:: *P*\ :sub:`CW` +.. |P_tw| replace:: *P*\ :sub:`TW` *MDPOW* is a python package that automates the calculation of solvation free energies via molecular dynamics (MD) simulations. In @@ -14,7 +15,8 @@ coefficients. Currently implemented: - *water-octanol* partition coefficient (|P_ow|) - *water-cyclohexane* partition coefficient (|P_cw|) - +- *water-toluene* partition coefficient (|P_tw|) + Calculations are performed with the Gromacs_ MD software package [#GromacsWrapperNote]_. Currently, *OPLS-AA*, *CHARMM/CGENFF*, and *AMBER/GAFF* parameters are supported. @@ -47,7 +49,7 @@ See `INSTALL`_ for detailed instructions. MDPOW currently supports and is tested with Python 3.8 to 3.10. You will also need `Gromacs`_ (currently tested with versions 4.6.5, -2018, 2020, 2021 but 2016 and 2019 should also work). +2018, 2020, 2021, 2022, 2023 but 2016 and 2019 should also work). Development version diff --git a/doc/sphinx/source/index.txt b/doc/sphinx/source/index.txt index 1c4986d9..b5a3d884 100644 --- a/doc/sphinx/source/index.txt +++ b/doc/sphinx/source/index.txt @@ -7,7 +7,7 @@ .. |POW| replace:: *P*\ :sub:`OW` .. |P_ow| replace:: *P*\ :sub:`OW` .. |P_cw| replace:: *P*\ :sub:`CW` - +.. |P_tw| replace:: *P*\ :sub:`TW` MDPOW documentation @@ -19,15 +19,16 @@ MDPOW documentation **MDPOW** is a python package that automates the calculation of solvation free energies via molecular dynamics (MD) simulations. In -particular, it facilitates the computation of partition coeffcients. Currently implemented: +particular, it facilitates the computation of partition +coeffcients. Currently implemented: - *water-octanol* partition coefficient (|P_ow|) - *water-cyclohexane* partition coefficient (|P_cw|) - -.. warning:: Development is still very much in flux and the - documentation is at least partially out of date. If - something appears unclear or just wrong, then please ask - questions on the `MDPOW Issue Tracker`_. +- *water-toluene* partition coefficient (|P_tw|) + +The package is being actively developed and incorporates recent ideas +and advances. If something appears unclear or just wrong, then please +ask questions on the `MDPOW Issue Tracker`_. .. _`MDPOW Issue Tracker`: https://github.com/Becksteinlab/mdpow/issues @@ -44,6 +45,8 @@ software package [#GromacsWrapperFramework]_. MDPOW is tested with * Gromacs 2018.6 * Gromacs 2020.6 * Gromacs 2021.1 +* Gromacs 2022.4 +* Gromacs 2023.1 but versions 5.x, 2016.x, and 2019.x should also work. It should be possible to use any of these Gromacs versions without