From 49d51a00c8b6956c3f506ad42007a051c4a503dd Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 8 Nov 2023 22:23:24 -0500 Subject: [PATCH 1/3] updated CI environments - remove six from all environments (should have been in PR #265, part of #259) - add sphinx_rtd_theme to the RTD CI as it is apparently no longer installed automatically by RTD. (fix #267) --- ci/conda-envs/test_env.yaml | 1 - ci/readthedocs/environment.yml | 2 +- ci/readthedocs/requirements.txt | 1 - 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/ci/conda-envs/test_env.yaml b/ci/conda-envs/test_env.yaml index 28698900..20c28775 100644 --- a/ci/conda-envs/test_env.yaml +++ b/ci/conda-envs/test_env.yaml @@ -3,7 +3,6 @@ channels: - conda-forge dependencies: - python -- six - numpy>=1.0 - matplotlib - pandas>=0.17 diff --git a/ci/readthedocs/environment.yml b/ci/readthedocs/environment.yml index 76164c1d..a5eb0473 100644 --- a/ci/readthedocs/environment.yml +++ b/ci/readthedocs/environment.yml @@ -4,9 +4,9 @@ channels: - defaults dependencies: - python=3.11 -- six - numpy>=1.0 - matplotlib-base - pandas - numkit>=1.0 - gromacs==2023.1 +- sphinx_rtd_theme diff --git a/ci/readthedocs/requirements.txt b/ci/readthedocs/requirements.txt index 5cc2477e..939d390c 100644 --- a/ci/readthedocs/requirements.txt +++ b/ci/readthedocs/requirements.txt @@ -1,4 +1,3 @@ -six numpy>=1.0 matplotlib pandas From be290079e848e1d5a464f353fdbd4d255c5ed087 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 8 Nov 2023 23:31:13 -0500 Subject: [PATCH 2/3] add gromacs_py to alternatives --- doc/sphinx/source/alternatives.txt | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/doc/sphinx/source/alternatives.txt b/doc/sphinx/source/alternatives.txt index 9646c055..db2872d0 100644 --- a/doc/sphinx/source/alternatives.txt +++ b/doc/sphinx/source/alternatives.txt @@ -24,11 +24,20 @@ gmxapi_ (M.E. Irrgang, J.M. Hays, and P.M. Kasson) `10.1093/bioinformatics/bty484 `_ +`gromacs_py`_ (Samuel Murail, Maxence Delaunay, Damien Espana) + Gromacs_py is a Python library allowing a simplified use of the + Gromacs MD simulation software. Gromacs_py can build a system + topologie based on a pdb file, create the simulation system (pbc + box, adding water and ions) and run minimisation, equilibration and + production runs. One of the main objective of the Gromacs_py + wrapper is to automatize routine operations for MD simulation of + multiple systems. + MDAnalysis_ (N. Michaud-Agrawal, E. J. Dennning, and O. Beckstein) Reads various trajectories (dcd, xtc, trr) and makes coordinates available as numpy_ arrays. It also has a fairly sophisticated selection language, similar to Charmm_ or VMD_. - + ParmEd_ A general tool for working with topology files for all the popular MD codes, including the `parmed.gromacs`_ module for ITP and TOP @@ -160,3 +169,4 @@ they can be added here. Thanks. .. _issue tracker: https://github.com/Becksteinlab/GromacsWrapper/issues .. _ParmEd: http://parmed.github.io/ParmEd/html/index.html .. _parmed.gromacs: http://parmed.github.io/ParmEd/html/api/parmed/parmed.gromacs.html +.. _`gromacs_py`: https://github.com/samuelmurail/gromacs_py From 793f4c582ad5f7288557ce125daa4c3fe2624a71 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 8 Nov 2023 23:35:18 -0500 Subject: [PATCH 3/3] removed supported Python versions from doc index page Supported Python can be found in the installation page. I only want one place in the docs that I need to keep updated. --- doc/sphinx/source/index.txt | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/doc/sphinx/source/index.txt b/doc/sphinx/source/index.txt index 3d241a03..2c1abc57 100644 --- a/doc/sphinx/source/index.txt +++ b/doc/sphinx/source/index.txt @@ -2,21 +2,21 @@ .. GromacsWrapper documentation master file, created by sphinx-quickstart on Tue Jun 23 19:38:56 2009. ==================================================== - GromacsWrapper --- a Python framework for Gromacs + GromacsWrapper --- a Python framework for GROMACS ==================================================== :Release: |release| :Date: |today| -**GromacsWrapper** is a Python package (Python 2.7.x and Python ≥ 3.6) -that wraps system calls to GROMACS_ tools into thin classes. This -allows for fairly seamless integration of the gromacs tools into -Python_ scripts. This is generally superior to shell scripts because -of Python's better error handling and superior data structures. It -also allows for modularization and code re-use. In addition, commands, -warnings and errors are logged to a file so that there exists a -complete history of what has been done. +**GromacsWrapper** is a pure Python package that wraps system calls to +GROMACS_ tools into thin classes. This allows for fairly seamless +integration of the GROMACS tools into Python_ scripts. This is +generally superior to shell scripts because of Python's better error +handling and superior data structures. It also allows for +modularization and code re-use. In addition, commands, warnings and +errors are logged to a file so that there exists a complete history of +what has been done. GROMACS_ versions 4.6.x, 2016.x, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x, and 2023.x are all supported. GromacsWrapper detects your @@ -24,8 +24,8 @@ Gromacs tools and provides them as :func:`gromacs.grompp`, :func:`gromacs.mdrun`, etc, regardless of your Gromacs version, which allows one to write scripts that are broadly Gromacs-version agnostic. Source your ``GMXRC`` file or make the :program:`gmx` binary -(for versions ≥ 5.x) or all the Gromacs tools available on your -:envvar:`PATH` for GromacsWrapper to find the Gromacs installation. +(for versions ≥ 5.x) or all the GROMACS tools available on your +:envvar:`PATH` for GromacsWrapper to find the GROMACS installation. .. warning:: @@ -51,9 +51,9 @@ you're fixing. Getting started =============== -See :ref:`installation` for download and installation instructions. The -:ref:`quickstart` provides a brief example of how to use -GromacsWrapper in the most basic fashion. +See :ref:`installation` for supported versions of Python and download +and installation instructions. The :ref:`quickstart` provides a brief +example of how to use GromacsWrapper in the most basic fashion. The source code itself is available in the `GromacsWrapper git repository`_.