From 360922fae169290de66789eddeb27a2a35474fad Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 13 Mar 2023 11:39:13 -0700 Subject: [PATCH] updated conda installation instructions - conda package was moved from bioconda to conda-forge - updated installation in README and docs - fixed some remnants of master->main - close #109 --- CHANGES | 2 ++ README.rst | 26 +++++++++++---------- doc/sphinx/source/index.txt | 2 +- doc/sphinx/source/installation.txt | 37 ++++++++++++++++-------------- 4 files changed, 37 insertions(+), 30 deletions(-) diff --git a/CHANGES b/CHANGES index 87eaf578..cbb7adfe 100644 --- a/CHANGES +++ b/CHANGES @@ -11,6 +11,8 @@ orbeckst * replaced deprecated numpy.bool with bool in a test (#234) * fixed use of moved collections.Iterable in test (#235) +NOTE: since 0.8.3, the conda package is available from conda-forge + (thanks to @njzjz) 2021-09-09 0.8.2 orbeckst, simonbray diff --git a/README.rst b/README.rst index 3fbef3d7..c5c82667 100644 --- a/README.rst +++ b/README.rst @@ -31,7 +31,7 @@ running simulations with sensible parameters. https://gromacswrapper.readthedocs.org/en/latest/ .. _GromacsWrapper git repository: https://github.com/Becksteinlab/GromacsWrapper -.. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=master +.. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=main :target: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml :alt: Build Status .. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/badge.svg @@ -46,10 +46,11 @@ running simulations with sensible parameters. :alt: Documentation .. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg :target: http://makeapullrequest.com - :alt: PRs Welcome! -.. |anaconda| image:: https://anaconda.org/bioconda/gromacswrapper/badges/version.svg - :target: https://anaconda.org/bioconda/gromacswrapper + :alt: PRs Welcome! +.. |anaconda| image:: https://anaconda.org/conda-forge/gromacswrapper/badges/version.svg + :target: https://anaconda.org/conda-forge/gromacswrapper :alt: Anaconda.org package + Quick Start @@ -114,24 +115,24 @@ with :: pip install GromacsWrapper -or as a `bioconda package`_ with ``conda`` from the *bioconda* channel :: +or as a `conda-forge package`_ with ``conda`` from the *conda-forge* channel :: - conda install -c conda-forge -c bioconda gromacswrapper + conda install -c conda-forge gromacswrapper .. _`latest version of GromacsWrapper from PyPi`: https://pypi.org/project/GromacsWrapper/ -.. _`bioconda package`: - https://anaconda.org/bioconda/GromacsWrapper - +.. _`conda-forge package`: + https://anaconda.org/conda-forge/gromacswrapper + + Development version ------------------- The *main* branch in the GitHub source repository generally contains useful code but nevertheless, things can break in weird and -wonderful ways. Please report issues through the `Issue Tracker`_ and -mention that you used the *develop branch*. +wonderful ways. Please report issues through the `Issue Tracker`_. To use the *development code base*: checkout the ``main`` branch:: @@ -167,12 +168,13 @@ Reporting Bugs and Contributing to GromacsWrapper ================================================= Please use the `Issue Tracker`_ to report bugs, installation problems, -and feature requests. +and feature requests. Ask questions in the `Discussion forum`_. **Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a general introduction on how make a pull request and contribute to open source projects. .. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues +.. _Discussion forum: https://github.com/Becksteinlab/GromacsWrapper/discussions Building Documentation diff --git a/doc/sphinx/source/index.txt b/doc/sphinx/source/index.txt index c13e4e64..6c33f776 100644 --- a/doc/sphinx/source/index.txt +++ b/doc/sphinx/source/index.txt @@ -101,7 +101,7 @@ or in the Acknowledgements section. Thank you. .. _AUTHORS: - https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/master/AUTHORS + https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/main/AUTHORS .. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper diff --git a/doc/sphinx/source/installation.txt b/doc/sphinx/source/installation.txt index d6572b47..8844dcfc 100644 --- a/doc/sphinx/source/installation.txt +++ b/doc/sphinx/source/installation.txt @@ -36,28 +36,31 @@ GromacsWrapper from PyPi`_.) ====================== .. versionadded:: 0.8.1 +.. versionchanged:: 0.8.3 + Package migrated from *bioconda* to *conda-forge*. -Install as a `bioconda package`_ with the `conda`_ package manager from the -`bioconda`_ channel :: +Install as a `conda-forge package`_ with the `conda`_ package manager from the +`conda-forge`_ channel :: - conda install -c conda-forge -c bioconda gromacswrapper + conda install -c conda-forge gromacswrapper -Both the *conda-forge* and the *bioconda* channel should be specified. +The *conda-forge* channel should be explicitly specified if you are +not already using it by default. .. Note:: - The *bioconda* channel also contains `bioconda packages for - GROMACS`_, which can be used for testing and system setup; for - running in a high-performance environment you are advised to - carefully benchmark and possibly compile a version of GROMACS_ that - is tuned for the system. + The *conda-forge* channel also contains `conda-forge packages for + GROMACS`_ (earlier versions ≤ 2021.x are available as `GROMACS + bioconda packages`_), which can be used for testing and system + setup; for running in a high-performance environment you are + advised to carefully benchmark and possibly compile a version of + GROMACS_ that is tuned for the system. .. _conda: https://docs.conda.io -.. _bioconda: https://bioconda.github.io/ -.. _`bioconda package`: - https://anaconda.org/bioconda/GromacsWrapper -.. _`bioconda packages for GROMACS`: - https://anaconda.org/bioconda/gromacs/ +.. _conda-forge: https://conda-forge.org/ +.. _`conda-forge package`: https://anaconda.org/conda-forge/GromacsWrapper +.. _`conda-forge packages for GROMACS`: https://anaconda.org/conda-forge/gromacs/ +.. _`GROMACS bioconda packages`: https://anaconda.org/bioconda/gromacs/ .. _GROMACS: http://www.gromacs.org/ @@ -68,12 +71,12 @@ If your prefer to download manually, get the latest stable release from https://github.com/Becksteinlab/GromacsWrapper/releases and either :: - pip install GromacsWrapper-0.8.2.tar.gz + pip install GromacsWrapper-0.8.3.tar.gz or install from the unpacked source:: - tar -zxvf GromacsWrapper-0.8.2.tar.gz - cd GromacsWrapper-0.8.2 + tar -zxvf GromacsWrapper-0.8.3.tar.gz + cd GromacsWrapper-0.8.3 python setup.py install