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

@@ -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

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

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

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