diff --git a/.github/ISSUE_TEMPLATE/questions.md b/.github/ISSUE_TEMPLATE/questions.md index fd8bad08428..39cfcd83bb4 100644 --- a/.github/ISSUE_TEMPLATE/questions.md +++ b/.github/ISSUE_TEMPLATE/questions.md @@ -1,6 +1,6 @@ --- name: Questions -about: If you want to ask a question please use the mailing list! +about: If you want to ask a question please use GitHub Discussions! --- @@ -11,13 +11,13 @@ If you have a **QUESTION** such as - what output means - ... or similar questions related to *USING* MDAnalysis -then please *ask this question on the user mailing list* +then please *ask this question on GitHub Discussions* - https://groups.google.com/forum/#!forum/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions -The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and decisions on the API. In order to keep the volume of work on the issue tracker manageable for our volunteer developers, we will **IMMEDIATELY CLOSE ISSUES WITH QUESTIONS** as these questions are better answered on the mailing list. +The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and decisions on the API. In order to keep the volume of work on the issue tracker manageable for our volunteer developers, we will migrate issues with questions to [GitHub Discussions](https://github.com/MDAnalysis/mdanalysis/discussions). -We really appreciate you getting in touch with us --- no matter what you want to discuss. But we need your help keeping the amount of work manageable so please use the mailing list for questions and the issue tracker for code-related issues. +We really appreciate you getting in touch with us --- no matter what you want to discuss. But we need your help keeping the amount of work manageable so please use [GitHub Discussions](https://github.com/MDAnalysis/mdanalysis/discussions) for questions and the issue tracker for code-related issues. Thank you! diff --git a/.github/workflows/greetings.yaml b/.github/workflows/greetings.yaml index aa7a6ff9b6f..a0e5903d585 100644 --- a/.github/workflows/greetings.yaml +++ b/.github/workflows/greetings.yaml @@ -17,4 +17,4 @@ jobs: - uses: actions/first-interaction@v1 with: repo-token: ${{ secrets.GITHUB_TOKEN }} - pr-message: 'Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our [Code of Conduct](https://www.mdanalysis.org/pages/conduct/) and that first time contributors introduce themselves on the [developer mailing list](https://groups.google.com/g/mdnalysis-devel) so we can get to know you. You can learn more about [participating here](https://www.mdanalysis.org/#participating). Please also add yourself to `package/AUTHORS` as part of this PR.' + pr-message: 'Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our [Code of Conduct](https://www.mdanalysis.org/pages/conduct/) and that first time contributors introduce themselves on [GitHub Discussions](https://github.com/MDAnalysis/mdanalysis/discussions) so we can get to know you. You can learn more about [participating here](https://www.mdanalysis.org/#participating). Please also add yourself to `package/AUTHORS` as part of this PR.' diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 70953c07dda..7b6b459a78d 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -41,7 +41,7 @@ welcome reports](#reporting) by filling out [*this form*][conduct-form]. This code applies equally to founders, developers, mentors and new community members, in all spaces managed by MDAnalysis. This -includes the mailing lists, our GitHub organizations, our chat rooms, +includes GitHub Discussions, our GitHub organizations, our chat rooms, in-person events, and any other forums created by the project team. In addition, violations of this code outside these spaces may affect a person's ability to participate within them. @@ -49,7 +49,7 @@ person's ability to participate within them. By embracing the following principles, guidelines and actions to follow or avoid, you will help us make MDAnalysis a welcoming and productive community. If that doesn't answer your questions, feel free to contact us -at our [*user-mailing-list*](mailto:mdnalysis-discussions@googlegroups.com). +via [GitHub Discussions](https://github.com/MDAnalysis/mdanalysis/discussions). 1. **Be friendly and patient**. diff --git a/GOVERNANCE.md b/GOVERNANCE.md index 6c716aeae2f..812b3b98a9c 100644 --- a/GOVERNANCE.md +++ b/GOVERNANCE.md @@ -6,7 +6,7 @@ Below is a summary of the governance model (but note that if the text on this pa ---- -Project leadership is provided by a subset of contributors, the **MDAnalysis Core Developers** ([@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs)) who have produced substantial contributions over extended lengths of time and who remain active in reviewing issues and discussions on the various mailing lists. MDAnalysis Core Developers are granted commit rights (write access) to the GitHub source code repository. New MDAnalysis Core Developers are elected with a simple majority of current MDAnalysis Core Developers. +Project leadership is provided by a subset of contributors, the **MDAnalysis Core Developers** ([@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs)) who have produced substantial contributions over extended lengths of time and who remain active in reviewing issues and discussions on the various discussion channels. MDAnalysis Core Developers are granted commit rights (write access) to the GitHub source code repository. New MDAnalysis Core Developers are elected with a simple majority of current MDAnalysis Core Developers. All decisions are made by simple majority of the MDAnalysis Core Developers. diff --git a/README.rst b/README.rst index df365c7e0f4..c539704e74a 100644 --- a/README.rst +++ b/README.rst @@ -2,9 +2,13 @@ MDAnalysis Repository README ================================ -|numfocus| |build| |cron| |cirruscron| |linters| |cov| +|numfocus| -|docs| |devdocs| |usergroup| |developergroup| |anaconda| |asv| +|build| |cron| |cirruscron| |linters| |cov| + +|docs| |devdocs| |discussions| + +|anaconda| |asv| MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. @@ -84,10 +88,10 @@ Contributing ============ Please report **bugs** or **enhancement requests** through the `Issue -Tracker`_. Questions can also be asked on the `user mailing list`_. +Tracker`_. Questions can also be asked on `GitHub Discussions`_. If you are a **new developer** who would like to start contributing to -MDAnalysis get in touch on the `developer mailing list`_. To set up a +MDAnalysis get in touch on `GitHub Discussions`_. To set up a development environment and run the test suite read the `developer guide`_. @@ -135,26 +139,15 @@ For citations of included algorithms and sub-modules please see the references_. .. _`MDAnalysis API docs`: https://docs.mdanalysis.org .. _`Issue Tracker`: https://github.com/mdanalysis/mdanalysis/issues -.. _`user mailing list`: - https://groups.google.com/group/mdnalysis-discussion +.. _`GitHub Discussions`: + https://github.com/MDAnalysis/mdanalysis/discussions .. _`developer guide`: https://userguide.mdanalysis.org/contributing.html -.. _`developer mailing list`: - https://groups.google.com/group/mdnalysis-devel .. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787 .. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e .. _references: https://docs.mdanalysis.org/documentation_pages/references.html .. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis - -.. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg - :alt: User Google Group - :target: https://groups.google.com/group/mdnalysis-discussion - -.. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg - :alt: Developer Google Group - :target: https://groups.google.com/group/mdnalysis-devel - .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg :alt: Documentation (latest release) :target: https://docs.mdanalysis.org @@ -198,3 +191,7 @@ For citations of included algorithms and sub-modules please see the references_. .. |powered_by_MDA| image:: https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=15&logo=data:image/x-icon;base64,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA :alt: Powered by MDAnalysis :target: https://www.mdanalysis.org + +.. |discussions| image:: https://img.shields.io/github/discussions/MDAnalysis/MDAnalysis + :alt: GitHub Discussions + :target: https://github.com/MDAnalysis/mdanalysis/discussions \ No newline at end of file diff --git a/package/INSTALL b/package/INSTALL index a6b9a2a876f..71c04e7760e 100644 --- a/package/INSTALL +++ b/package/INSTALL @@ -53,9 +53,9 @@ file) and README and check the MDAnalysis project pages at in particular https://github.com/MDAnalysis/mdanalysis/wiki/Install and related pages. -You can always ask questions on the MDAnalysis mailing list: +You can always ask questions on GitHub Discussions: - http://groups.google.com/group/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation People there are very happy to help. When posting please remember to mention the release of MDAnalysis you are trying to install (e.g. "tar diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py index b72908d765c..1813cb27f32 100644 --- a/package/MDAnalysis/__init__.py +++ b/package/MDAnalysis/__init__.py @@ -36,8 +36,8 @@ also be manipulated (for instance, fit to a reference structure) and written out. Time-critical code is written in C for speed. -Help is also available through the mailinglist at -http://groups.google.com/group/mdnalysis-discussion +Help is also available through GitHub Discussions at +https://github.com/MDAnalysis/mdanalysis/discussions Please report bugs and feature requests through the issue tracker at https://github.com/MDAnalysis/mdanalysis/issues diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 2d41ff09207..ae59073dbc5 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -31,7 +31,7 @@ ---- Support for AMBER is still somewhat *experimental* and feedback and contributions are highly appreciated. Use the `Issue Tracker`_ or get in touch -on the `MDAnalysis mailinglist`_. +on the `GitHub Discussions`_. .. rubric:: Units @@ -126,7 +126,7 @@ .. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml .. _NetCDF: http://www.unidata.ucar.edu/software/netcdf .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues -.. _MDAnalysis mailinglist: https://groups.google.com/group/mdnalysis-discussion +.. _GitHub Discussions: https://github.com/MDAnalysis/mdanalysis/discussions """ import scipy.io.netcdf diff --git a/package/README b/package/README index cd73289a955..277c62dfed3 100644 --- a/package/README +++ b/package/README @@ -90,7 +90,7 @@ Please report bugs and feature requests through the Issue Tracker at https://github.com/MDAnalysis/mdanalysis/issues -Help is also available through the mailing list +Help is also available through GitHub Discussions - http://groups.google.com/group/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions diff --git a/package/doc/README b/package/doc/README index 432b0db8292..0a25ed3b4e4 100644 --- a/package/doc/README +++ b/package/doc/README @@ -45,7 +45,7 @@ The manual includes all the doc strings with some additional text; it is a work in progress and suggestions to improve it are welcome. File them via the Issue Tracker at https://github.com/MDAnalysis/mdanalysis/issues/ or mention it on the -mailing list http://groups.google.com/group/mdnalysis-discussion . +GitHub Discussions https://github.com/MDAnalysis/mdanalysis/discussions. Wiki and online docs diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index ec50cc43290..e6171630c28 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -46,15 +46,14 @@ Getting involved ================ Please report **bugs** or **enhancement requests** through the `Issue -Tracker`_. Questions can also be asked on the `mdnalysis-discussion mailing -list`_. +Tracker`_. Questions can also be asked on the `GitHub Discussions`_. The MDAnalysis community subscribes to a `Code of Conduct`_ that all community members agree and adhere to --- please read it. .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues -.. _`mdnalysis-discussion mailing list`: - http://groups.google.com/group/mdnalysis-discussion +.. _`GitHub Discussions`: + https://github.com/MDAnalysis/mdanalysis/discussions .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/ diff --git a/package/setup.py b/package/setup.py index 20833734c99..045b644b8a5 100755 --- a/package/setup.py +++ b/package/setup.py @@ -35,12 +35,10 @@ https://github.com/MDAnalysis/mdanalysis/wiki/INSTALL -Also free to ask on the MDAnalysis mailing list for help: +Also free to ask on GitHub Discussions for help: - http://groups.google.com/group/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation -(Note that the group really is called `mdnalysis-discussion' because -Google groups forbids any name that contains the string `anal'.) """ from setuptools import setup, Extension, find_packages diff --git a/testsuite/INSTALL b/testsuite/INSTALL index b0db41ed077..d70142f6b58 100644 --- a/testsuite/INSTALL +++ b/testsuite/INSTALL @@ -23,9 +23,9 @@ file) and README and check the MDAnalysis project pages at in particular https://github.com/MDAnalysis/mdanalysis/wiki/INSTALL and related pages. -You can always ask questions on the MDAnalysis mailing list: +You can always ask questions on GitHub Discussions: - https://groups.google.com/group/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation People there are very happy to help. When posting please remember to mention the release of MDAnalysis you are trying to install (e.g. "tar file diff --git a/testsuite/README b/testsuite/README index a2627534cfa..77e568e2019 100644 --- a/testsuite/README +++ b/testsuite/README @@ -2,7 +2,7 @@ MDAnalysisTests =================== -|build| |cov| |devdocs| |developergroup| +|build| |cov| |devdocs| MDAnalysis_ is a Python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Amber, NAMD, LAMMPS, or Gromacs. @@ -30,9 +30,9 @@ Contact Please report bugs and feature requests through the `Issue Tracker`_. -Help is also available through the user mailing list at https://groups.google.com/group/mdnalysis-discussion. +Help is also available through GitHub Discussions at https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation. -For questions and discussions for code development, join the developer list https://groups.google.com/group/mdnalysis-devel. +For questions and discussions for code development, use GitHub Discussions. .. Links .. _MDAnalysis: https://www.mdanalysis.org @@ -53,8 +53,4 @@ For questions and discussions for code development, join the developer list http .. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg :alt: Documentation (development version) - :target: https://docs.mdanalysis.org/dev - -.. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg - :alt: Developer Google Group - :target: https://groups.google.com/group/mdnalysis-devel + :target: https://docs.mdanalysis.org/dev \ No newline at end of file diff --git a/testsuite/setup.py b/testsuite/setup.py index 154b7dba99b..b61a740e90f 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -34,9 +34,9 @@ https://github.com/MDAnalysis/mdanalysis/wiki/INSTALL -Also free to ask on the MDAnalysis mailing list for help: +Also free to ask on GitHub Discussions for help: - http://groups.google.com/group/mdnalysis-discussion + https://github.com/MDAnalysis/mdanalysis/discussions (Note that the group really is called `mdnalysis-discussion' because Google groups forbids any name that contains the string `anal'.)