Oliver Beckstein edited this page Jun 2, 2016 · 5 revisions

This is a historical document and is of no relevance anymore.

As oulined in Issue 223, Google Code is closing down and we need to move the MDAnalysis project. The (current) choice is GitHub. This page collects the issues we need to consider. Important documentation on the whole procedure can be found in the GitHubExporterFAQ.


We'd like to do a clean transition where we

  1. stop using Google code
  2. transition to GitHub
  3. then start using GitHub.

From reading the issues for export our best hope appears to be to use the export wizard Export to GitHub (instead of manual tools) but the wizard cannot update an existing repository and so we want to avoid having to manually sync later changes from Google Code to Git Hub.

TASKS by Person

  • Issue Tracker (Issue 231): richardjgowers (Richard) will
    1. check if there are any open issues that have attachments. If yes, then
    2. download the attachments from all open issues and store them in individual directories named IssueNNN/CommentMM with the original file names (NNN is the issue id number, eg 055 for Issue 55 and MM is the comment number, eg 01 for comment #1 or 00 for the initial issue report).
    3. prepare a zip file (and wait for further instructions until we figure out a way to put everything back together)
  • team (Issue 232): orbeckst (Oliver)
    1. collect GitHub usernames from all current contributors
  • Repository (Issue 233): orbeckst (Oliver) will
    1. remove commit access to Google Code from everyone
    2. create a final snapshot (via Takeout) of the project and save the admin and people data
    3. use the Export Wizard to transfer the repository to GitHub (code history, issue tracker (without attachments), wiki)
    4. split off applications into individual repositories
    5. set up new access lists (based on the currently active committors)
  • Wiki (Issue 234): TBN will
    1. turn the wiki branch into a GitHub wiki (see Wiki)
    2. manually fix up pages where necessary
    3. start filing issues re: wiki where community cleanup is needed
  • Online docs (development branch) (Issue 235): TBN will
    1. devise a workflow that allows us to publish the html docs as a gh-pages branch in the repository
  • MDAnalysis home page (Issue 236): TBN
    1. Set up as a GitHub pages site using either pure html or Jekyll (see the preliminary notes on web site development).
    2. populate and maintain the site

Repository Organization

On GitHub, the project will be owned by the Github Organization MDAnalysis. Using an organization will allow us to maintain multiple repositories with appropriate user permissions.

Required GitHub Repositories

We will initially set up repositories for


  • prune feature branches on google code:
    • Which feature branches are still important?
    • Remove those that are fully merged or will not be developed further (check with commit authors)
  • move the following components to GitHub
    1. Code (mdanalysis repository)
    2. Wiki (wiki repository)
    3. Issue Tracker
    4. home page contents
    • summary
    • people
    • links (e.g. to mailing lists)

Points 1-3 should be handled by the Google Code export wizard although the FAQ also shows how to do this manually.

Point 4 needs to be done manually (easiest is to snapshot the admin page); the contributors page will be snapshot, too. All the information is probably also in the Takeout JSON file but that needs to be verified).

Point 5 needs to be done manually by getting (wget/curl) the individual tarballs from the old download page; perhaps we put them up on PyPi just for historical reasons (if this is possible).


We plan to use the export to GitHub wizard (new button in the repo). Oliver (orbeckst) will do this (as a owner). It will be initially moved to orbeckst's personal GitHub space (a limitation of the export procedure) and then transferred inside GitHub to the MDAnalysis Organization.

Oliver can also use Google Takeout to obtain a big JSON file that contains all the project metadata (including the issue tracker except attachments). This provides a fall-back for manual transfer.

Issue Tracker

  • attachments will not be transferred
    • need to manually save any attachments that we want to keep
    • assign one person to go through the open issues and
      • download attachments
      • keep a note of issue and comment number
  • issue owners and commenters might not be tranferred; in principle I have this information in the Takeout dump but we cannot change this information on GitHub.



  • By default, the wiki will be converted to markdown and placed in a wiki branch, as described in the FAQ: here did my Google Code wikis go?.
  • Will the wiki be transformed into a GitHub wiki? No, but according to the FAQ there exists a tool finishGoogleCodeGitHubWikiMigration to move the wiki files from the wiki branch into the repo's wiki section.

Project Information

GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
Core Developers


Release Notes
Guide for Developers
Google Summer of Code

Code of Conduct


@mdanalysis on Twitter
Downloads (PyPi)
Mailing Lists:
User discussion group
Developer mailing list

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