IMK Extracting Authorship from git, 2023-08-03

When moving code from one project to another, original authorship and attribution is easily lost in the process. Fortunately, if you’re using git, this information travels with the repository and anyone who had a part in publishing code is identifiable. In this post, we are concerned with identifying the authors who were involved with the ENCORE analysis module in MDAnalysis and giving proper attribution in the new mdaencore MDAKit AUTHOR.md.

While GitHub does show the historical information we want, this is much easier accomplished on the command line with a local copy of the repository. From within the original code base, at the same level as the encore analysis module, we can run the git log command 

$ git log --pretty="%an <%ae>|%ai" encore/ \
| sort -k2 -t'|' \
| awk -F"|" '!_[$1]++'

and then output the contents to a file or less for easier viewing. This will show all authors (%an) along with their email (%ae) and their commit times (%ai). We can separate the author information from the times with a |, so we can later sort the output by date using the pipe symbol as a delimiter. This is then passed to awk to remove duplicate authors (based on their name and email combination) but maintaining chronological order. Unfortunately, as is common with git histories, many authors will have multiple email addresses and can show up multiple times in a history. In this case it’s best to just pick the most reliable contact address.

The output of the above command yields a list of authors (with real emails removed for scraping reasons) 

Matteo Tiberti <XYZ@ABC.COM>|2016-01-26 15:43:49 +0000
Tone Bengtsen <XYZ@ABC.COM>|2016-02-16 13:40:41 +0100
Wouter Boomsma <XYZ@ABC.COM>|2016-02-20 23:05:27 +0100
Wouter Boomsma <XYZ@ABC.COM>|2016-09-11 22:36:33 +0200
Richard Gowers <XYZ@ABC.COM>|2016-10-13 14:40:48 +0100
Oliver Beckstein <XYZ@ABC.COM>|2016-10-27 23:26:26 -0700
Wouter Boomsma <XYZ@ABC.COM>|2016-11-03 09:31:43 +0100
Max Linke <XYZ@ABC.COM>|2016-11-30 18:03:45 +0100
Max Linke <XYZ@ABC.COM>|2016-12-30 22:23:16 +0100
Jonathan Barnoud <XYZ@ABC.COM>|2017-01-12 22:14:39 +0100
richardjgowers <XYZ@ABC.COM>|2018-04-24 13:47:05 -0400
Tyler Reddy <XYZ@ABC.COM>|2018-05-02 15:32:20 -0600
zeman <XYZ@ABC.COM>|2018-06-11 11:28:45 +0200
Matthijs Tadema <XYZ@ABC.COM>|2019-07-16 14:56:55 +0200
Matthijs Tadema <XYZ@ABC.COM>|2019-07-17 14:12:10 +0200
Rocco Meli <XYZ@ABC.COM>|2020-02-15 08:39:12 +0000
shfrz <XYZ@ABC.COM>|2020-03-19 14:56:59 +0530
Irfan Alibay <XYZ@ABC.COM>|2020-06-15 08:13:38 +0100
Philip Loche <XYZ@ABC.COM>|2021-02-04 10:57:15 +0100
Paarth Thadani <XYZ@ABC.COM>|2021-04-07 20:06:14 +0530
Aya Alaa <XYZ@ABC.COM>|2022-03-23 17:06:12 +0200
Estefania Barreto-Ojeda <XYZ@ABC.COM>|2022-07-25 02:28:09 -0600
chrispfae <XYZ@ABC.COM>|2023-02-24 23:16:15 +0100

The repeated authors in this case used different email addresses between their commits. This list of authors can then be used to populate an AUTHORS.md file like the one in mdaencore.

Occasionally, authors names won’t be resolved properly, such as zeman, shfrz and chrispfae. At this point, you can try and get more information about these users by looking outside of just these files. Most of this information is probably already in the AUTHORS.md from the original repository, but depending on their GitHub username it may not be clear who they actually are. Using shfrz as an example, we can collect all of the commits made by this author using

git log --author=shfrz

which yields a commit history of 

commit 9a5467db55584eebbbe068bac0ba273f33713a6c
Author: shfrz <39633713+shfrz@users.noreply.github.com>
Date:   Mon Mar 30 04:14:36 2020 +0530

Updated mdamath (#2634)

FIxes issue #2632

## Changes made in this PR
- When lowerbound roundoff errors occur in `mdamath.angle` (i.e. the internal value of `x` becomes < -1.0), the returned angle is now `np.pi` rather than `-np.pi`.
- The `if`/`else` construct for roundoff errors has now been switched to an `np.clip()` call.

## Files changed
- MDAnalysis/lib/mdamath.py
- MDAnalysisTests/lib/test_util.py
- CHANGELOG

commit a78307f0d99b7310707ef015cab2908ce4770a4e
Author: shfrz <39633713+shfrz@users.noreply.github.com>
Date:   Thu Mar 19 14:56:59 2020 +0530

Remove details from ClusterMethods [Fixes #2575] (#2620)

Fixes issue #2575

## Work done in this PR:

Here the always-empty `details` dictionary which used to be returned by ClusterMethods has been removed.

## Files changed

- ClusterMethods.py (removed details).
- test_encore.py (removed details).
- cluster.py (removed details).
- AUTHORS and CHANGELOG updated accordingly.

commit bc2f1a54695b4fc9256a2b8d500fd65028e34110
Author: shfrz <39633713+shfrz@users.noreply.github.com>
Date:   Tue Mar 3 06:42:02 2020 +0530

Updated Readme (#2552)

Fixed typos in README.rst.

From this we can see that AUTHORS was updated by this user in commit a78307f0d99b7310707ef015cab2908ce4770a4e, which likely has the information we would actually include. The fastest way to show what changes were made is by using the command

git show a78307f0d99b7310707ef015cab2908ce4770a4e

which returns

commit a78307f0d99b7310707ef015cab2908ce4770a4e
Author: shfrz <39633713+shfrz@users.noreply.github.com>
Date:   Thu Mar 19 14:56:59 2020 +0530

Remove details from ClusterMethods [Fixes #2575] (#2620)

Fixes issue #2575

## Work done in this PR:

Here the always-empty `details` dictionary which used to be returned by ClusterMethods has been removed.

## Files changed

- ClusterMethods.py (removed details).
- test_encore.py (removed details).
- cluster.py (removed details).
- AUTHORS and CHANGELOG updated accordingly.

diff --git a/package/AUTHORS b/package/AUTHORS
index af90aaba3..a83cea075 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -138,6 +138,7 @@ Chronological list of authors
- Yuxuan Zhuang
- Abhishek Shandilya
- Morgan L. Nance
+  - Faraaz Shah

From the last line here, we were able to quickly confirm their identity, with particular emphasis on the way they chose to share it.