[Bioc-devel] lessons learned: negative experiences with git log

[Nitesh Turaga]

Hi Kasper,

Is this what you are looking for? (My understanding of your question is you want to see which files changed as part of a ‘merge’ commit)

The command below lists 5 commits 

	-n : number of commits 

	-m : This option makes diff output for merge commits to be shown in the default format. (More details here: https://git-scm.com/docs/git-show)

	-—name-only: will display only the names of the files


Rgraphviz ❯❯❯ git log -m --name-only -n 5                                                                                                                   

commit 50a89903830505a1a686570825304f7a30e194f1 (HEAD -> master, origin/master, origin/HEAD)
Author: kasperdanielhansen <kasperdanielhansen using gmail.com>
Date:   Thu Aug 12 21:19:44 2021 -0400

    fixing seg fault

DESCRIPTION
src/doLayout.c

commit 43207afdc87afc04bbc8b2a1acbbdb3b531d25b3
Author: kasperdanielhansen <kasperdanielhansen using gmail.com>
Date:   Thu Aug 12 21:18:02 2021 -0400

    removing testing vignette

vignettes/testing.Rmd

commit 955e30b3ae316265b4f5f130ab6f12c33081da54
Author: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
Date:   Wed Aug 11 08:52:11 2021 -0400

    Fixing length condition error

DESCRIPTION
man/agopenSimple.Rd

commit 15204d879d974de8d40b0342b2f853c88f4bf9a3 (from 7c1433d9f6025e3195f27ccc18a1439398221ffc)
Merge: 7c1433d b01ad95
Author: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
Date:   Wed Aug 11 08:26:09 2021 -0400

    Merge remote-tracking branch 'upstream/master'

DESCRIPTION

commit 15204d879d974de8d40b0342b2f853c88f4bf9a3 (from b01ad9552737978b3b7db6815323a078ceafe041)
Merge: 7c1433d b01ad95
Author: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
Date:   Wed Aug 11 08:26:09 2021 -0400

    Merge remote-tracking branch 'upstream/master'

R/plotGraph.R
src/doLayout.c
vignettes/testing.Rmd


As you can see above, the files which changed are listed. You can also see “only” merge commits and the files that change with this command,

	git log --merges -m --name-only -n 5


Hope this helps. 


Best regards,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Aug 13, 2021, at 9:34 AM, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
> 
> Here are my experiences as a novice in git.
> 
> Yesterday I was working on fixing a condition length error in Rgraphviz, a
> package which has not been touched in years. After I fixed this, I got a
> segmentation fault in examples / tests / vignettes; all over the place.
> 
> This could have been related to a small git snafu I had on my laptop
> because I had not synchronized  laptop / Github / bioc git for a _long_
> time (read: years).
> 
> No matter, I thought, git history will easily reveal this, and since there
> has been no changes to the package in years, it should be really easy to
> just list which file had changed. However, running
>  git log --name-status
> I got this
> 
> ==== START git log ======
> commit 955e30b3ae316265b4f5f130ab6f12c33081da54
> Author: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
> Date:   Wed Aug 11 08:52:11 2021 -0400
> 
>    Fixing length condition error
> 
> :100644 100644 25e24de 3aee690 M        DESCRIPTION
> :100644 100644 f8e077f b73b052 M        man/agopenSimple.Rd
> 
> commit 15204d879d974de8d40b0342b2f853c88f4bf9a3
> Merge: 7c1433d b01ad95
> Author: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
> Date:   Wed Aug 11 08:26:09 2021 -0400
> 
>    Merge remote-tracking branch 'upstream/master'
> 
> commit b01ad9552737978b3b7db6815323a078ceafe041
> Author: Nitesh Turaga <nitesh.turaga using gmail.com>
> Date:   Wed May 19 15:33:11 2021 +0000
> 
>    bump x.y.z version to odd y following creation of RELEASE_3_13 branch
> 
> :100644 100644 78243eb 25e24de M        DESCRIPTION
> ====== END git log ======
> 
> This suggests that no files apart from DESCRIPTION and a man page were
> touched recently (it looks the same if I go back longer). Look at the
> second message with "Merge remote-tracking". No files are listed!
> 
> It turns out that files were indeed touched as part of the "Merge
> remote-tracking ..." commit. I can see this by a
>  git diff b01ad9552737978b3b7db6815323a078ceafe041
> but in reality I had given up on git and did a standard recursive diff on
> the stable release tarball and my codebase.
> 
> I have not been able to figure out what options I need to give git log to
> display which files changed as part of that commit, and I find that
> perplexing and -- frankly -- pretty worrying.
> 
> Anyway, just some scary lessons on git log and merge.
> 
> Best
> 
> -- 
> Best,
> Kasper
> 
> 	[[alternative HTML version deleted]]
> 
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