Grappling with git...

Trying to control git in the command line. It's difficult to keep it all straight in my mind. 

I think part of the mix up is the Vi editor. 

Press Esc

Type :wq

For write quit. 

Some information here:

https://stackoverflow.com/questions/33504984/adding-a-git-commit-message-using-vi-on-os-x

https://medium.com/@steveamaza/how-to-write-a-proper-git-commit-message-e028865e5791

https://chris.beams.io/posts/git-commit/

git commit -m"Fix typo in introduction to user guide"

Checking drawProteins package...

 So I want to be sure that drawProteins will be updated with the adjusted function that creates a chain when one is missing. 

I've opened up R-Studio. 

It says RELEASE_3_11. 

I think this is the correct release for the next Bioconductor release - cut off time tomorrow and release date?

Does it add a chain when one is missing?

This should be done by the feature_to_dataframe() function. 

OK: so   # Add 1 chain if missing 

is missing. 

But, # Add 1 chain if missing

is on (REMOTE: UPSTREAM) master. 

Will this be used to update the package?

I think so but how do I know this?

Check Build - Looks good.

Build talk about version number 1.9.0 and talks about Last Changed Date so that is 9 Oct 2020. 

Good news. 

Key details on how to develop are here: https://bioconductor.org/developers/how-to/git/push-to-github-bioc/

OK, so 

Released version of drawProteins is 1.8.0 and is here: http://bioconductor.org/packages/release/bioc/html/drawProteins.html

Development version of drawProteins is 1.9.0 and is here:http://bioconductor.org/packages/3.12/bioc/html/drawProteins.html

To check, I can open another R-Studio Project and download development version:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("drawProteins")

This is quite annoying. I think I have version 1.9.0 downloaded. That's what the session info says but it is NOT adding the chain making plotting impossible. 

So something is not quite correct. 

But WHAT???

I'm in a confusion mess. 

Session info says: drawProteins_1.9.0

BUT 

drawProteins::extract_feat_acc(feat1[[1]])

gives an object with only one element and no chain. 

Because the drawProteins::extract_feat_acc function doesn't have the if statement that adds the chain. 

OK. What to do?

# Uniprot entry without chains: 

# A0A024QZX5

to check!!

It is line 122 in master branch...

OH, wow... 

I did some merging on Github. 

Everything says it is synced but Upstream RELEASE_3_11 still says Version: 1.8.0

Still confused:

Check master through R-Studio - version 1.9.1

Check RELEASE_3_11 - version 1.8.0

Version 1.8.0 does NOT have the add chain when missing code. 

Question sent to Bioconductor 

RESPONSE:

The version scheme is outlined at https://bioconductor.org/developers/how-to/version-numbering/

Within a 'release', the version x.y.z is always bumped in the z field. You are at 1.8.0 in release, so the version bump is to 1.8.1, 1.8.2, ...

Meanwhile, in devel you were at 1.9.0, so the version bumps are 1.9.1, 1.9.2, ...

The solution to your current dilemma is to bump the version of the RELEASE_3_11 branch to 1.8.1. But beware that this will be your last shot at committing to the RELEASE_3_11 branch, because commits to the 3_11 branch will stop tomorrow -- I'd only bump the release version if this were an important bug fix, and you were sure you'd got it right.

'devel' will become 'release' on October 27 (see https://bioconductor.org/developers/release-schedule/) when the BIOCONUCTOR team will create a new 'RELEASE_3_12' branch from your current 'devel' branch. The 3_12 release will have version 1.10.0. the 'devel' branch will also be incremented, to 1.11.0. Subsequently, your version bumps are 1.10.1, 1.10.2, ... in RELEASE_3_12, and 1.11.1, 1.11.2, ... in devel.

--- END ---

So I bumped RELEASE_3_11 to 1.8.1.

It should work!!!

Git resources...

This page is important as I learned about accessing remote branches: http://gitready.com/intermediate/2009/02/13/list-remote-branches.html

Also lots about git on Bioconductor:

Pulling and pushing changes: http://bioconductor.org/developers/how-to/git/