[Bioc-devel] Bioconductor package tidybulk

Thu, Jun 4, 2020 6:10 AM
The master branch is the development branch (Bioc 3.12) .  The version  of  x.y.z   The y is always odd in devel  and even in release.  This is the very first section on the page you referenced.  http://bioconductor.org/developers/how-to/version-numbering/

We do not jump full y versions in the middle of a release.

The current RELEASE_3_11  version is  1.0.0  =  the appropriate version bump on this branch is  1.0.1

The current master version is 1.1.0  = the appropriate version bump on this branch is  1.1.1


If you are unfamiliar with git and github branches I encourage you to read more documentation about it.  There are many helpful tutorials.
You can have as many branches on your local github repository as you like. We recommend creating unique branches for bioconductor releases to mimic our branch structure.   In general, and to make it less confusing we would highly recommend using the master branch as the development branch and link that to the master (development version) of Bioconductor.   This would be consistent and then you can following the guides and tutorials listed on the Bioconductor help pages

http://bioconductor.org/developers/how-to/git/


The release branch is designed to always be a stable branch and should only be updated for bug corrections.
The master branch should be for development and new features.



We will assume you ran the following to set up your remotes as recommended:
git remote add upstream git at git.bioconductor.org:packages/tidybulk.git


if you do
git remote -v

you should see something similar:
origin  <link to your github> (fetch)
origin  <link to your github> (push)
upstream git at git.bioconductor.org:packages/tidybulk.git (fetch)
upstream git at git.bioconductor.org:packages/tidybulk.git (push)


To create and work on a release branch:

git fetch --all
# this gets all branches from all remotes


# The following would only need to be run once EVER!
git checkout -b RELEASE_3_11  upstream/RELEASE_3_11

# this says checkout  a branch (-b)  call it RELEASE_3_11  and have it copied/link to the code at  upstream/RELEASE_3_11 (the #bioconductor upstream remote branch of RELEASE_3_11)

After it is created, to switch to this branch on a daily basis you can simply:
git checkout RELEASE_3_11



git pull upstream RELEASE_3_11
# pulls changes from the upstream RELEASE_3_11 remote


# The following would only need to be run once EVER!   It creates a branch on your local github called RELEASE_3_11
git push -u origin RELEASE_3_11



Make your code changes to fix bugs! Make sure to do a valid version bump by bumping the  z  of version  x.y.z

git add <files>
git commit    # give an informative commit message


git push upstream RELEASE_3_11
# This should push to the Bioconductor git repository

git push origin RELEASE_3_11
# This should push to your github local git repository


git checkout master
# Switch back to your master branch for development and code changes


If you are ever confused on what branch you are on you can do
git branch


To work on the devel master branch the commands would be similar to above but using master

git pull upstream master  # pulls from git bioconductor
git pull origin master        # pull from your individual github

# make changes, commit changes

git push upstream master  # pushes to git Bioconductor
git push origin master   # push to your github


Hopefully that helped clarified and will get you started.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
[Bioc-devel] Bioconductor package tidybulk

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