GitHub: pushing local changes to the remote version (updated)

After fumbling around for a while, I finally got a grip on how to use GitHub.
If you're as slow a learner as me, it might take you a couple of days to really get used to it, but it's also a skill worthwhile to learn.

For now, I'm just using github for remote access, and version control for my scripts.

I assume, you already have a github project initiated.

The best in-depth explanation I could find:
https://www.atlassian.com/git/tutorials/comparing-workflows/centralized-workflow

 

Task:

Editing some file of the program locally, then merge it with the remote version.

Get a local copy of your own rep

git clone https://github.com/davidries84/bwa_parallel_arrays.git

Edit some files.

If it is your own rep in which you changed files and you just want to update the master:

git commit -am "change time tracking"

-a means all files you changed will be pushed to the remote repository
-m is used to state the changes you did in a short message

By 'pushing' the changes up to the remote version of your code, you update that remote version:

git push -u origin master

If you added some files, instead of only editing already existing files:

git add .
git commit -am "adding test files"git push -u origin master

Editing the 'master' should only be done for failsave changes (like comments). The master should always be fully functional code. So for implementing new features or bugfixes, you should use 'branches', which get merged into the master, when the new code is ready and finished.


In your local directory, create a new branch for your intended changes.
By creating a new branch, you automatically change (checkout) into that branch.

git checkout -b update_Readme

Do your changes, i.e.

gedit README.md

"commit" your changes:

 from the man "git commit" pages:

Stores the current contents of the index in a new commit along with a log message from the user describing the changes.

The content to be added can be specified in several ways:
...
4. by using the -a switch with the commit command to automatically
"add" changes from all known files (i.e. all files that are already
listed in the index) and to automatically "rm" files in the index
that have been removed from the working tree, and then perform the
actual commit;

So we commit everything (-a) and add a message describing the change (-m)

git commit -am "added some text to readme"

To update the repository, we have to "push" the local branch "update_Readme", to the origin.
git push " Updates remote refs using local refs, while sending objects necessary to complete the given refs."

 git push origin update_Readme 

Afterwards, we can checkout back to the master.

git checkout master 

After accepting your own changes (using the website), it makes sense to sync your local master with your remote master, thus bringing it up to date.
git-fetch - Download objects and refs from another repository

git fetch upstream

git-rebase - Forward-port local commits to the updated upstream head

git rebase upstream/master