Github is an ideal place to work together with colleagues and also external parties. In the new organization https://github.com/Deltares-research, there are a few ways to work with outside collaborators:

1. Use PULL REQUESTS. Allow your repository to accept pull requests. This way collaborators do not require to be added (and managed) as 'Outside collaborators'. This works well for PUBLIC repositories.
2. Invite an outside collaborator to your organization and then assign them to your repository. For PUBLIC repositories no license is claimed for PRIVATE repositories 1 license is claimed. No additional costs for adding the same collaborator to multiple repositories.

I want to use my own Github account that I've used thus far (linked to my private e-mail address). Can I do that and if yes, how?

It is possible to use your existing GITHUB account. However if you work for Deltares, you will have to assign your Deltares email to your GITHUB account. All Deltares employees will be invited using their Deltares email address.

When you receive an invitation email:

When you are invited to join the Deltares GITHUB Enterprise, an invitation email will be sent to your Deltares email address. By following the link in the invitation you will be redirected to GITHUB where you are required to login to MyDeltares:

Use the Deltares Login button at the bottom of the login form. If you do not yet have a MyDeltares account, one will automatically be created for you. After login your MyDeltares account will be linked to your Github account.

Login directly to the Deltares GITHUB Enterprise:

When you browse to the Deltares Enterprise in GITHUB you will see all public repositories. It is however not possible to join the enterprise from here using your existing unlinked GITHUB account. You need to be invited by one of the repository owners first.

Problem

I want to request a new Github repository for my project or software product, but I do not know which of the two Deltares organizations I must choose: Deltares or Deltares-research

Solution

You do not need to choose anything, this will be done for you based on the information provided during the registration process.

What is the difference between the two organizations?

Deltares organization: This organization is meant to house all repositories that are linked to a Product Management Team (PMT) and contain production ripe software.

Deltares-research: All repositories that do not fit into the Deltares organization.

Problem

After your repository is moved from https://github.com/Deltares to the new organization https://github.com/Deltares-research, it is possible that you are required to re-authorize your account in one or more of your local applications, such as VS Code, TortoiseGIT or on the GIT command line.

Solution

Follow the following steps to refresh you authorization token:

1. Open the Credential Manager in Widows. ( type 'Credential Manager')
2. In Credential Manager select 'Windows Credentials'
   
   
   
3. Lookup the credentials for git:https://github.com and remove this.
4. Re-initialise the cred manager in git bash: git config --global credential.helper manager-core
5. Re-run git pull and follow the pop-up instructions to authenticate in a browser (which happened automatically for me with SSO).

After your repository is moved from https://github.com/Deltares to the new organization https://github.com/Deltares-research, the list of collaborators has been cleared. Each repository is assigned one administrator who is tasked with inviting new collaborators.

Inviting new collaborator can be done by the Administrator using the 'Add people' button.

For bigger repositories it is advised to user teams instead of adding individual users. At present it is not possible for administrators to create a Team. In such cases the administrator should send a request to the Github support group: github-support@deltares.nl

No there is not.

When you have questions regarding the new GITHUB environment you can post them to the GITHUB support team. We can then try to connect you to people who already have experience with GITHUB. Otherwise we suggest you contact your department head for funding.

There is no fixed definition of 'production-ripe' software. It is up to the Product Management Teams (PMT) to decide if they wish to designate certain repositories / products as production ripe or as research. 

All repositories under the Deltares organisations should be linked to one of the PMT;s. If unsure about the status of your repository please contact the PMT and discuss with them where your repository fits best.

In the current Deltares organization, co-pilot has been enabled. There are 24 licenses available, all of which are currently taken. At present co-pilot is not enabled in the Deltares-research organization. This will change once the Deltares organization has been added to the Deltares enterprise.

How we plan to use co-pilot in the future and how we plan to manage the licenses has not yet been worked out. For more information please contact: github-owners@deltares.nl .

Apparently some users can no longer see their repositories in Zenodo. Even when their repositories have not been moved from the Deltares organization. Why this is the case is still unclear however the resolution is that one of the organization owners logs into Zenodo using ones Github account and activates the required repositories.

Deltares does not support the use of GITHUB's own Large File Storage (LFS) environment. However it is possible to connect your repository to the Deltares S3 bucket (MinIO) using GIT-LFS.

Please read the information on the following page: How to connect your GITHUB repository to a LFS?:

If you wish to connect your repository to the Data Version Control (DVC) tool, then please read the information on the following page: How to connect your GITHUB repository to a LFS?:

Setup your GITHUB repository:

First you must setup your GITHUB repository by cloning this to your computer. If you do not yet have a GITHUB repository, you can request one 'Request a repository' page.

Once your GITHUB repository is in place and up-to-date, continue with the GIT-LFS instructions.

Setup GIT-LFS:

Go to the GIT-LFS website and follow the instructions on how to download and install GIT-LFS. A good starting point is the 'Getting Started' section on the home page.

GIT-LFS configuration files:

.gitattributes:    Stored in the root folder of your repository. This file contains patterns of all files that GIT-LFS should track and manage as 'large files'.

*.bin filter=lfs diff=lfs merge=lfs -text

Useful examples for .gitattributes can be found here

.lfsconfig:   Stored in the root folder of your repository. This file is necessary to point GIT-LFS to the MinIO server of Deltares instead of the default GITHUB LFS.

[lfs]
url = "http://localhost:8080"

Setup GIT-LFS API Proxy

A Git LFS API proxy is needed to seamlessly integrate GIT-LFS with the S3-based MinIO API. The proxy serves as a bridge between GIT-LFS and the S3 storage protocol, and will translate Git LFS API calls into S3 API calls, ensuring that files tracked by Git LFS are correctly stored on S3.
( See N:\Deltabox\Publications\2023\ict\git-lfs-minio\ for Windows and Linux executables with example config.json )

config.json:    Stored outside of the root folder of your repository. This file contains the MinIO end-point server of Deltares

{
    "serverListenAddr": ":8080",
    "minioHost": "s3.deltares.nl",
    "minioAccessKey": "gitlfs",
    "minioSecretKey": "UPONREQUEST",
    "minioBucket": "gitlfs",
    "minioURLExpires": 3600
}

Setup credentials:

(THIS NEEDS TO BE UPDATED: The GIT-LFS credentials are separate from GITHUB ) In order for GIT-LFS to login to the MinIO API, it is required to provide credentials. This can be configured in the Windows Credential Manager on your (Windows) computer.

Open the Credential Manager tool from the Control Panel and the credentials for the MinIO API as a new Generic Credentials entry.

Setup your GITHUB repository:

First you must setup your GITHUB repository by cloning this to your computer. If you do not yet have a GITHUB repository, you can request one 'Request a repository' page.

Once your GITHUB repository is in place and up-to-date, continue with the DVC instructions.

Setup DVC:

Go to the DVC website and follow the instructions on how to download and install DVC. A good starting point is the 'Get Started' page.

DVC configuration files:

.dvcignore:    Stored in the root folder of your DVC project. This file contains patterns of all files that DVC should ignore.

# Add patterns of files dvc should ignore, which could improve
# the performance. Learn more at
# https://dvc.org/doc/user-guide/dvcignore

# Ignore secrets file
.dvc/config.local

.dvc/.gitignore:    Stored in the .dvc folder. This file is similar to the .dvcignore file however this file contains patterns of all files that GIT should ignore.

/config.local
/tmp
/cache

.dvc/config:    Stored in the .dvc folder. Contains all DVC configuration that can be shared and can be uploaded into your repository.

 [core]
    remote = miniostorage
    autostage = true
['remote "miniostorage"']
    url = s3://<path to your bucket>
    endpointurl = https://s3.avi.deltares.nl
    ssl_verify = false

.dvc/config.local:    Stored in the .dvc folder. Contains all DVC configuration that cannot be shared nor uploaded into your repository

['remote "miniostorage"']
    access_key_id = 
    secret_access_key = 

How you will setup your scripting environment will strongly depend on the codding language of the source code in your GITHUB repository. But in all cases you can take advantage of the REWIND functionality of MinIO. This functionality allows you to restore your data folder of files to a given point in time. 

For Python an example can be found here: https://github.com/robin-deltares/minio-py-rewind/blob/main/minio_rewind.py

from minio import Minio
import minio_rewind

# For access
myMinioServer = 'my.minio.server'
myAccessKey   = 'my_access_key'
mySecretKey   = 'my_secret_key'

# The path that will be recursively downloaded
myBucketName = 'my_bucket_name'
myPathName   = 'my_path_name'
myRewind     = '2023.05.10T16:00' # Notation that mc uses

# Minio client connection
myClient = Minio(myMinioServer,
                 access_key=myAccessKey,
                 secret_key=mySecretKey)

# Prepare the rewind-settings
rewinder = minio_rewind.Rewinder(myClient,myRewind)

# Download the objects
rewinder.download(myBucketName,myPathName)

GIT-LFS

git-lfs is intended to be transparent to git, therefore it requires a customized server. Its learning process is short and fast. Some configuration commands, and bang! it is running, storing large files independently of the git repository. That's its only function, and it does it fine. Having an additional server is not a drawback, but instead a requirement for such transparency. Once configured, files are just handled by git, by means of git hooks (endpoints that are activated after git operations).

Limitations of GIT-LFS can are documented here.

DVC

dvc is intended to provide independent management of large files for the final user. What dvc basically does is this: it just makes git ignore the files that you wish to control (adding them to .gitignore) and instead, it generates an additional file with the same name and the extension .dvc. So, in order to push a commit with its corresponding files, the user is required to manually "add" (equivalent to git commit, not to git add; there's no equivalent for the git stage in dvc) and "push" to both systems. This is not a drawback, but a necessary level of control. In exchange, the remote large-files-holder is just any remote filesystem, accessible directly by its path, via ssh or via multiple drivers (google drive, amazon, etc.). Anyway, hooks are also available for dvc, which would simplify the use of large files, if having additional files is not annoying to one, and saving files to the remote would require additional operations, remember that they are .gitignored! So, if you modify a file stored in dvc, such change will not be noticed by git status, and you might lose such change, except if you make the additional check with dvc.

Some comparisons with related technologies can be found here.

Custom scripts

scripting is the most flexible way to go. It allows you to access all MinIO's API functionality in the language of your preference. To help you get started MinIO offers the user a variety of SDKs. Scripting does imply that you as developer have enough coding skills  are also the maintainer. However with enough real-word examples this option should not be too difficult.

Note to developers: Please provide your examples to github-support@deltares.nl so we can incorporate them into this manual.