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mih committed Nov 15, 2023
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4 changes: 3 additions & 1 deletion docs/basics/101-138-sharethirdparty.rst
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Expand Up @@ -76,11 +76,13 @@ or Gitea_.
But while anything that is managed by Git is accessible in repository hosting services, they usually don't support storing annexed data [#f2]_.

When you want to publish a dataset to a Git repository hosting service to allow others to easily find and clone it, but you also want others to be able to retrieve annexed files in this dataset via :dlcmd:`get`, annexed contents need to be pushed to additional storage hosting services.
The hosting services can be all kinds of private, institutional, or commercial services, and their location will be registered in the dataset under the concept of a :term:`special remote`.
The hosting services can be all kinds of private, institutional, or commercial services, and their location will be registered in the dataset under the concept of a :term:`special remote`. Check the :find-out-more:`on this <fom-special-remote>` for some background on this git-annex concept.

.. index::
pair: special remote; git-annex concept
.. find-out-more:: What is a special remote
:name: fom-special-remote
:float: tb

A special-remote is an extension to Git’s concept of remotes, and can
enable :term:`git-annex` to transfer data from and possibly to places that are not Git
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7 changes: 5 additions & 2 deletions docs/basics/101-139-hostingservices.rst
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Expand Up @@ -53,6 +53,7 @@ How to add a sibling on a Git repository hosting site: The manual way
.. _sshkey:
.. find-out-more:: What is an SSH key and how can I create one?
:name: fom-sshkey
:float: tb

An SSH key is an access credential in the :term:`SSH` protocol that can be used
to login from one system to remote servers and services, such as from your private
Expand Down Expand Up @@ -126,10 +127,12 @@ What is a token?

Personal access tokens are an alternative to authenticating via your password, and take the form of a long character string, associated with a human-readable name or description.
If you are prompted for ``username`` and ``password`` in the command line, you would enter your token in place of the ``password`` [#f3]_.
Note that you do not have to type your token at every authentication -- your token will be stored on your system the first time you have used it and automatically reused whenever relevant.
Note that you do not have to type your token at every authentication -- your token will be stored on your system the first time you have used it and automatically reused whenever relevant. Check the :find-out-more:`on credential storage <fom-credential-storage>` to learn how this is done.

.. index:: credential; storage
.. find-out-more:: How does the authentication storage work?
.. find-out-more:: Where are credentials stored?
:name: fom-credential-storage
:float: tb

Passwords, user names, tokens, or any other login information is stored in
your system's (encrypted) `keyring <https://en.wikipedia.org/wiki/GNOME_Keyring>`_.
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5 changes: 4 additions & 1 deletion docs/basics/101-139-privacy.rst
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Expand Up @@ -22,12 +22,15 @@ Having the file annexed allows you to specifically not share its contents, even
However, it is highly important to realize that while annexed file's *contents* are not saved into Git, annex file's *names* are.
If private information such as a medical patients non-anonymized ID or other potentially identifying information becomes a part of the file name, this information is exposed in the Git history of the dataset.
Keep in mind that this applies even if you renamed the file.
Check the :find-out-more:`on removing information committed to Git <fom-uncommit>` in case sensitive would ever leak into one of your datasets.

.. index::
pair: remove sensitive information; with Git
.. find-out-more:: Help! I accidentally saved sensitive information to Git!
:name: fom-uncommit
:float: tb

The only lasting way to remove contents from the dataset history completely is to substantially rewrite the dataset's history via tools such as ``git-filter-repo`` or ``git filter-branch``, two very dangerous and potentially destructive operations.
The only lasting way to remove contents from the dataset history completely is to substantially rewrite the dataset's history via tools such as ``git-filter-repo`` or ``git filter-branch``, two very dangerous and potentially destructive operations.


Strategy 2: Restrict access via third party service or file system permissions
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9 changes: 6 additions & 3 deletions docs/basics/101-141-push.rst
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Expand Up @@ -28,6 +28,7 @@ In order to publish a dataset, the dataset needs to have a sibling to push to.
This, for instance, can be a :term:`GitHub`, :term:`GitLab`, or :term:`GIN`
repository, but it can also be a Remote Indexed Archive (RIA) store for backup
or storage of datasets [#f1]_, or a regular clone.
See the :find-out-more:`on configuring siblings <fom-all-siblings>` for an overview.

.. index::
pair: create-sibling-github; DataLad command
Expand All @@ -38,6 +39,8 @@ or storage of datasets [#f1]_, or a regular clone.
pair: RIA; dataset hosting
pair: create sibling; with DataLad
.. find-out-more:: All of the ways to configure siblings
:name: fom-all-siblings
:float: tb

- Add an existing repository as a sibling with the :dlcmd:`siblings`
command. Here are common examples:
Expand Down Expand Up @@ -74,7 +77,7 @@ from the command line:
If you have more than one :term:`branch` in your dataset, note that a
:dlcmd:`push` command will by default update only the current branch.
If updating multiple branches is relevant for your workflow, please check out
the :ref:`find-out-more about this <fom-push-branch>`.
the :find-out-more:`about this <fom-push-branch>`.

By default, :dlcmd:`push` will make the last saved state of the dataset
available. Consequently, if the sibling is in the same state as the dataset,
Expand Down Expand Up @@ -126,9 +129,9 @@ targets are configured throughout the dataset hierarchy.

.. index::
pair: configure which branches to push; with Git
.. find-out-more:: Pushing more than the current branch
.. find-out-more:: Push more than the current branch
:name: fom-push-branch
:float:
:float: tb

If you have more than one :term:`branch` in your
dataset, a :dlcmd:`push --to <sibling>` will by default only push
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