datalad-handbook/docs/basics/101-123-config2.rst

.. _config2:

More on DIY configurations
--------------------------

As the last section already suggest, within a Git repository,
``.git/config`` is not the only configuration file.
There are also ``.gitmodules`` and ``.gitattributes``, and in DataLad datasets
there also is a ``.datalad/config`` file.

All of these files store configurations, but have an important difference:
They are version controlled, and upon sharing a dataset these configurations
will be shared as well. An example for a shared configuration
is the one that the ``text2git`` configuration template applied:
In the shared copy of your dataset from :ref:`sibling`, text files are also saved with Git,
and not git-annex. The configuration responsible
for this behavior is in a ``.gitattributes`` file, and we'll start this
section by looking into it.

.. index:: ! configuration file; .gitattributes

``.gitattributes``
^^^^^^^^^^^^^^^^^^

This file lies right in the root of your superdataset:

.. runrecord:: _examples/DL-101-123-101
   :language: console
   :workdir: dl-101/DataLad-101

   $ cat .gitattributes

This looks neither spectacular nor pretty. Also, it does not follow the ``section-option-value``
organization of the ``.git/config`` file anymore. Instead, there are three lines,
and all of these seem to have something to do with the configuration of git-annex.
There even is one key word that you recognize: MD5E.
If you have read the :ref:`Find-out-more on object trees <objecttree>`
you will recognize it as a reference to the type of
key used by git-annex to identify and store file content in the object-tree.
The first row, ``* annex.backend=MD5E``, therefore translates to "The ``MD5E`` git-annex backend should be used for any file".
But what is the rest? We'll start with the last row:

.. code-block:: bash

   * annex.largefiles=((mimeencoding=binary)and(largerthan=0))

Uhhh, cryptic. The lecturer explains: "git-annex will *annex*, that is, *store in the object-tree*,
anything it considers to be a "large file". By default, anything
in your dataset would be a "large file", that means anything would be annexed.
However, in section :ref:`symlink` I already mentioned that exceptions to this
behavior can be defined based on

#. file size

#. and/or path/pattern, and thus for example file extensions,
   or names, or file types (e.g., text files, as with the
   ``text2git`` configuration template).

"In ``.gitattributes``, you can define what a large file and what is not
by simply telling git-annex by writing such rules."

What you can see in this ``.gitattributes`` file is a rule based on **file types**:
With ``(mimeencoding=binary))`` [#f1]_, the ``text2git`` configuration template
configured git-annex to regard all files of type "binary" as a large file.
Thanks to this little line, your text files are not annexed, but stored
directly in Git.

The patterns ``*`` and ``**`` are so-called "wildcards" you might recognize from used in :term:`globbing`.
In Git configuration files, an asterisk "*" matches anything except a slash.
The third row therefore
translates to "Do not annex anything that is a text file" for git-annex.
Two leading "``**``" followed by a slash matches
*recursively* in all directories.
Therefore, the second row instructs git-annex to regard nothing starting with ``.git`` as a "large file", including contents inside of ``.git`` directories.
This way, the ``.git`` repositories are protected from being annexed.
If you had a single file (``myfile.pdf``) you would not want annexed, specifying a rule such as:

.. code-block:: bash

   myfile.pdf annex.largefiles=nothing

will keep it stored in Git. To see an example of this, navigate into the longnow subdataset,
and view this dataset's ``.gitattributes`` file:

.. runrecord:: _examples/DL-101-123-102
   :language: console
   :workdir: dl-101/DataLad-101

   $ cat recordings/longnow/.gitattributes

The relevant part is ``README.md annex.largefiles=nothing``.
This instructs git-annex to specifically not annex ``README.md``.

Lastly, if you wanted to configure a rule based on **size**, you could add a row such as:

.. code-block:: bash

   ** annex.largefiles=(largerthan=20kb)

to store only files exceeding 20KB in size in git-annex [#f2]_.

As you may have noticed, unlike ``.git/config`` files,
there can be multiple ``.gitattributes`` files within a dataset. So far, you have seen one
in the root of the superdataset, and in the root of the ``longnow`` subdataset.
In principle, you can add one to every directory-level of your dataset.
For example, there is another ``.gitattributes`` file within the
``.datalad`` directory:

.. runrecord:: _examples/DL-101-123-103
   :language: console
   :workdir: dl-101/DataLad-101

   $ cat .datalad/.gitattributes

As with Git configuration files, more specific or lower-level configurations take precedence
over more general or higher-level configurations. Specifications in a subdirectory can
therefore overrule specifications made in the ``.gitattributes`` file of the parent
directory.

In summary, the ``.gitattributes`` files will give you the possibility to configure
what should be annexed and what should not be annexed up to individual file level.
This can be very handy, and allows you to tune your dataset to your custom needs.
For example, files you will often edit by hand could be stored in Git if they are
not too large to ease modifying them [#f3]_.
Once you know the basics of this type of configuration syntax, writing
your own rules is easy. For more tips on how configure git-annex's content
management in ``.gitattributes``, take a look at `the git-annex documentation <https://git-annex.branchable.com/tips/largefiles>`_.
Later however you will see preconfigured DataLad *procedures* such as ``text2git`` that
can apply useful configurations for you, just as ``text2git`` added the last line
in the root ``.gitattributes`` file.

.. index:: ! configuration file; .gitmodules

``.gitmodules``
^^^^^^^^^^^^^^^

On last configuration file that Git creates is the ``.gitmodules`` file.
There is one right in the root of your dataset:

.. runrecord:: _examples/DL-101-123-104
   :language: console
   :workdir: dl-101/DataLad-101

   $ cat .gitmodules

Based on these contents, you might have already guessed what this file
stores. The ``.gitmodules`` file is a configuration file that stores the mapping between
your own dataset and any subdatasets you have installed in it.
There will be an entry for each submodule (subdataset) in your dataset.
The name *submodule* is Git terminology, and describes a Git repository inside of
another Git repository, i.e., the super- and subdataset principles.
Upon sharing your dataset, the information about subdatasets and where to retrieve
them from is stored and shared with this file.
In addition to modifying it with the ``git config`` command or by hand, the ``datalad subdatasets`` command also has a ``--set-property NAME VALUE`` option that you can use to set subdataset properties.

Section :ref:`sharelocal1` already mentioned one additional configuration option in a footnote: The ``datalad-recursiveinstall`` key.
This key is defined on a per subdataset basis, and if set to "``skip``", the given subdataset will not be recursively installed unless it is explicitly specified as a path to :dlcmd:`get [-n/--no-data] -r`.
If you are a maintainer of a superdataset with monstrous amounts of subdatasets, you can set this option and share it together with the dataset to prevent an accidental, large recursive installation in particularly deeply nested subdatasets.
Below is a minimally functional example on how to apply the configuration and how it works:

Let's create a dataset hierarchy in a temporary location as an example to work with (note that we concatenate multiple commands into a single line using bash's "and" ``&&`` operator):

.. code-block:: console

    $ # create a superdataset with two subdatasets in a temporary directory
    $ datalad create superds && datalad -C superds create -d . subds1 && datalad -C superds create -d . subds2
    create(ok): /tmp/superds (dataset)
    add(ok): subds1 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subds1 (dataset)
    add(ok): subds2 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subds2 (dataset)

Next, we create subdatasets in the subdatasets:

.. code-block:: console

    $ # create two subdatasets in subds1
    $ datalad -C superds/subds1 create -d . subsubds1 && datalad -C superds/subds1 create -d . subsubds2
    add(ok): subsubds1 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subsubds1 (dataset)
    add(ok): subsubds2 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subsubds2 (dataset)

    $ # create two subdatasets in subds2
    $ datalad -C superds/subds2 create -d . subsubds1 && datalad -C superds/subds2 create -d . subsubds2
    add(ok): subsubds1 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subsubds1 (dataset)
    add(ok): subsubds2 (file)
    add(ok): .gitmodules (file)
    save(ok): . (dataset)
    create(ok): subsubds2 (dataset)

Here is the directory structure:

.. code-block:: console

    $ cd superds/ && tree
    .
    ├── subds1
    │   ├── subsubds1
    │   └── subsubds2
    └── subds2
        ├── subsubds1
        └── subsubds2

    $ # save in the superdataset
    datalad save -m "add a few sub and subsub datasets"
    add(ok): subds1 (file)
    add(ok): subds2 (file)
    save(ok): . (dataset)

Now, we can apply the ``datalad-recursiveinstall`` configuration to skip recursive installations for ``subds1``

.. code-block:: console

    $ git config -f .gitmodules --add submodule.subds1.datalad-recursiveinstall skip

    $ # save this configuration
    $ datalad save -m "prevent recursion into subds1, unless explicitly given as path"
    add(ok): .gitmodules (file)
    save(ok): . (dataset)


If the dataset is cloned, and someone runs a recursive :dlcmd:`get`, the subdatasets of ``subds1`` will not be installed, the subdatasets of ``subds2``, however, will be.

.. code-block:: console

    $ # clone the dataset somewhere else
    $ cd ../ && datalad clone superds clone_of_superds
    [INFO   ] Cloning superds into '/tmp/clone_of_superds'
    install(ok): /tmp/clone_of_superds (dataset)

    $ # recursively get all contents (without data)
    $ cd clone_of_superds && datalad get -n -r .
    get(ok): /tmp/clone_of_superds/subds2 (dataset)
    get(ok): /tmp/clone_of_superds/subds2/subsubds1 (dataset)
    get(ok): /tmp/clone_of_superds/subds2/subsubds2 (dataset)

    $ # only subsubds of subds2 are installed, not of subds1:
    $ tree
    .
    ├── subds1
    └── subds2
        ├── subsubds1
        └── subsubds2

    4 directories, 0 files

Nevertheless, if ``subds1`` is provided with an explicit path, its subdataset ``subsubds`` will be cloned, essentially overriding the configuration:

.. code-block:: console

    $  datalad get -n -r subds1 && tree
    install(ok): /tmp/clone_of_superds/subds1 (dataset) [Installed subdataset in order to get /tmp/clone_of_superds/subds1]
    .
    ├── subds1
    │   ├── subsubds1
    │   └── subsubds2
    └── subds2
        ├── subsubds1
        └── subsubds2

    6 directories, 0 files


.. index:: ! configuration file; .datalad/config

``.datalad/config``
^^^^^^^^^^^^^^^^^^^

DataLad adds a repository-specific configuration file as well.
It can be found in the ``.datalad`` directory, and just like ``.gitattributes``
and ``.gitmodules`` it is version controlled and is thus shared together with
the dataset. One can configure
`many options <https://docs.datalad.org/en/latest/generated/datalad.config.html>`_,
but currently, our ``.datalad/config`` file only stores a :term:`dataset ID`.
This ID serves to identify a dataset as a unit, across its entire history and flavors.
In a geeky way, this is your dataset's social security number: It will only exist
one time on this planet.

.. runrecord:: _examples/DL-101-123-105
   :language: console
   :workdir: dl-101/DataLad-101

   $ cat .datalad/config

Note, though, that local configurations within a Git configuration file
will take precedence over configurations that can be distributed with a dataset.
Otherwise, dataset updates with :dlcmd:`update` (or, for Git-users,
:gitcmd:`pull`) could suddenly and unintentionally alter local DataLad
behavior that was specifically configured.
Also, :term:`Git` and :term:`git-annex` will not query this file for configurations, so please store only sticky options that are specific to DataLad (i.e., under the ``datalad.*`` namespace) in it.

.. index::
   pair: modify configuration; with Git

Writing to configuration files other than ``.git/config``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

"Didn't you say that knowing the :gitcmd:`config` command is already
half of what I need to know?" you ask. "Now there are three other configuration
files, and I do not know with which command I can write into these files."

"Excellent question", you hear in return, "but in reality, you **do** know:
it's also the :gitcmd:`config` command. The only part of it you need to
adjust is the ``-f``, ``--file`` parameter. By default, the command writes to
a Git config file. But it can write to a different file if you specify it
appropriately. For example,

   ``git config --file=.gitmodules --replace-all submodule."name".url "new URL"``

will update your submodule's URL. Keep in mind though that you would need
to commit this change, as ``.gitmodules`` is version controlled".

Let's try this:

.. runrecord:: _examples/DL-101-123-106
   :workdir: dl-101/DataLad-101
   :language: console

   $ git config --file=.gitmodules --replace-all submodule."recordings/longnow".url "git@github.com:datalad-datasets/longnow-podcasts.git"

This command will replace the submodule's https URL with an SSH URL.
The latter is often used if someone has an *SSH key pair* and added the
public key to their GitHub account (you can read more about this
`here <https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories>`_).
We will revert this change shortly, but use it to show the difference between
a :gitcmd:`config` on a ``.git/config`` file and on a version controlled file:

.. runrecord:: _examples/DL-101-123-107
   :workdir: dl-101/DataLad-101
   :language: console

   $ datalad status

.. runrecord:: _examples/DL-101-123-108
   :workdir: dl-101/DataLad-101
   :language: console

   $ git diff

As these two commands show, the ``.gitmodules`` file is modified. The https URL
has been deleted (note the ``-``), and a SSH URL has been added. To keep these
changes, we would need to :dlcmd:`save` them. However, as we want to stay with
https URLs, we will just *checkout* this change -- using a Git tool to undo an
unstaged modification.

.. runrecord:: _examples/DL-101-123-109
   :workdir: dl-101/DataLad-101
   :language: console

   $ git checkout .gitmodules
   $ datalad status

Note, though, that the ``.gitattributes`` file cannot be modified with a :gitcmd:`config`
command. This is due to its different format that does not comply to the
``section.variable.value`` structure of all other configuration files. This file, therefore,
has to be edited by hand, with an editor of your choice.

.. index:: ! environment variable
.. _envvars:

Environment variables
^^^^^^^^^^^^^^^^^^^^^

An :term:`environment variable` is a variable set up in your shell
that affects the way the shell or certain software works -- for example,
the environment variables ``HOME``, ``PWD``, or ``PATH``.
Configuration options that determine the behavior of Git, git-annex, and
DataLad that could be defined in a configuration file can also be set (or overridden)
by the associated environment variables of these configuration options.
Many configuration items have associated environment variables.
If this environment variable is set, it takes precedence over options set in
configuration files, thus providing both an alternative way to define configurations
as well as an override mechanism. For example, the ``user.name``
configuration of Git can be overridden by its associated environment variable,
``GIT_AUTHOR_NAME``. Likewise, one can define the environment variable instead
of setting the ``user.name`` configuration in a configuration file.

.. index:: configuration item; datalad.log.level

Git, git-annex, and DataLad have more environment variables than anyone would want to
remember. `The ProGit book <https://git-scm.com/book/en/v2/Git-Internals-Environment-Variables>`__
has a good overview on Git's most useful available environment variables for a start.
All of DataLad's configuration options can be translated to their
associated environment variables. Any environment variable with a name that starts with ``DATALAD_``
will be available as the corresponding ``datalad.`` configuration variable,
replacing any ``__`` (two underscores) with a hyphen, then any ``_`` (single underscore)
with a dot, and finally converting all letters to lower case. The ``datalad.log.level``
configuration option thus is the environment variable ``DATALAD_LOG_LEVEL``.

.. index:: operating system concept; environment variable
.. find-out-more:: Some more general information on environment variables
   :name: fom-envvar

   Names of environment variables are often all-uppercase. While the ``$`` is not part of
   the name of the environment variable, it is necessary to *refer* to the environment
   variable: To reference the value of the environment variable ``HOME``, for example, you would
   need to use ``echo $HOME`` and not ``echo HOME``. However, environment variables are
   set without a leading ``$``. There are several ways to set an environment variable
   (note that there are no spaces before and after the ``=`` !), leading to different
   levels of availability of the variable:

   - ``THEANSWER=42 <command>`` makes the variable ``THEANSWER`` available for the process in ``<command>``.
     For example, ``DATALAD_LOG_LEVEL=debug datalad get <file>`` will execute the :dlcmd:`get`
     command (and only this one) with the log level set to "debug".
   - ``export THEANSWER=42`` makes the variable ``THEANSWER`` available for other processes in the
     same session, but it will not be available to other shells.
   - ``echo 'export THEANSWER=42' >> ~/.bashrc`` will write the variable definition in the
     ``.bashrc`` file and thus available to all future shells of the user (i.e., this will make
     the variable permanent for the user)

   To list all of the configured environment variables, type ``env`` into your terminal.


Summary
^^^^^^^

This has been an intense lecture, you have to admit. One definite
take-away from it has been that you now know a second reason why the hidden
``.git`` and ``.datalad`` directory contents and also the contents of ``.gitmodules`` and
``.gitattributes`` should not be carelessly tampered with -- they contain all of
the repository's configurations.

But you now also know how to modify these configurations with enough
care and background knowledge such that nothing should go wrong once you
want to work with and change them. You can use the :gitcmd:`config` command
for Git configuration files on different scopes, and even the ``.gitmodules`` or ``datalad/config``
files. Of course you do not yet know all of the available configuration options. However,
you already know some core Git configurations such as name, email, and editor. Even more
important, you know how to configure git-annex's content management based on ``largefile``
rules, and you understand the  variables within ``.gitmodules`` or the sections
in ``.git/config``. Slowly, you realize with pride,
you are more and more becoming a DataLad power-user.

Write a note about configurations in datasets into ``notes.txt``.

.. runrecord:: _examples/DL-101-123-110
   :workdir: dl-101/DataLad-101
   :language: console

   $ cat << EOT >> notes.txt
   Configurations for datasets exist on different levels (systemwide,
   global, and local), and in different types of files (not version
   controlled (git)config files, or version controlled .datalad/config,
   .gitattributes, or gitmodules files), or environment variables.
   With the exception of .gitattributes, all configuration files share a
   common structure, and can be modified with the git config command, but
   also with an editor by hand.

   Depending on whether a configuration file is version controlled or
   not, the configurations will be shared together with the dataset.
   More specific configurations and not-shared configurations will always
   take precedence over more global or hared configurations, and
   environment variables take precedence over configurations in files.

   The "git config --list --show-origin" command is a useful tool to give
   an overview over existing configurations. Particularly important may
   be the .gitattributes file, in which one can set rules for git-annex
   about which files should be version-controlled with Git instead of
   being annexed.

   EOT

.. runrecord:: _examples/DL-101-123-111
   :workdir: dl-101/DataLad-101
   :language: console

   $ datalad save -m "add note on configurations and git config"

.. only:: adminmode

   Add a tag at the section end.

     .. runrecord:: _examples/DL-101-123-112
        :language: console
        :workdir: dl-101/DataLad-101

        $ git branch sct_more_on_DYI_configurations


.. rubric:: Footnotes

.. [#f1] When opening any file on a UNIX system, the file does not need to have a file
         extension (such as ``.txt``, ``.pdf``, ``.jpg``) for the operating system to know
         how to open or use this file (in contrast to Windows, which does not know how to
         open a file without an extension). To do this, Unix systems rely on a file's
         MIME type -- an information about a file's content. A ``.txt`` file, for example,
         has MIME type ``text/plain`` as does a bash script (``.sh``), a Python
         script has MIME type ``text/x-python``, a ``.jpg`` file is ``image/jpg``, and
         a ``.pdf`` file has MIME type ``application/pdf``. You can find out the MIME type
         of a file by running:

         .. code-block:: console

            $ file --mime-type path/to/file

.. [#f2] Specifying annex.largefiles in your .gitattributes file will make the configuration
         "portable" -- shared copies of your dataset will retain these configurations.
         You could however also set largefiles rules in your ``.git/config`` file. Rules
         specified in there take precedence over rules in ``.gitattributes``. You can set
         them using the :gitcmd:`config` command:

         .. code-block:: console

            $ git config annex.largefiles 'largerthan=100kb and not (include=*.c or include=*.h)'

         The above command annexes files larger than 100KB, and will never annex files with a
         ``.c`` or ``.h`` extension.

.. [#f3] Should you ever need to, this file is also where one would change the git-annex
         backend in order to store new files with a new backend. Switching the backend of
         *all* files (new as well as existing ones) requires the :gitannexcmd:`migrate`
         command
         (see `the documentation <https://git-annex.branchable.com/git-annex-migrate>`_ for
         more information on this command).