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In Basics, remove 'below' when refering to things that can float away
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docs/basics/101-101-create.rst

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@@ -43,8 +43,7 @@ Note the command structure of :dlcmd:`create` (optional bits are enclosed in ``[
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datalad create --description "course on DataLad-101 on my private laptop" -c text2git DataLad-101
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If you want, use the above command instead of the :dlcmd:`create` command below
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to provide a description. Its use will not be immediately clear, the chapter
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If you want, use the above command instead to provide a description. Its use will not be immediately clear, the chapter
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:ref:`chapter_collaboration` will show you where this description
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ends up and how it may be useful.
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docs/basics/101-103-modify.rst

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@@ -18,7 +18,7 @@ Let's write a short summary of how to create a DataLad dataset from scratch:
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This is meant to be a note you would take in an educational course.
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You can take this note and write it to a file with an editor of your choice.
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The code below, however, contains this note within the start and end part of a
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The code snippet, however, contains this note within the start and end part of a
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`heredoc <https://en.wikipedia.org/wiki/Here_document>`_.
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You can also copy the full code snippet, starting
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from ``cat << EOT > notes.txt``, including the ``EOT`` in the last line, in your
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.. index:: here-document, heredoc
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.. find-out-more:: How does a heredoc (here-document) work?
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The code snippet below makes sure to write lines of text into a
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The code snippet makes sure to write lines of text into a
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file (that so far does not exist) called ``notes.txt``.
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To do this, the content of the "document" is wrapped in between
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you create and modify a ``.txt`` file over the course of the Basics part of this
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handbook.
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Running the command below will create ``notes.txt`` in the
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Running this command will create ``notes.txt`` in the
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root of your ``DataLad-101`` dataset:
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.. index:: heredoc
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Modify this file by adding another note. After all, you already know how to use
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:dlcmd:`save`, so write a short summary on that as well.
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Again, the example below uses Unix commands (``cat`` and redirection, this time however
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Again, the example uses Unix commands (``cat`` and redirection, this time however
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with ``>>`` to *append* new content to the existing file)
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to accomplish this, but you can take any editor of your choice.
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docs/basics/101-105-install.rst

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@@ -75,7 +75,7 @@ the podcasts as a *subdataset* of ``DataLad-101``. Because we are in the root
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of the ``DataLad-101`` dataset, the pointer to the dataset is a ``.`` (which is Unix'
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way of saying "current directory").
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As before with long commands, we line break the code below with a ``\``. You can
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As before with long commands, we line break the code with a ``\``. You can
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copy it as it is presented here into your terminal, but in your own work you
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can write commands like this into a single line.
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docs/basics/101-106-nesting.rst

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@@ -117,8 +117,9 @@ we can set subdatasets to previous states, or *update* them.
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In the upcoming sections, we'll experience the perks of dataset nesting
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frequently, and everything that might seem vague at this point will become
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clearer. To conclude this demonstration,
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the figure below illustrates the current state of our dataset, ``DataLad-101``, with its nested subdataset.
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figure :numref:`fignesting` illustrates the current state of our dataset, ``DataLad-101``, with its nested subdataset.
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.. _fignesting:
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.. figure:: ../artwork/src/virtual_dstree_dl101.svg
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:width: 70%
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docs/basics/101-108-run.rst

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@@ -68,8 +68,7 @@ Inside of ``DataLad-101/code``, create a simple shell script ``list_titles.sh``.
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This script will carry out a simple task:
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It will loop through the file names of the ``.mp3`` files and
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write out speaker names and talk titles in a very basic fashion.
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The content of this script is written below -- the ``cat`` command
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will write it into the script.
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The ``cat`` command will write the script content into ``code/list_titles.sh``.
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.. windows-wit:: Here's a script for Windows users
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docs/basics/101-115-symlinks.rst

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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Are you using DataLad on the Windows Subsystem for Linux?
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If so, please take a look into the Windows Wit below.
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If so, please take a look into the Windows Wit.
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.. index::
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pair: access WSL2 symlinked files; on Windows

docs/basics/101-116-sharelocal.rst

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$ datalad get -n recordings/longnow
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The section below will elaborate on :dlcmd:`get` and the
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``-n/--no-data`` option, but for now, let's first see what has changed after
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Before we look further into :dlcmd:`get` and the
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``-n/--no-data`` option, let's first see what has changed after
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running the above command (excerpt):
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.. runrecord:: _examples/DL-101-116-108

docs/basics/101-119-sharelocal4.rst

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PS: You might wonder what a plain :dlcmd:`update` command with no option does.
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If you are a Git-user and know about branches and merging you can read the
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``Note for Git-users`` below. However, a thorough explanation
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``Note for Git-users``. However, a thorough explanation
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and demonstration will be in the next section.
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.. index::

docs/basics/101-124-procedures.rst

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write their own ones in addition, and deploy them on individual machines,
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or ship them within DataLad datasets. This allows to
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automate routine configurations or tasks in a dataset, or share configurations that would otherwise not "stick" to the dataset.
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Some general rules for creating a custom procedure are outlined
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below:
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Here are some general rules for creating a custom procedure:
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- A procedure can be any executable. Executables must have the
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appropriate permissions and, in the case of a script,

docs/basics/101-130-yodaproject.rst

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proportion of the previous handbook content as a prerequisite. In order to be
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not too overwhelmingly detailed, the upcoming sections will approach
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:dlcmd:`push` from a "learning-by-doing" perspective:
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You will see a first :dlcmd:`push` to GitHub below, and the :ref:`Findoutmore on the published dataset <fom-midtermclone>`
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First, you will see a :dlcmd:`push` to GitHub, and the :ref:`Findoutmore on the published dataset <fom-midtermclone>`
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at the end of this section will already give a practical glimpse into the
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difference between annexed contents and contents stored in Git when pushed
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to GitHub. The chapter :ref:`chapter_thirdparty` will extend on this,
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$ datalad push --to github
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Thus, you have now published your dataset's history to a public place for others
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to see and clone. Below we will explore how this may look and feel for others.
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to see and clone. Now we will explore how this may look and feel for others.
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There is one important detail first, though: By default, your tags will not be published.
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Thus, the tag ``ready4analysis`` is not pushed to GitHub, and currently this
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Therefore, you decide to install this dataset into a new location on your
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Replace the ``url`` in the :dlcmd:`clone` command below with the path
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Replace the ``url`` in the :dlcmd:`clone` command with the path
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to your own ``midtermproject`` GitHub repository, or clone the "public"
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``midterm_project`` repository that is available via the Handbook's GitHub
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organization at `github.com/datalad-handbook/midterm_project <https://github.com/datalad-handbook/midterm_project>`_:

docs/basics/101-135-help.rst

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:term:`Debugging` and :term:`logging` are not as complex as these terms may sound if you have never consciously debugged.
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Procedurally, it can be as easy as adding an additional flag to a command call, and cognitively, it can be as easy as engaging your visual system in a visual search task for the color red or the word "error", or reading more DataLad output than you're used to.
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The paragraphs below start with the general concepts, and collect concrete debugging strategies for different problems.
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We will start with the general concepts, and then collect concrete debugging strategies for different problems.
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.. _logging:
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docs/basics/101-136-cheatsheet.rst

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.. only:: html
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Click on the image below to obtain a PDF version of the cheat sheet. Individual
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Click on the image to obtain a PDF version of the cheat sheet. Individual
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sections are linked to chapters or technical docs.
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.. figure:: ../artwork/src/datalad-cheatsheet_p1.png

docs/basics/101-139-figshare.rst

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The screenshot below shows how the ``DataLad-101`` dataset looks like in exported form:
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The screenshot in :numref:`figfigshare` shows how the ``DataLad-101`` dataset looks like in exported form:
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.. _figfigshare:
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.. figure:: ../artwork/src/figshare_screenshot.png
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The dataset export on Figshare
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You could then extend the dataset with metadata, obtain a `DOI <https://www.doi.org/driven_by_DOI.html>`_ for it and make it citable, and point others to it in order to download it as an archive of files.
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Beyond this, as the command :dlcmd:`export-archive` is used by it to prepare content for upload to Figshare, annexed files also will be annotated as available from the archive on Figshare using ``datalad-archive`` special remote.

docs/basics/101-139-hostingservices.rst

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Projects are single repositories, and groups can be used to manage one or more projects at the same time.
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In order to use ``create-sibling-gitlab``, a user **must** `create a group <https://docs.gitlab.com/ee/user/group/#create-a-group>`_ via the web interface, or specify a pre-existing group, because `GitLab does not allow root-level groups to be created via their API <https://docs.gitlab.com/ee/api/groups.html#new-group>`_.
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Only when there already is a "parent" group DataLad and other tools can create sub-groups and projects automatically.
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In the screenshots below, a new group ``my-datalad-root-level-group`` is created right underneath the user account.
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In the screenshots :numref:`fig-rootgroup-gitlab1` and :numref:`fig-rootgroup-gitlab2`, a new group ``my-datalad-root-level-group`` is created right underneath the user account.
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The group name as shown in the URL bar is what DataLad needs in order to create sibling datasets.
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.. _fig-rootgroup-gitlab1:
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.. figure:: ../artwork/src/gitlab-rootgroup.png
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Webinterface to create a root-level group on GitLab.
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.. _fig-rootgroup-gitlab2:
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.. figure:: ../artwork/src/gitlab-rootgroup2.png
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docs/basics/101-139-s3.rst

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Lastly, for git-annex to be able to download files from the bucket without requiring your
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AWS credentials, it needs to know where to find the bucket. We do this by setting the bucket
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URL, which takes a standard format incorporating the bucket name and location (see the code blocl below).
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URL, which takes a standard format incorporating the bucket name and location (see the code block below).
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Alternatively, this URL can also be copied from your AWS console.
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.. code-block:: bash

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