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Merge pull request #1147 from datalad-handbook/res
Resolve all 're contractions in the Basics
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docs/basics/101-102-populate.rst

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@@ -226,7 +226,7 @@ in the same commit. And ... what happens if I have files I do not want to track?
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:dlcmd:`save -m "some commit message"` would save all of what is currently
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untracked or modified in the dataset into the history!"
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Regarding your first remark, you're absolutely right!
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Regarding your first remark, you are absolutely right!
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It is good practice to save only those changes
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together that belong together. We do not want to squish completely unrelated changes
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into the same spot of our history, because it would get very nasty should we want to
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$ datalad save -m "add reference book about git" books/progit.pdf
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Regarding your second remark, you're right that a :dlcmd:`save` without a
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Regarding your second remark, you are right that a :dlcmd:`save` without a
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path specification would write all of the currently untracked files or modifications
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to the history. But check the :find-out-more:`on how to tell it otherwise <fom-save-updated-only>`.
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docs/basics/101-103-modify.rst

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@@ -145,7 +145,7 @@ and save the file in DataLad:
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$ datalad save -m "add note on datalad save"
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Let's take another look into our history to see the development of this file.
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We're using :gitcmd:`log -p -n 2` to see last two commits and explore
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We are using :gitcmd:`log -p -n 2` to see last two commits and explore
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the difference to the previous state of a file within each commit.
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.. runrecord:: _examples/DL-101-103-107

docs/basics/101-105-install.rst

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@@ -36,7 +36,7 @@ of a DataLad dataset! Shall we try whether we can install that?"
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now instead of looking at slides for hours is my preferred type of learning anyway",
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you think as you fire up your terminal and navigate into your ``DataLad-101`` dataset.
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In this demonstration, we're using one of the many openly available datasets that
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In this demonstration, we are using one of the many openly available datasets that
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DataLad provides in a public registry that anyone can access. One of these datasets is a
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collection of audio recordings of a great podcast, the longnow seminar series [#f2]_.
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It consists of audio recordings about long-term thinking, and while the DataLad-101

docs/basics/101-108-run.rst

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@@ -36,12 +36,12 @@ list of speakers and titles to cross out what they've already listened
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to, and ask you to prepare such a list.
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"Mhh... probably there is a DataLad way to do this... wasn't there also
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a note about metadata extraction at some point?" But as we're not that
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a note about metadata extraction at some point?" But as we are not that
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far into the lectures, you decide to write a short shell script
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to generate a text file that lists speaker and title
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name instead.
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To do this, we're following a best practice that will reappear in the
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To do this, we are following a best practice that will reappear in the
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later section on :ref:`YODA principles <yoda>`: Collecting all
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additional scripts that work with content of a subdataset *outside*
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of this subdataset, in a dedicated ``code/`` directory,

docs/basics/101-109-rerun.rst

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@@ -110,7 +110,7 @@ So you go ahead and find the commit :term:`shasum` in your history:
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Take that shasum and paste it after :dlcmd:`rerun`
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(the first 6-8 characters of the shasum would be sufficient,
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here we're using all of them).
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here we are using all of them).
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.. runrecord:: _examples/DL-101-109-106
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:language: console

docs/basics/101-110-run2.rst

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@@ -39,14 +39,14 @@ in the hidden paths
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.. runrecord:: _examples/DL-101-110-101
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:language: console
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:workdir: dl-101/DataLad-101
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:notes: We saw a very simple datalad run. Now we're going to extend it with useful options. Narrative: prepare talk about dataset, add logo to slides. For this, we'll try to resize a logo in the meta data of the subdataset
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:notes: We saw a very simple datalad run. Now we are going to extend it with useful options. Narrative: prepare talk about dataset, add logo to slides. For this, we'll try to resize a logo in the meta data of the subdataset
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:cast: 02_reproducible_execution
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$ ls recordings/longnow/.datalad/feed_metadata/*jpg
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For the slides you decide to prepare images of size 400x400 px, but
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the logos' original size is much larger (both are 3000x3000 pixel). Therefore
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let's try to resize the images -- currently, they're far too large to fit on a slide.
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let's try to resize the images -- currently, they are far too large to fit on a slide.
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To resize an image from the command line we can use the Unix
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command ``convert -resize`` from the `ImageMagick tool <https://imagemagick.org/index.php>`_.

docs/basics/101-114-txt2git.rst

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@@ -15,10 +15,10 @@ I was able to modify this despite giving it to DataLad to track, with
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no permission denied errors whatsoever! How does that work?"
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This night, though, your question stays unanswered and you fall into a restless
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sleep filled with bad dreams about "permission denied" errors. The next day you're
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sleep filled with bad dreams about "permission denied" errors. The next day you are
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the first student in your lecturer's office hours.
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"Oh, you're really attentive. This is a great question!" our lecturer starts
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"Oh, you are really attentive. This is a great question!" our lecturer starts
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to explain.
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.. figure:: ../artwork/src/teacher.svg

docs/basics/101-116-sharelocal.rst

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@@ -39,7 +39,7 @@ of undesired, or uncontrolled modification.
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To demonstrate how to share a DataLad dataset on a common file system,
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we will pretend that your personal computer
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can be accessed by other users. Let's say that
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your room mate has access, and you're making sure that there is
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your room mate has access, and you are making sure that there is
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a ``DataLad-101`` dataset in a different place on the file system
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for him to access and work with.
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one or more projects.
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"Awesome!" exclaims your room mate as you take out your laptop to
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share the dataset. "You're really saving my ass
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share the dataset. "You are really saving my ass
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here. I'll make up for it when we prepare for the final", he promises.
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To install ``DataLad-101`` into a different part

docs/basics/101-119-sharelocal4.rst

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@@ -9,13 +9,13 @@ All of what you have seen about sharing dataset was really
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cool, and for the most part also surprisingly intuitive.
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:dlcmd:`run` commands or file retrieval worked exactly as
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you imagined it to work, and you begin to think that slowly but
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steadily you're getting a feel about how DataLad really works.
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steadily you are getting a feel about how DataLad really works.
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But to be honest, so far, sharing the dataset with DataLad was
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also remarkably unexciting given that you already knew most of
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the dataset magic that your room mate currently is still
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mesmerized about.
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To be honest, you're not yet certain whether
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To be honest, you are not yet certain whether
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sharing data with DataLad really improves your life up
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until this point. After all, you could have just copied
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your directory into your ``mock_user`` directory and

docs/basics/101-121-siblings.rst

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@@ -335,7 +335,7 @@ do not use Git, but a later section will get into the details of what
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the meaning of ":term:`merge`", ":term:`branch`", "refs"
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or ":term:`main`" is.
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For now, you're happy to have the changes your room mate made available.
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For now, you are happy to have the changes your room mate made available.
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This is how it should be! You helped him, and he helps you. Awesome!
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There actually is a wonderful word for it: *Collaboration*.
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Thus, without noticing, you have successfully collaborated for the first

docs/basics/101-122-config.rst

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@@ -35,7 +35,7 @@ student from the row behind you. Personally, you'd also
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be much more excited
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about any hands-on lecture filled with commands. But the
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recent lecture about :term:`git-annex` and the :term:`object-tree`
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was surprisingly captivating, so you're actually looking forward to today.
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was surprisingly captivating, so you are actually looking forward to today.
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"Shht! I want to hear this!", you shush him with a wink.
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"We will start by looking into the very first configuration
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and DataLad -- can be configured using the :gitcmd:`config`
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command [#f1]_. Therefore, once you understand the syntax of this
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command, you already know half of what's relevant. The other half
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is understanding what you're doing. Now then, let's learn *how*
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to configure settings, but also *understand* what we're doing
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is understanding what you are doing. Now then, let's learn *how*
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to configure settings, but also *understand* what we are doing
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with these configurations."
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"This seems easy enough", you think. Let's see what types of

docs/basics/101-123-config2.rst

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@@ -444,7 +444,7 @@ you already know some core Git configurations such as name, email, and editor. E
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important, you know how to configure git-annex's content management based on ``largefile``
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rules, and you understand the variables within ``.gitmodules`` or the sections
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in ``.git/config``. Slowly, you realize with pride,
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you're more and more becoming a DataLad power-user.
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you are more and more becoming a DataLad power-user.
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Write a note about configurations in datasets into ``notes.txt``.
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docs/basics/101-130-yodaproject.rst

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.. importantnote:: Turn data analysis into dynamically generated documents
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Beyond the contents of this section, we have transformed the example analysis also into a template to write a reproducible paper.
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If you're interested in checking that out, please head over to `github.com/datalad-handbook/repro-paper-sketch/ <https://github.com/datalad-handbook/repro-paper-sketch>`_.
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If you are interested in checking that out, please head over to `github.com/datalad-handbook/repro-paper-sketch/ <https://github.com/datalad-handbook/repro-paper-sketch>`_.
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Raw data as a modular, independent entity
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/basics/101-133-containersrun.rst

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@@ -143,7 +143,7 @@ For this, we will pull an image from Singularity hub. This image was made
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for the handbook, and it contains the relevant Python setup for
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the analysis. Its recipe lives in the handbook's
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`resources repository <https://github.com/datalad-handbook/resources>`_.
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If you're curious how to create a Singularity image, the :find-out-more:`on this topic <fom-container-creation>` has some pointers:
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If you are curious how to create a Singularity image, the :find-out-more:`on this topic <fom-container-creation>` has some pointers:
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.. index::
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pair: build container image; with Singularity

docs/basics/101-135-help.rst

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This allows you to gain more insights into the actions DataLad and its underlying tools are taking, where *exactly* they fail, and to even play around with the program at the state of the failure.
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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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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 are 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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.. _logging:

docs/basics/101-136-filesystem.rst

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management operations, and each question outlines caveats and
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solutions with code examples you can paste into your own terminal.
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Because these code snippets will add many commits to your
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dataset, we're cleaning up within each segment with
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dataset, we are cleaning up within each segment with
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common git operations that manipulate the datasets
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history -- be sure to execute these commands as well (and
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be sure to be in the correct dataset).
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$ git reset --hard HEAD~1
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Now we are checking out how to rename files and commit this operation
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using only Git:
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A Git-specific way to rename files is the ``git mv`` command:
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dataset contents cannot be published to these services.
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Even though you could find a third party service of your choice
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and publish your dataset *and* the annexed data (see section :ref:`sharethirdparty`),
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you're feeling lazy today. And since it
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you are feeling lazy today. And since it
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is only two files, and they are quite small, you decide to store them in Git --
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store.

docs/basics/101-137-history.rst

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Fixing (empty) commit messages
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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From the back of the lecture hall comes a question you're really glad
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From the back of the lecture hall comes a question you are really glad
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someone asked: "It has happened to me that I accidentally did a
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:dlcmd:`save` and forgot to specify the commit message,
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how can I fix this?".

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