Merge pull request #569 from datalad-handbook/dvc

DataLad as DVC for ML analysis

Makefile

@@ -19,6 +19,12 @@ clean-examples:
 	# wipe out the RIA store
 	@rm -vrf /home/me/myriastore
 
+# do not touch whats in the DataLad narrative, only certain unrelated wdirs and examples
+clean-DVC:
+	# wipe out the DVC comparison
+	@find docs/beyond_basics/_examples -name DL-101-168* -type f | xargs rm -vrf
+	@chmod +w -R /home/me/DVCvsDL; rm -vrf /home/me/DVCvsDL
+
 # wipe out usecases
 clean-usecases:
 	# check if we have something like .xsession or a .bashrc
@@ -38,4 +44,6 @@ clean:
 	@chmod +w -R /home/me/pushes; rm -vrf /home/me/pushes
 	@rm -vrf /home/me/makepushtarget.py
 	# wipe out the RIA store
-	@rm -vrf /home/me/myriastore
+	@rm -vrf /home/me/myriastore
+	# wipe out the DVC comparison
+	@chmod +w -R /home/me/DVCvsDL; rm -vrf /home/me/DVCvsDL

docs/basics/101-127-yoda.rst

@@ -343,6 +343,8 @@ of all the contents you created in the wake of your analysis project.
 This established trust in your results, and enables others to understand
 where files derive from.
 
+.. _yodaproc:
+
 The YODA procedure
 ^^^^^^^^^^^^^^^^^^
 

docs/basics/101-138-sharethirdparty.rst

@@ -57,7 +57,7 @@ web server, but also a third party services cloud storage such as
 `Google <https://google.com>`_,
 `Amazon S3 buckets <https://aws.amazon.com/s3/?nc1=h_ls>`_,
 `Box.com <https://www.box.com/en-gb/home>`_,
-`Figshare <https://figshare.com/>`_,
+`Figshare <https://figshare.com/>`__,
 `owncloud <https://owncloud.org/>`_,
 `sciebo <https://sciebo.de/>`_,
 or many more. The key to achieve this lies within :term:`git-annex`.
@@ -497,6 +497,7 @@ books, or the cropped logos from chapter :ref:`chapter_run`::
    $ datalad get books/TLCL.pdf
    get(ok): /home/some/other/user/DataLad-101/books/TLCL.pdf (file) [from dropbox-for-friends]
 
+.. _gitlfs:
 
 Use GitHub for sharing content
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -545,6 +546,7 @@ from GitHub.
    Unfortunately, it is impossible to :command:`drop` contents from Git LFS:
    `help.github.com/en/github/managing-large-files <https://help.github.com/en/github/managing-large-files/removing-files-from-git-large-file-storage#git-lfs-objects-in-your-repository>`_
 
+.. _figshare:
 
 Built-in data export
 ^^^^^^^^^^^^^^^^^^^^
@@ -563,7 +565,7 @@ special features a DataLad dataset provides will be available, such as its
 history or configurations.
 
 Another example is :command:`export-to-figshare`. Running this command allows
-you to publish the dataset to `Figshare <https://figshare.com/>`_.  As the
+you to publish the dataset to `Figshare <https://figshare.com/>`__.  As the
 :command:`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.  As a result, if you publish
@@ -577,7 +579,7 @@ be able to fetch content from the tarball shared on Figshare via DataLad.
          access to the server and client side of your GitLab instance. Find out more
          `here <https://docs.gitlab.com/ee/administration/git_annex.html>`_.
          Alternatively, GitHub can integrate with
-         `GitLFS <https://git-lfs.github.com/>`_, a non-free, centralized service
+         `GitLFS <https://git-lfs.github.com/>`__, a non-free, centralized service
          that allows to store large file contents. The last paragraph in this
          section shows an example on how to use their free trial version.
 

docs/basics/101-180-FAQ.rst

@@ -388,6 +388,12 @@ that it appears similar to git-annex.
 A more elaborate delineation from related solutions can be found in the DataLad
 `developer documentation <http://docs.datalad.org/en/latest/related.html>`_.
 
+What is the difference between DataLad and DVC?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+`DVC <https://dvc.org/>`_ is a version control system for machine learning projects.
+We have compared the two tools in a dedicated handbook section, :ref:`dvc`.
+
 DataLad version-controls my large files -- great. But how much is saved in total?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -443,6 +449,7 @@ MEG, EEG, iEEG, and ECoG data. It publishes hosted data as DataLad datasets on
 obtain the datasets just as any other DataLad datasets with :command:`datalad clone`
 or :command:`datalad install`.
 
+.. _gitannexbranch:
 
 What is the git-annex branch?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^