diff --git a/docs/basics/101-106-nesting.rst b/docs/basics/101-106-nesting.rst
index ef3f22535..1793e4f26 100644
--- a/docs/basics/101-106-nesting.rst
+++ b/docs/basics/101-106-nesting.rst
@@ -84,8 +84,14 @@ we can set subdatasets to previous states, or *update* them.
Previously, we used :command:`cd` to navigate into the subdataset, and
subsequently opened the Git log. This is necessary, because a :command:`git log`
- in the superdataset would only return the superdatasets history. There is one
- trick, though: ``git -C`` lets you perform any Git command in a provided path.
+ in the superdataset would only return the superdatasets history.
+ While moving around with ``cd`` is straightforward, you also found it
+ slightly annoying from time to time to use the ``cd`` command so often and also
+ to remember in which directory you currently are in. There is one
+ trick, though: ``git -C`` (note that it is a capital C) lets you perform any
+ Git command in a provided path. Providing this option together with a path to
+ a Git command let's you run the command as if Git was started in this path
+ instead of the current working directory.
Thus, from the root of ``DataLad-101``, this command would have given you the
subdatasets history as well::
diff --git a/docs/basics/101-130-yodaproject.rst b/docs/basics/101-130-yodaproject.rst
index 17cff706b..99cdd156f 100644
--- a/docs/basics/101-130-yodaproject.rst
+++ b/docs/basics/101-130-yodaproject.rst
@@ -1,3 +1,5 @@
+.. _yoda_project:
+
YODA-compliant data analysis projects
-------------------------------------
diff --git a/docs/basics/101-132-advancednesting.rst b/docs/basics/101-132-advancednesting.rst
index e051bb278..614c015c9 100644
--- a/docs/basics/101-132-advancednesting.rst
+++ b/docs/basics/101-132-advancednesting.rst
@@ -39,8 +39,11 @@ evolved. Let's query the superdataset what it thinks about this.
$ datalad status
From the superdataset's perspective, the subdataset appears as being
-"modified". Note that these modifications of the subdataset are not
-automatically recorded to the superdataset! This makes sense -- after all it
+"modified". Note how it is not individual files that show up as "modified", but
+indeed the complete subdataset as a single entity.
+
+What this shows you is that the modifications of the subdataset you performed are not
+automatically recorded to the superdataset. This makes sense -- after all it
should be up to you to decide whether you want record something or not --,
but it is worth repeating: If you modify a subdataset, you will need to save
this *in the superdataset* in order to have a clean superdataset status.
@@ -163,13 +166,42 @@ interested in this, checkout the hidden section below.
$ datalad status --recursive
Let's save the modification of the subdataset into the history of the
-superdataset:
+superdataset. For this, to avoid confusion, you can specify explicitly to
+which dataset you want to save a modification. ``-d .`` specifies the current
+dataset, i.e., ``DataLad-101``, as the dataset to save to:
.. runrecord:: _examples/DL-101-132-110
:language: console
:workdir: dl-101/DataLad-101/
- $ datalad save -m "finished my midterm project"
+ $ datalad save -d . -m "finished my midterm project!" midterm_project
+
+.. findoutmore:: More on how save can operate on nested datasets
+
+ In a superdataset with subdatasets, :command:`datalad save` by default
+ tries to figure out on its own which dataset's history of all available
+ datasets a :command:`save` should be written to. However, it can reduce
+ confusion or allow specific operations to be very explicit in the command
+ call and tell DataLad where to save what kind of modifications to.
+
+ If you want to save the current state of the subdataset into the superdataset
+ (as necessary here), start a ``save`` from the superdataset and have the
+ ``-d/--dataset`` option point to its root::
+
+ # in the root of the superds
+ $ datalad save -d . -m "update subdataset"
+
+ If you are in the superdataset, and you want to save an unsaved modification
+ in a subdataset to the *subdatasets* history, let ``-d/--dataset`` point to
+ the subdataset::
+
+ # in the superds
+ $ datalad save -d path/to/subds -m "modified XY"
+
+ The recursive option allows you to save any content underneath the specified
+ directory, and recurse into any potential subdatasets::
+
+ $ datalad save . --recursive
Let's check which subproject commit is now recorded in the superdataset:
diff --git a/docs/basics/101-132-gitC.rst b/docs/basics/101-132-gitC.rst
deleted file mode 100644
index e5b21c348..000000000
--- a/docs/basics/101-132-gitC.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-Working in (sub-)datasets from afar
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Up until now, we made sure to diligently ``cd`` into the precise dataset or
-subdataset we wanted to work with. This was straightforward and easy, but, to
-be honest, you found it slightly annoying from time to time as well.
-
-Luckily, Git has an option to run commands in a path different from the current
-working directory: ``-C`` (note that it is a capital C). Providing this
-option together with a path to any Git command let's you run the command as
-if Git was started in this path instead of the current working directory.
-
-.. todo::
-
- this needs some examples and practice.
\ No newline at end of file
diff --git a/docs/basics/101-133-containersrun.rst b/docs/basics/101-133-containersrun.rst
new file mode 100644
index 000000000..3e674bfc2
--- /dev/null
+++ b/docs/basics/101-133-containersrun.rst
@@ -0,0 +1,320 @@
+.. _containersrun:
+
+Computational reproducibility with software containers
+------------------------------------------------------
+
+Just after submitting your midterm data analysis project, you get together
+with your friends. "I'm curious: So what kind of analyses did y'all carry out?"
+you ask. The variety of methods and datasets the others used is huge, and
+one analysis interests you in particular. Later that day, you decide to
+install this particular analysis dataset to learn more about the methods used
+in there. However, when you :command:`re-run` your friends analysis script,
+it throws an error. Hastily, you call her -- maybe she can quickly fix her
+script and resubmit the project with only minor delays. "I don't know what
+you mean", you hear in return.
+"On my machine, everything works fine!"
+
+
+On its own, DataLad datasets can contain almost anything that is relevant to
+ensure reproducibility: Data, code, human-readable analysis descriptions
+(e.g., ``README.md`` files), provenance on the origin of all files
+obtained from elsewhere, and machine-readable records that link generated
+outputs to the commands, scripts, and data they were created from.
+
+This however may not be sufficient to ensure that an analysis *reproduces*
+(i.e., produces the same or highly similar results), let alone *works* on a
+computer different than the one it was initially composed on. This is because
+the analysis does not only depend on data and code, but also the
+*software environment* that it is conducted in.
+
+A lack of information about the operating system of the computer, the precise
+versions of installed software, or their configurations may
+make it impossible to replicate your analysis on a different machine, or even
+on your own machine once a new software update is installed. Therefore, it is
+important to communicate all details about the computational environment for
+an analysis as thoroughly as possible. Luckily, DataLad provides an extension
+that can link computational environments to datasets, the
+`datalad containers `_
+extension [#f1]_.
+
+This section will give a quick overview on what containers are and
+demonstrate how ``datalad-containers`` helps to capture full provenance of an
+analysis by linking containers to datasets and analyses.
+
+Containers
+^^^^^^^^^^
+
+To put it simple, computational containers are cut-down virtual machines that
+allow you to package all software libraries and their dependencies (all in the
+precise version your analysis requires) into a bundle you can share with
+others. On your own and other's machines, the container constitutes a secluded
+software environment that
+
+- contains the exact software environment that you specified, ready to run
+ analyses in
+- does not effect any software outside of the container
+
+Unlike virtual machines, software containers do not have their own operating
+system. Instead, they use basic services of the underlying operating system
+of the computer they run on (in a read-only fashion). This makes them
+lightweight and portable. By sharing software environments with containers,
+others (and also yourself) have easy access to the correct software
+without the need to modify the software environment of the machine the
+container runs on. Thus, containers are ideal to encapsulate the software
+environment and share it together with the analysis code and data to ensure
+computational reproducibility of your analyses, or to create a suitable
+software environment on a computer that you do not have permissions to deploy
+software on.
+
+There are a number of different tools to create and use containers, with
+`Docker `_ being one of the most well-known of them.
+While being a powerful tool, it is only rarely used on high performance computing
+(HPC) infrastructure [#f2]_. An alternative is `Singularity `_.
+Both of these tools share core terminology:
+
+**Recipe**
+ A text file template that lists all required components of the computational environment.
+ It is made by a human user.
+
+**Image**
+ This is *built* from the recipe file. It is a static filesystem inside a file,
+ populated with the software specified in the recipe, and some initial configuration.
+
+**Container**
+ A running instance of an Image that you can actually use for your computations.
+ If you want to create and run your own software container, you start by writing
+ a recipe file and build an Image from it. Alternatively, you can can also *pull*
+ an Image built from a publicly shared recipe from the *Hub* of the tool you are using.
+
+**Hub**
+ A storage resource to share and consume images. There is
+ `Singularity-Hub `_ and
+ `Docker-Hub `_. Both are optional, additional services
+ not required to use software containers, but a convenient way to share recipes
+ and have imaged built from them by a service (instead of building them
+ manually and locally).
+
+Note that as of now, the ``datalad-containers`` extension supports
+Singularity and Docker images.
+Singularity furthermore is compatible with Docker -- you can use
+Docker Images as a basis for Singularity Images, or run Docker Images with
+Singularity (even without having Docker installed).
+
+.. note::
+
+ In order to use Singularity containers (and thus ``datalad containers``), you have to
+ `install `_ the software singularity.
+
+Using ``datalad containers``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. index:: ! datalad command; containers-add
+.. index:: ! datalad command; containers-run
+
+One core feature of the ``datalad containers`` extension is that it registers
+computational containers to a dataset. This is done with the
+:command:`datalad containers-add` command.
+Once a container is registered, arbitrary commands can be executed inside of
+it, i.e., in the precise software environment the container encapsulates. All it
+needs for this it to swap the :command:`datalad run` command introduced in
+section :ref:`run` with the :command:`datalad containers-run` command.
+
+Let's see this in action for the ``midterm_analysis`` dataset by rerunning
+the analysis you did for the midterm project within a Singularity container.
+We start by registering a container to the dataset.
+For this, we will pull an Image from Singularity hub. This Image was made
+for the handbook, and it contains the relevant Python setup for
+the analysis. Its recipe lives in the handbook's
+`resources repository `_, and the
+Image is built from the recipe via Singularity hub.
+If you're curious how to create a Singularity Image, the hidden
+section below has some pointers:
+
+.. findoutmore:: How to make a Singularity Image
+
+ Singularity containers are build from Image files, often
+ called "recipes", that hold a "definition" of the software container and its
+ contents and components. The
+ `singularity documentation `_
+ has its own tutorial on how to build such Images from scratch.
+ An alternative to writing the Image file by hand is to use
+ `Neurodocker `_. This
+ command-line program can help you generate custom Singularity recipes (and
+ also ``Dockerfiles``, from which Docker Images are build). A wonderful tutorial
+ on how to use Neurodocker is
+ `this introduction `_
+ by Michael Notter.
+
+ Once a recipe exists, the command
+
+ .. code-block:: bash
+
+ sudo singularity build
+
+ will build a container (called ````) from the recipe. Note that this
+ command requires ``root`` privileges ("``sudo``"). You can build the container
+ on any machine, though, not necessarily the one that is later supposed to
+ actually run the analysis, e.g., your own laptop versus a compute cluster.
+ Alternatively, `Singularity Hub `_ integrates
+ with Github and builds containers from Images pushed to repositories on Github.
+ `The docs `_
+ give you a set of instructions on how to do this.
+
+The :command:`datalad containers-add` command takes an arbitrary
+name to give to the container, and a path or url to a container Image:
+
+.. runrecord:: _examples/DL-101-133-101
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ # we are in the midterm_project subdataset
+ $ datalad containers-add midterm-software --url shub://adswa/resources:1
+
+
+This command downloaded the container from Singularity Hub, added it to
+the ``midterm_project`` dataset, and recorded basic information on the
+container under its name "midterm-software" in the dataset's configuration at
+``.datalad/config``.
+
+.. findoutmore:: What has been added to .datalad/config?
+
+ .. runrecord:: _examples/DL-101-133-102
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ $ cat .datalad/config
+
+ This recorded the Image's origin on Singularity-Hub, the location of the
+ Image in the dataset under ``.datalad/environments//image``, and it
+ specifies the way in which the container should be used: The line
+
+ .. code-block:: bash
+
+ cmdexec = singularity exec {img} {cmd}
+
+ can be read as: "If this container is used, take the ``cmd`` (what you wrap in a
+ :command:`datalad containers-run` command) and plug it into a
+ :command:`singularity exec` command. The mode of calling Singularity,
+ namely ``exec``, means that the command will be executed inside of the container.
+
+ Note that the Image is saved under ``.datalad/environments`` and the
+ configuration is done in ``.datalad/config`` -- as these files are version
+ controlled and shared with together with a dataset, your software
+ container and the information where it can be re-obtained from are linked
+ to your dataset.
+
+ This is how the ``containers-add`` command is recorded in your history:
+
+ .. runrecord:: _examples/DL-101-133-103
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ $ git log -n 1 -p
+
+Now that we have a complete computational environment linked to the ``midterm_project``
+dataset, we can execute commands in this environment. Let us for example try to repeat
+the :command:`datalad run` command from the section :ref:`yoda_project` as a
+:command:`datalad containers-run` command.
+
+The previous ``run`` command looked like this::
+
+ $ datalad run -m "analyze iris data with classification analysis" \
+ --input "input/iris.csv" \
+ --output "prediction_report.csv" \
+ --output "pairwise_relationships.png" \
+ "python3 code/script.py"
+
+How would it look like as a ``containers-run`` command?
+
+.. runrecord:: _examples/DL-101-133-104
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ $ datalad containers-run -m "rerun analysis in container" \
+ --container-name midterm-software \
+ --input "input/iris.csv" \
+ --output "prediction_report.csv" \
+ --output "pairwise_relationships.png" \
+ "python3 code/script.py"
+
+Almost exactly like a :command:`datalad run` command! The only additional parameter
+is ``container-name``. At this point, though, the ``--container-name``
+flag is even *optional* because there is only a single container registered to the dataset.
+But if your dataset contains more than one container you will *need* to specify
+the name of the container you want to use in your command.
+The complete command's structure looks like this::
+
+ $ datalad containers-run --name [-m ...] [--input ...] [--output ...]
+
+.. index:: ! datalad command; containers-remove
+.. index:: ! datalad command; containers-list
+
+.. findoutmore:: How can I list available containers or remove them?
+
+ The command :command:`datalad containers-list` will list all containers in
+ the current dataset:
+
+ .. runrecord:: _examples/DL-101-133-110
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+
+ $ datalad containers-list
+
+ The command :command:`datalad containers-remove` will remove a container
+ from the dataset, if there exists a container with name given to the
+ command. Note that this will remove not only the Image from the dataset,
+ but also the configuration for it in ``.datalad/config``.
+
+
+Here is how the history entry looks like:
+
+.. runrecord:: _examples/DL-101-133-111
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ $ git log -p -n 1
+
+If you would :command:`rerun` this commit, it would be re-executed in the
+software container registered to the dataset. If you would share the dataset
+with a friend and they would :command:`rerun` this commit, the Image would first
+be obtained from its registered url, and thus your
+friend can obtain the correct execution environment automatically.
+
+Note that because this new :command:`containers-run` command modified the
+``midterm_project`` subdirectory, we need to also save
+the most recent state of the subdataset to the superdataset ``DataLad-101``.
+
+.. runrecord:: _examples/DL-101-133-112
+ :language: console
+ :workdir: dl-101/DataLad-101/midterm_project
+
+ $ cd ../
+ $ datalad status
+
+.. runrecord:: _examples/DL-101-133-113
+ :language: console
+ :workdir: dl-101/DataLad-101
+
+ $ datalad save -d . -m "add container and execute analysis within container" midterm_project
+
+
+Software containers, the ``datalad-containers`` extension, and DataLad thus work well together
+to make your analysis completely reproducible -- by not only linking code, data,
+and outputs, but also the software environment of an analysis. And this does not
+only benefit your future self, but also whomever you share your dataset with, as
+the information about the container is shared together with the dataset. How cool
+is that?
+
+If you are interested in more, you can read about another example of :command:`datalad containers-run`
+in the usecase :ref:`usecase_reproduce_neuroimg`.
+
+.. rubric:: Footnotes
+
+.. [#f1] To read more about DataLad's extensions, see section :ref:`extensions_intro`.
+.. [#f2] The main reason why Docker is not deployed on HPC systems is because
+ it grants users "`superuser privileges `_".
+ On multi-user systems such as HPC, users should not have those
+ privileges, as it would enable them to temper with other's or shared
+ data and resources, posing a severe security threat.
diff --git a/docs/basics/101-134-summary.rst b/docs/basics/101-134-summary.rst
new file mode 100644
index 000000000..026169118
--- /dev/null
+++ b/docs/basics/101-134-summary.rst
@@ -0,0 +1,57 @@
+.. _summary_containers:
+
+Summary
+-------
+
+The last two sections have first of all extended your knowledge on dataset nesting:
+
+- When subdatasets are created or installed, they are registered to the superdataset
+ in their current version state (as identified by their most recent commit's hash).
+ For a freshly created subdatasets, the most recent commit is at the same time its
+ first commit.
+
+- Once the subdataset evolves, the superdataset recognizes this as a ``modification``
+ of the subdatasets version state. If you want to record this, you need to
+ :command:`save` it in the superdataset::
+
+ $ datalad save -m "a short summary of changes in subds"
+
+But more than nesting concepts, they have also extended your knowledge on
+reproducible analyses with :command:`datalad run` and you have experienced
+for yourself why and how software containers can go hand-in-hand with DataLad:
+
+- A software container encapsulates a complete software environment, independent
+ from the environment of the computer it runs on. This allows you to create or
+ use secluded software and also share it together with your analysis to ensure
+ computational reproducibility.
+
+- The command :command:`datalad containers-add` registers an Image from a path or
+ url to your dataset.
+
+- If you use :command:`datalad containers-run` instead of :command:`datalad run`,
+ you can reproducibly execute a command of your choice *within* the software
+ environment.
+
+- A :command:`datalad rerun` of a commit produced with :command:`datalad containers-run`
+ will re-execute the command in the same software environment.
+
+Now what can I do with it?
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For one, you will not be surprised if you ever see a subdataset being shown as
+``modified`` by :command:`datalad status`: You now know that if a subdataset
+evolves, it's most recent state needs to be explicitly saved to the superdatasets
+history.
+
+On a different matter, you are now able to capture and share analysis provenance that
+includes the relevant software environment. This does not only make your analyses
+projects automatically reproducible, but automatically *computationally* reproducible -
+you can make sure that your analyses runs on any computer with Singularity,
+regardless of the software environment on this computer. Even if you are unsure how you can wrap up an
+environment into a software container Image at this point, you could make use of
+hundreds of publicly available Images on `Singularity-Hub `_ and
+`Docker-Hub `_.
+
+With this, you have also gotten a first glimpse into an extension of DataLad: A
+Python module you can install with Python package managers such as ``pip`` that
+extends DataLad's functionality.
diff --git a/docs/basics/101-144-intro_extensions.rst b/docs/basics/101-144-intro_extensions.rst
new file mode 100644
index 000000000..e4c6a3422
--- /dev/null
+++ b/docs/basics/101-144-intro_extensions.rst
@@ -0,0 +1,57 @@
+.. _extensions_intro:
+
+DataLad's extensions
+--------------------
+
+The commands DataLad provides cover a broad range of domain-agnostic use cases.
+However, there are extension packages that can add (domain-specific)
+functionality and new commands.
+
+Such extensions are shipped as separate Python packages, and are *not* included in
+DataLad itself. Instead, users with the need for a particular extension can
+install the extension package -- either on top of DataLad if DataLad is already
+installed, or on its own (the extension will then pull in DataLad core
+automatically, with no need to first or simultaneously install DataLad itself
+explicitly). The installation is done with
+standard Python package managers, such as :term:`pip`, and beyond installation
+of the package, no additional setup is required.
+
+Among others (a full list can be found on `PyPi `_),
+the following DataLad extensions are available:
+
+.. list-table::
+ :widths: 50 100
+ :header-rows: 1
+
+ * - Extension name
+ - Description
+ * - `DataLad Container `_
+ - Equips DataLad's :command:`run`/:command:`rerun` functionality with
+ the ability to transparently execute commands in containerized
+ computational environments. The section :ref:`containersrun` demonstrates
+ how this extension can be used, as well as the usecase :ref:`usecase_reproduce_neuroimg`.
+ * - `DataLad Neuroimaging `_
+ - Metadata extraction support for a range of standards common to
+ neuroimaging data. The usecase :ref:`usecase_reproduce_neuroimg` demonstrates
+ how this extension can be used.
+ * - `DataLad Metalad `_
+ - Equips DataLad with an alternative command suite and advanced tooling
+ for metadata handling (extraction, aggregation, reporting).
+
+ .. todo::
+
+ once section on metadata is done, link it here
+
+To install a DataLad extension, use
+
+.. code-block:: bash
+
+ $ pip install
+
+such as in
+
+.. code-block:: bash
+
+ $ pip install datalad-container
+
+Afterwards, the new DataLad functionality the extension provides is readily available.
\ No newline at end of file
diff --git a/docs/basics/_examples/DL-101-101-103 b/docs/basics/_examples/DL-101-101-103
index 1d6d17cd1..8ed885834 100644
--- a/docs/basics/_examples/DL-101-101-103
+++ b/docs/basics/_examples/DL-101-101-103
@@ -1,12 +1,12 @@
$ git log
-commit 758f0af5a5d8865db0f8aac4717d8fa93771d8a4
+commit 6c2e4854217a5cbb06eb9b3d0c476573ee2b3ced
Author: Elena Piscopia
-Date: Mon Nov 18 10:49:52 2019 +0100
+Date: Wed Dec 4 16:21:12 2019 +0100
Instruct annex to add text files to Git
-commit 715acb08af2fdab8d901180c3d9985a5335b0584
+commit 623d3f641b8c6e948a036a7be9ec4f056d1ae024
Author: Elena Piscopia
-Date: Mon Nov 18 10:49:52 2019 +0100
+Date: Wed Dec 4 16:21:12 2019 +0100
[DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-102-103 b/docs/basics/_examples/DL-101-102-103
index 935d1f3ac..238150f7b 100644
--- a/docs/basics/_examples/DL-101-102-103
+++ b/docs/basics/_examples/DL-101-102-103
@@ -3,5 +3,5 @@ $ wget https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01
$ wget https://www.gitbook.com/download/pdf/book/swaroopch/byte-of-python -O byte-of-python.pdf
# get back into the root of the dataset
$ cd ../
-2019-11-18 10:50:31 URL:https://vorboss.dl.sourceforge.net/project/linuxcommand/TLCL/19.01/TLCL-19.01.pdf [2120211/2120211] -> "TLCL.pdf" [1]
-2019-11-18 10:50:35 URL:https://legacy.gitbook.com/download/pdf/book/swaroopch/byte-of-python [4407669] -> "byte-of-python.pdf" [1]
+2019-12-04 16:21:19 URL:https://netcologne.dl.sourceforge.net/project/linuxcommand/TLCL/19.01/TLCL-19.01.pdf [2120211/2120211] -> "TLCL.pdf" [1]
+2019-12-04 16:21:21 URL:https://legacy.gitbook.com/download/pdf/book/swaroopch/byte-of-python [4407669] -> "byte-of-python.pdf" [1]
diff --git a/docs/basics/_examples/DL-101-102-107 b/docs/basics/_examples/DL-101-102-107
index fe7591bac..2e0db66ba 100644
--- a/docs/basics/_examples/DL-101-102-107
+++ b/docs/basics/_examples/DL-101-102-107
@@ -1,7 +1,7 @@
$ git log -p -n 1
-commit 464b1e50a588101cff01de9d0a95ad1f7cfc0457
+commit c2dcdaaf0107c3aceac2fc430f8e28da257434d1
Author: Elena Piscopia
-Date: Mon Nov 18 10:50:36 2019 +0100
+Date: Wed Dec 4 16:21:22 2019 +0100
add books on Python and Unix to read later
diff --git a/docs/basics/_examples/DL-101-102-108 b/docs/basics/_examples/DL-101-102-108
index 92b366f4d..1706ccf4e 100644
--- a/docs/basics/_examples/DL-101-102-108
+++ b/docs/basics/_examples/DL-101-102-108
@@ -1,4 +1,4 @@
$ cd books
$ wget https://github.com/progit/progit2/releases/download/2.1.154/progit.pdf
$ cd ../
-2019-11-18 10:51:14 URL:https://github-production-release-asset-2e65be.s3.amazonaws.com/15400220/57552a00-9a49-11e9-9144-d9607ed4c2db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20191118%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191118T095037Z&X-Amz-Expires=300&X-Amz-Signature=ee3c1f736354cc22e799692c8f5ffe9a7501eac269b98a4f0d915e1d08264530&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dprogit.pdf&response-content-type=application%2Foctet-stream [12465653/12465653] -> "progit.pdf" [1]
+2019-12-04 16:21:24 URL:https://github-production-release-asset-2e65be.s3.amazonaws.com/15400220/57552a00-9a49-11e9-9144-d9607ed4c2db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20191204%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191204T152122Z&X-Amz-Expires=300&X-Amz-Signature=66df788d2f7db5a587cd679928904ddf3735912c6589aa767a65fdb322422ec5&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dprogit.pdf&response-content-type=application%2Foctet-stream [12465653/12465653] -> "progit.pdf" [1]
diff --git a/docs/basics/_examples/DL-101-102-111 b/docs/basics/_examples/DL-101-102-111
index 2678b3f23..405300987 100644
--- a/docs/basics/_examples/DL-101-102-111
+++ b/docs/basics/_examples/DL-101-102-111
@@ -1,6 +1,6 @@
# lets make the output a bit more concise with the --oneline option
$ git log --oneline
-8d6a681 add reference book about git
-464b1e5 add books on Python and Unix to read later
-758f0af Instruct annex to add text files to Git
-715acb0 [DATALAD] new dataset
+3d3987b add reference book about git
+c2dcdaa add books on Python and Unix to read later
+6c2e485 Instruct annex to add text files to Git
+623d3f6 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-103-107 b/docs/basics/_examples/DL-101-103-107
index 69b27d27d..fa3c87deb 100644
--- a/docs/basics/_examples/DL-101-103-107
+++ b/docs/basics/_examples/DL-101-103-107
@@ -1,7 +1,7 @@
$ git log -p -n 2
-commit 84ce7c5a1a47f2ff9b27b7e9865c269d0d46eee8
+commit c56f7cb5c0637dee0ad15c5e0d99e68e1d7fd4f5
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:15 2019 +0100
+Date: Wed Dec 4 16:21:25 2019 +0100
add note on datalad save
@@ -18,9 +18,9 @@ index 3a7a1fe..bfa64d7 100644
+Always use informative, concise commit messages.
+
-commit d792dfb3711a31f407dad8705a3f3283372844bf
+commit 242271452e13ca4f06e578b82788099a1317c158
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:15 2019 +0100
+Date: Wed Dec 4 16:21:25 2019 +0100
Add notes on datalad create
diff --git a/docs/basics/_examples/DL-101-106-101 b/docs/basics/_examples/DL-101-106-101
index 268e0d76a..25b6f27c9 100644
--- a/docs/basics/_examples/DL-101-106-101
+++ b/docs/basics/_examples/DL-101-106-101
@@ -1,7 +1,7 @@
$ git log -p -n 2
-commit fd5cbf6987e377b5a38c4f4df304c22da8d6b597
+commit 8db7558a987c679de83e63788611cf2ff34143e9
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:29 2019 +0100
+Date: Wed Dec 4 16:21:39 2019 +0100
Add note on datalad install
@@ -20,9 +20,9 @@ index bfa64d7..6d8cdce 100644
+root of the superdataset with the '-d' option.
+
-commit d4b91a53f95557adc4b78521af5b131c02fc35f6
+commit ab0b11f4292c900b81f633cda09ee8bf749195e8
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:18 2019 +0100
+Date: Wed Dec 4 16:21:27 2019 +0100
[DATALAD] Recorded changes
@@ -44,9 +44,9 @@ index 0000000..dcc34fb
@@ -0,0 +1 @@
+Subproject commit dcc34fbe669b06ced84ced381ba0db21cf5e665f
-commit 84ce7c5a1a47f2ff9b27b7e9865c269d0d46eee8
+commit c56f7cb5c0637dee0ad15c5e0d99e68e1d7fd4f5
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:15 2019 +0100
+Date: Wed Dec 4 16:21:25 2019 +0100
add note on datalad save
@@ -63,9 +63,9 @@ index 3a7a1fe..bfa64d7 100644
+Always use informative, concise commit messages.
+
-commit d792dfb3711a31f407dad8705a3f3283372844bf
+commit 242271452e13ca4f06e578b82788099a1317c158
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:15 2019 +0100
+Date: Wed Dec 4 16:21:25 2019 +0100
Add notes on datalad create
@@ -79,9 +79,9 @@ index 0000000..3a7a1fe
+The dataset is created empty
+
-commit 8d6a681c2145aacaebf4855f675e892355560640
+commit 3d3987be908a115c4cd044705af0d51a25e2f47d
Author: Elena Piscopia
-Date: Mon Nov 18 10:51:14 2019 +0100
+Date: Wed Dec 4 16:21:24 2019 +0100
add reference book about git
@@ -94,9 +94,9 @@ index 0000000..c5d2ab2
+../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf
\ No newline at end of file
-commit 464b1e50a588101cff01de9d0a95ad1f7cfc0457
+commit c2dcdaaf0107c3aceac2fc430f8e28da257434d1
Author: Elena Piscopia
-Date: Mon Nov 18 10:50:36 2019 +0100
+Date: Wed Dec 4 16:21:22 2019 +0100
add books on Python and Unix to read later
@@ -117,9 +117,9 @@ index 0000000..9a812a0
+../.git/annex/objects/ZZ/f1/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf
\ No newline at end of file
-commit 758f0af5a5d8865db0f8aac4717d8fa93771d8a4
+commit 6c2e4854217a5cbb06eb9b3d0c476573ee2b3ced
Author: Elena Piscopia
-Date: Mon Nov 18 10:49:52 2019 +0100
+Date: Wed Dec 4 16:21:12 2019 +0100
Instruct annex to add text files to Git
@@ -136,9 +136,9 @@ index c3aaefe..b223f34 100644
+* annex.largefiles=(not(mimetype=text/*)and(largerthan=0))
\ No newline at end of file
-commit 715acb08af2fdab8d901180c3d9985a5335b0584
+commit 623d3f641b8c6e948a036a7be9ec4f056d1ae024
Author: Elena Piscopia
-Date: Mon Nov 18 10:49:52 2019 +0100
+Date: Wed Dec 4 16:21:12 2019 +0100
[DATALAD] new dataset
@@ -155,12 +155,12 @@ index 0000000..b540820
\ No newline at end of file
diff --git a/.datalad/config b/.datalad/config
new file mode 100644
-index 0000000..ea9d4d6
+index 0000000..95115e5
--- /dev/null
+++ b/.datalad/config
@@ -0,0 +1,2 @@
+[datalad "dataset"]
-+ id = c4755e2a-09e8-11ea-98f1-e86a64c8054c
++ id = b47220ee-16a9-11ea-b652-d0c637c523bc
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..c3aaefe
diff --git a/docs/basics/_examples/DL-101-108-104 b/docs/basics/_examples/DL-101-108-104
index 62a99527f..f92f6b8c0 100644
--- a/docs/basics/_examples/DL-101-108-104
+++ b/docs/basics/_examples/DL-101-108-104
@@ -1,4 +1,4 @@
-$ datalad save -m "Add simple script to write a list of podcast speakers and titles"
+$ datalad save -m "Add short script to write a list of podcast speakers and titles"
add(ok): code/list_titles.sh (file)
save(ok): . (dataset)
action summary:
diff --git a/docs/basics/_examples/DL-101-108-106 b/docs/basics/_examples/DL-101-108-106
index 60692351a..bb82894b9 100644
--- a/docs/basics/_examples/DL-101-108-106
+++ b/docs/basics/_examples/DL-101-108-106
@@ -1,7 +1,7 @@
$ git log -p -n 1
-commit c64173fe0a41bac4865c71f814bcbb84cd1c8146
+commit 281a9a48a1451e85c5a9284b6b908c93a987654c
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:30 2019 +0100
+Date: Wed Dec 4 16:21:41 2019 +0100
[DATALAD RUNCMD] create a list of podcast titles
@@ -9,7 +9,7 @@ Date: Mon Nov 18 10:52:30 2019 +0100
{
"chain": [],
"cmd": "bash code/list_titles.sh > recordings/podcasts.tsv",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [],
diff --git a/docs/basics/_examples/DL-101-108-108 b/docs/basics/_examples/DL-101-108-108
index 3a485e03d..3480ce1a3 100644
--- a/docs/basics/_examples/DL-101-108-108
+++ b/docs/basics/_examples/DL-101-108-108
@@ -1,11 +1,11 @@
$ git log --oneline
-c64173f [DATALAD RUNCMD] create a list of podcast titles
-9d578af Add simple script to write a list of podcast speakers and titles
-fd5cbf6 Add note on datalad install
-d4b91a5 [DATALAD] Recorded changes
-84ce7c5 add note on datalad save
-d792dfb Add notes on datalad create
-8d6a681 add reference book about git
-464b1e5 add books on Python and Unix to read later
-758f0af Instruct annex to add text files to Git
-715acb0 [DATALAD] new dataset
+281a9a4 [DATALAD RUNCMD] create a list of podcast titles
+61f3a4d Add short script to write a list of podcast speakers and titles
+8db7558 Add note on datalad install
+ab0b11f [DATALAD] Recorded changes
+c56f7cb add note on datalad save
+2422714 Add notes on datalad create
+3d3987b add reference book about git
+c2dcdaa add books on Python and Unix to read later
+6c2e485 Instruct annex to add text files to Git
+623d3f6 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-108-113 b/docs/basics/_examples/DL-101-108-113
index b5e899e8e..8edee1219 100644
--- a/docs/basics/_examples/DL-101-108-113
+++ b/docs/basics/_examples/DL-101-108-113
@@ -1,13 +1,13 @@
$ git log -n 2
-commit 854a655e0fb6e822739a8e83c2460fe58c107204
+commit 16787003e96f58235c73d4865f899fe2fdd85b2f
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:32 2019 +0100
+Date: Wed Dec 4 16:21:42 2019 +0100
BF: list both directories content
-commit c64173fe0a41bac4865c71f814bcbb84cd1c8146
+commit 281a9a48a1451e85c5a9284b6b908c93a987654c
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:30 2019 +0100
+Date: Wed Dec 4 16:21:41 2019 +0100
[DATALAD RUNCMD] create a list of podcast titles
@@ -15,7 +15,7 @@ Date: Mon Nov 18 10:52:30 2019 +0100
{
"chain": [],
"cmd": "bash code/list_titles.sh > recordings/podcasts.tsv",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [],
diff --git a/docs/basics/_examples/DL-101-108-114 b/docs/basics/_examples/DL-101-108-114
index 91a031085..adfed2e41 100644
--- a/docs/basics/_examples/DL-101-108-114
+++ b/docs/basics/_examples/DL-101-108-114
@@ -1,5 +1,5 @@
-$ datalad rerun c64173fe0a41bac4865c71f814bcbb84cd1c8146
+$ datalad rerun 281a9a48a1451e85c5a9284b6b908c93a987654c
[INFO] == Command start (output follows) =====
[INFO] == Command exit (modification check follows) =====
add(ok): recordings/podcasts.tsv (file)
diff --git a/docs/basics/_examples/DL-101-108-115 b/docs/basics/_examples/DL-101-108-115
index 2058ba2b4..86d0c84f1 100644
--- a/docs/basics/_examples/DL-101-108-115
+++ b/docs/basics/_examples/DL-101-108-115
@@ -1,17 +1,17 @@
$ git log -n 1
-commit 406b44c6474d167fc9e497cc807c415f3a810e14
+commit b5497627adc2bac4cfba3de27cfea371f1447f6c
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:33 2019 +0100
+Date: Wed Dec 4 16:21:43 2019 +0100
[DATALAD RUNCMD] create a list of podcast titles
=== Do not change lines below ===
{
"chain": [
- "c64173fe0a41bac4865c71f814bcbb84cd1c8146"
+ "281a9a48a1451e85c5a9284b6b908c93a987654c"
],
"cmd": "bash code/list_titles.sh > recordings/podcasts.tsv",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [],
diff --git a/docs/basics/_examples/DL-101-108-120 b/docs/basics/_examples/DL-101-108-120
index 76ca906cf..6df34276a 100644
--- a/docs/basics/_examples/DL-101-108-120
+++ b/docs/basics/_examples/DL-101-108-120
@@ -1,17 +1,17 @@
$ git log -- recordings/podcasts.tsv
-commit 406b44c6474d167fc9e497cc807c415f3a810e14
+commit b5497627adc2bac4cfba3de27cfea371f1447f6c
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:33 2019 +0100
+Date: Wed Dec 4 16:21:43 2019 +0100
[DATALAD RUNCMD] create a list of podcast titles
=== Do not change lines below ===
{
"chain": [
- "c64173fe0a41bac4865c71f814bcbb84cd1c8146"
+ "281a9a48a1451e85c5a9284b6b908c93a987654c"
],
"cmd": "bash code/list_titles.sh > recordings/podcasts.tsv",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [],
@@ -20,9 +20,9 @@ Date: Mon Nov 18 10:52:33 2019 +0100
}
^^^ Do not change lines above ^^^
-commit c64173fe0a41bac4865c71f814bcbb84cd1c8146
+commit 281a9a48a1451e85c5a9284b6b908c93a987654c
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:30 2019 +0100
+Date: Wed Dec 4 16:21:41 2019 +0100
[DATALAD RUNCMD] create a list of podcast titles
@@ -30,7 +30,7 @@ Date: Mon Nov 18 10:52:30 2019 +0100
{
"chain": [],
"cmd": "bash code/list_titles.sh > recordings/podcasts.tsv",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [],
diff --git a/docs/basics/_examples/DL-101-112-109 b/docs/basics/_examples/DL-101-112-109
index 012c58354..b02d8922e 100644
--- a/docs/basics/_examples/DL-101-112-109
+++ b/docs/basics/_examples/DL-101-112-109
@@ -1,7 +1,7 @@
$ git log -p -n 2
-commit f609f69378303bfda1e6614d573ae59226dee8d5
+commit 199587fa10a7ea54885d3139b4d0ef042076da0d
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:43 2019 +0100
+Date: Wed Dec 4 16:21:52 2019 +0100
add note on clean datasets
@@ -21,9 +21,9 @@ index d1ba8fc..8f0124f 100644
+to the files listed with --output flags.
+
-commit 009c66d0f2b2a8890674e5e455c43bb9232c9c48
+commit dd726a625ba18ac0a25b744adf5feab33d9d6866
Author: Elena Piscopia
-Date: Mon Nov 18 10:52:42 2019 +0100
+Date: Wed Dec 4 16:21:51 2019 +0100
[DATALAD RUNCMD] Resize logo for slides
@@ -31,7 +31,7 @@ Date: Mon Nov 18 10:52:42 2019 +0100
{
"chain": [],
"cmd": "convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg",
- "dsid": "c4755e2a-09e8-11ea-98f1-e86a64c8054c",
+ "dsid": "b47220ee-16a9-11ea-b652-d0c637c523bc",
"exit": 0,
"extra_inputs": [],
"inputs": [
diff --git a/docs/basics/_examples/DL-101-114-101 b/docs/basics/_examples/DL-101-114-101
index 9dcbdd9f3..20e7d1e4d 100644
--- a/docs/basics/_examples/DL-101-114-101
+++ b/docs/basics/_examples/DL-101-114-101
@@ -1,22 +1,22 @@
$ git log --reverse --oneline
-715acb0 [DATALAD] new dataset
-758f0af Instruct annex to add text files to Git
-464b1e5 add books on Python and Unix to read later
-8d6a681 add reference book about git
-d792dfb Add notes on datalad create
-84ce7c5 add note on datalad save
-d4b91a5 [DATALAD] Recorded changes
-fd5cbf6 Add note on datalad install
-9d578af Add simple script to write a list of podcast speakers and titles
-c64173f [DATALAD RUNCMD] create a list of podcast titles
-854a655 BF: list both directories content
-406b44c [DATALAD RUNCMD] create a list of podcast titles
-e6e14a7 add note datalad and git diff
-15e7810 add note on basic datalad run and datalad rerun
-771909d [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
-dc84ec4 resized picture by hand
-054b821 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
-3b21c7d add additional notes on run options
-5e96512 [DATALAD RUNCMD] Resize logo for slides
-009c66d [DATALAD RUNCMD] Resize logo for slides
-f609f69 add note on clean datasets
+623d3f6 [DATALAD] new dataset
+6c2e485 Instruct annex to add text files to Git
+c2dcdaa add books on Python and Unix to read later
+3d3987b add reference book about git
+2422714 Add notes on datalad create
+c56f7cb add note on datalad save
+ab0b11f [DATALAD] Recorded changes
+8db7558 Add note on datalad install
+61f3a4d Add short script to write a list of podcast speakers and titles
+281a9a4 [DATALAD RUNCMD] create a list of podcast titles
+1678700 BF: list both directories content
+b549762 [DATALAD RUNCMD] create a list of podcast titles
+09c0513 add note datalad and git diff
+aadf74e add note on basic datalad run and datalad rerun
+86be52e [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
+bd42809 resized picture by hand
+3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
+b08d657 add additional notes on run options
+e4dd212 [DATALAD RUNCMD] Resize logo for slides
+dd726a6 [DATALAD RUNCMD] Resize logo for slides
+199587f add note on clean datasets
diff --git a/docs/basics/_examples/DL-101-115-103 b/docs/basics/_examples/DL-101-115-103
index 951b878a6..e2d8f8090 100644
--- a/docs/basics/_examples/DL-101-115-103
+++ b/docs/basics/_examples/DL-101-115-103
@@ -1,7 +1,7 @@
$ ls -lah
total 20K
-drwxr-xr-x 2 adina adina 4.0K Nov 18 10:51 .
-drwxr-xr-x 7 adina adina 4.0K Nov 18 10:52 ..
-lrwxrwxrwx 1 adina adina 131 Nov 18 10:50 byte-of-python.pdf -> ../.git/annex/objects/ZZ/f1/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf
+drwxr-xr-x 2 adina adina 4.0K Dec 4 16:21 .
+drwxr-xr-x 7 adina adina 4.0K Dec 4 16:21 ..
+lrwxrwxrwx 1 adina adina 131 Dec 4 16:21 byte-of-python.pdf -> ../.git/annex/objects/ZZ/f1/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf
lrwxrwxrwx 1 adina adina 133 Jun 29 17:39 progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf
lrwxrwxrwx 1 adina adina 131 Jan 28 2019 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
diff --git a/docs/basics/_examples/DL-101-116-105 b/docs/basics/_examples/DL-101-116-105
index cbbf57f11..d4ebc8d2d 100644
--- a/docs/basics/_examples/DL-101-116-105
+++ b/docs/basics/_examples/DL-101-116-105
@@ -1,4 +1,4 @@
$ git annex whereis books/TLCL.pdf
whereis books/TLCL.pdf (1 copy)
- a5e9c638-cc6b-4c27-99a5-14802c8a6898 -- course on DataLad-101 on my private Laptop [origin]
+ fdbcfeff-5296-4e58-84dc-913343e50f4d -- course on DataLad-101 on my private Laptop [origin]
ok
diff --git a/docs/basics/_examples/DL-101-117-101 b/docs/basics/_examples/DL-101-117-101
index 2221cf29c..bc2be8a2e 100644
--- a/docs/basics/_examples/DL-101-117-101
+++ b/docs/basics/_examples/DL-101-117-101
@@ -6,7 +6,7 @@ $ cd recordings/longnow
$ git annex whereis Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3
whereis Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 (3 copies)
00000000-0000-0000-0000-000000000001 -- web
- 1f1f78d5-c98d-4435-9f81-8bad94145ed5 -- me@muninn:~/dl-101/DataLad-101/recordings/longnow [origin]
+ 740557bc-bafe-41ed-b4ae-09cd5e5cbb03 -- me@muninn:~/dl-101/DataLad-101/recordings/longnow [origin]
da3bf937-5bd2-43ea-a07b-bcbe71f3b875 -- mih@medusa:/tmp/seminars-on-longterm-thinking
web: http://podcast.longnow.org/salt/redirect/salt-020031114-eno-podcast.mp3
diff --git a/docs/basics/_examples/DL-101-118-102 b/docs/basics/_examples/DL-101-118-102
index e660877a2..98954d804 100644
--- a/docs/basics/_examples/DL-101-118-102
+++ b/docs/basics/_examples/DL-101-118-102
@@ -1,23 +1,23 @@
# lets view the history
$ git log --oneline
-f609f69 add note on clean datasets
-009c66d [DATALAD RUNCMD] Resize logo for slides
-5e96512 [DATALAD RUNCMD] Resize logo for slides
-3b21c7d add additional notes on run options
-054b821 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
-dc84ec4 resized picture by hand
-771909d [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
-15e7810 add note on basic datalad run and datalad rerun
-e6e14a7 add note datalad and git diff
-406b44c [DATALAD RUNCMD] create a list of podcast titles
-854a655 BF: list both directories content
-c64173f [DATALAD RUNCMD] create a list of podcast titles
-9d578af Add simple script to write a list of podcast speakers and titles
-fd5cbf6 Add note on datalad install
-d4b91a5 [DATALAD] Recorded changes
-84ce7c5 add note on datalad save
-d792dfb Add notes on datalad create
-8d6a681 add reference book about git
-464b1e5 add books on Python and Unix to read later
-758f0af Instruct annex to add text files to Git
-715acb0 [DATALAD] new dataset
+199587f add note on clean datasets
+dd726a6 [DATALAD RUNCMD] Resize logo for slides
+e4dd212 [DATALAD RUNCMD] Resize logo for slides
+b08d657 add additional notes on run options
+3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
+bd42809 resized picture by hand
+86be52e [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
+aadf74e add note on basic datalad run and datalad rerun
+09c0513 add note datalad and git diff
+b549762 [DATALAD RUNCMD] create a list of podcast titles
+1678700 BF: list both directories content
+281a9a4 [DATALAD RUNCMD] create a list of podcast titles
+61f3a4d Add short script to write a list of podcast speakers and titles
+8db7558 Add note on datalad install
+ab0b11f [DATALAD] Recorded changes
+c56f7cb add note on datalad save
+2422714 Add notes on datalad create
+3d3987b add reference book about git
+c2dcdaa add books on Python and Unix to read later
+6c2e485 Instruct annex to add text files to Git
+623d3f6 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-118-103 b/docs/basics/_examples/DL-101-118-103
index fb296346f..a7f26b112 100644
--- a/docs/basics/_examples/DL-101-118-103
+++ b/docs/basics/_examples/DL-101-118-103
@@ -1,5 +1,5 @@
-$ datalad rerun 009c66d0f2b2a8890674e5e455c43bb9232c9c48
+$ datalad rerun dd726a625ba18ac0a25b744adf5feab33d9d6866
[INFO] Making sure inputs are available (this may take some time)
[WARNING] no content present; cannot unlock [unlock(/home/me/dl-101/mock_user/DataLad-101/recordings/salt_logo_small.jpg)]
[INFO] == Command start (output follows) =====
diff --git a/docs/basics/_examples/DL-101-121-103 b/docs/basics/_examples/DL-101-121-103
index 71f58d945..c591e7270 100644
--- a/docs/basics/_examples/DL-101-121-103
+++ b/docs/basics/_examples/DL-101-121-103
@@ -1,8 +1,7 @@
$ git log -n 1 -p
-
-commit 834615c670935bb5cb682ef301c6167d6786f02f
+commit aca517764b330a994c8523d74dd5320a7e54e3e8
Author: Elena Piscopia
-Date: Mon Nov 18 10:53:01 2019 +0100
+Date: Wed Dec 4 16:22:01 2019 +0100
Include nesting demo from datalad website
diff --git a/docs/basics/_examples/DL-101-121-112 b/docs/basics/_examples/DL-101-121-112
index f2d6047ae..4021bab28 100644
--- a/docs/basics/_examples/DL-101-121-112
+++ b/docs/basics/_examples/DL-101-121-112
@@ -1,28 +1,27 @@
$ git log --oneline
-db8aa3a Merge remote-tracking branch 'refs/remotes/roommate/master'
-834615c Include nesting demo from datalad website
-0e85c3e add note about datalad update
-2e7a3ad add note on git annex whereis
-73f44c4 add note about installing from paths and recursive installations
-dd6fef5 add note on clean datasets
-d9d0872 [DATALAD RUNCMD] Resize logo for slides
-36a9cfd [DATALAD RUNCMD] Resize logo for slides
-244c234 add additional notes on run options
-e3277e9 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
-257130b resized picture by hand
-6e624f5 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
-327fd83 add note on basic datalad run and datalad rerun
-4e3fb6e add note datalad and git diff
-d26a29b [DATALAD RUNCMD] create a list of podcast titles
-d04c4af BF: list both directories content
-ecde4e4 [DATALAD RUNCMD] create a list of podcast titles
-ef8b726 Add simple script to write a list of podcast speakers and titles
-e61c229 Add note on datalad install
-49e85d1 [DATALAD] Recorded changes
-5f98f2b add note on datalad save
-b72b237 Add notes on datalad create
-dac2fa7 add reference book about git
-9a6fb63 add books on Python and Unix to read later
-1a45fd4 Instruct annex to add text files to Git
-e85b950 [DATALAD] new dataset
-
+c15ea3e Merge remote-tracking branch 'refs/remotes/roommate/master'
+aca5177 Include nesting demo from datalad website
+1291140 add note about datalad update
+1b07d87 add note on git annex whereis
+ad17112 add note about installing from paths and recursive installations
+199587f add note on clean datasets
+dd726a6 [DATALAD RUNCMD] Resize logo for slides
+e4dd212 [DATALAD RUNCMD] Resize logo for slides
+b08d657 add additional notes on run options
+3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
+bd42809 resized picture by hand
+86be52e [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
+aadf74e add note on basic datalad run and datalad rerun
+09c0513 add note datalad and git diff
+b549762 [DATALAD RUNCMD] create a list of podcast titles
+1678700 BF: list both directories content
+281a9a4 [DATALAD RUNCMD] create a list of podcast titles
+61f3a4d Add short script to write a list of podcast speakers and titles
+8db7558 Add note on datalad install
+ab0b11f [DATALAD] Recorded changes
+c56f7cb add note on datalad save
+2422714 Add notes on datalad create
+3d3987b add reference book about git
+c2dcdaa add books on Python and Unix to read later
+6c2e485 Instruct annex to add text files to Git
+623d3f6 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-122-101 b/docs/basics/_examples/DL-101-122-101
index cfa33df00..e01bc1bb9 100644
--- a/docs/basics/_examples/DL-101-122-101
+++ b/docs/basics/_examples/DL-101-122-101
@@ -5,7 +5,7 @@ $ cat .git/config
bare = false
logallrefupdates = true
[annex]
- uuid = a5e9c638-cc6b-4c27-99a5-14802c8a6898
+ uuid = fdbcfeff-5296-4e58-84dc-913343e50f4d
version = 5
backends = MD5E
[submodule "recordings/longnow"]
@@ -14,5 +14,5 @@ $ cat .git/config
[remote "roommate"]
url = ../mock_user/DataLad-101
fetch = +refs/heads/*:refs/remotes/roommate/*
- annex-uuid = 838f9159-3b3d-4dd7-86b0-7dd7e51b05ed
+ annex-uuid = 0cfd3714-d3a7-45ab-8e70-2f741f23e8ed
annex-ignore = false
diff --git a/docs/basics/_examples/DL-101-122-103 b/docs/basics/_examples/DL-101-122-103
index 366348874..c68b5abfc 100644
--- a/docs/basics/_examples/DL-101-122-103
+++ b/docs/basics/_examples/DL-101-122-103
@@ -6,7 +6,7 @@ $ cat .git/config
logallrefupdates = true
editor = nano
[annex]
- uuid = a5e9c638-cc6b-4c27-99a5-14802c8a6898
+ uuid = fdbcfeff-5296-4e58-84dc-913343e50f4d
version = 5
backends = MD5E
[submodule "recordings/longnow"]
@@ -15,5 +15,5 @@ $ cat .git/config
[remote "roommate"]
url = ../mock_user/DataLad-101
fetch = +refs/heads/*:refs/remotes/roommate/*
- annex-uuid = 838f9159-3b3d-4dd7-86b0-7dd7e51b05ed
+ annex-uuid = 0cfd3714-d3a7-45ab-8e70-2f741f23e8ed
annex-ignore = false
diff --git a/docs/basics/_examples/DL-101-123-105 b/docs/basics/_examples/DL-101-123-105
index 59b332385..c9a3c5747 100644
--- a/docs/basics/_examples/DL-101-123-105
+++ b/docs/basics/_examples/DL-101-123-105
@@ -1,3 +1,3 @@
$ cat .datalad/config
[datalad "dataset"]
- id = 7256f1ae-000f-11ea-97b1-d0c637c523bc
+ id = b47220ee-16a9-11ea-b652-d0c637c523bc
diff --git a/docs/basics/_examples/DL-101-124-101 b/docs/basics/_examples/DL-101-124-101
index e0e3417d0..a05291e15 100644
--- a/docs/basics/_examples/DL-101-124-101
+++ b/docs/basics/_examples/DL-101-124-101
@@ -1,4 +1,5 @@
$ datalad run-procedure --discover
+cfg_hirni (../../../adina/env/handbook/lib/python3.7/site-packages/datalad_hirni/resources/procedures/cfg_hirni.py) [python_script]
cfg_bids (../../../adina/repos/datalad-neuroimaging/datalad_neuroimaging/resources/procedures/cfg_bids.py) [python_script]
cfg_metadatatypes (../../../adina/repos/datalad/datalad/resources/procedures/cfg_metadatatypes.py) [python_script]
cfg_text2git (../../../adina/repos/datalad/datalad/resources/procedures/cfg_text2git.py) [python_script]
diff --git a/docs/basics/_examples/DL-101-125-106 b/docs/basics/_examples/DL-101-125-106
deleted file mode 100644
index d2ef1c299..000000000
--- a/docs/basics/_examples/DL-101-125-106
+++ /dev/null
@@ -1,3 +0,0 @@
-$ cat .datalad/config
-[datalad "dataset"]
- id = c4755e2a-09e8-11ea-98f1-e86a64c8054c
diff --git a/docs/basics/_examples/DL-101-130-106 b/docs/basics/_examples/DL-101-130-106
index cb2b9fbee..8813ad4d1 100644
--- a/docs/basics/_examples/DL-101-130-106
+++ b/docs/basics/_examples/DL-101-130-106
@@ -1,5 +1,6 @@
$ cd ../
$ tree -d
+$ cd midterm_project
.
├── books
├── code
diff --git a/docs/basics/_examples/DL-101-130-107 b/docs/basics/_examples/DL-101-130-107
index b054945a4..e1813e993 100644
--- a/docs/basics/_examples/DL-101-130-107
+++ b/docs/basics/_examples/DL-101-130-107
@@ -9,7 +9,7 @@ from sklearn.metrics import classification_report
data = "input/iris.csv"
-# make sure that the data is obtained (get will also install linked sub-ds!):
+# make sure that the data are obtained (get will also install linked sub-ds!):
dl.get(data)
# prepare the data as a pandas dataframe
diff --git a/docs/basics/_examples/DL-101-130-110 b/docs/basics/_examples/DL-101-130-110
index 73f5f3199..020da785e 100644
--- a/docs/basics/_examples/DL-101-130-110
+++ b/docs/basics/_examples/DL-101-130-110
@@ -1,13 +1,13 @@
$ git show ready4analysis
-commit 789e6b445eac4f2245a05420289bff3e1580e9f7
+commit b0d252c3d692f42687b0fa9635f9cd188e4ecbb2
Author: Elena Piscopia
-Date: Mon Nov 18 16:13:18 2019 +0100
+Date: Wed Dec 4 16:22:11 2019 +0100
add script for kNN classification and plotting
diff --git a/code/script.py b/code/script.py
new file mode 100644
-index 0000000..d82606c
+index 0000000..e43d58e
--- /dev/null
+++ b/code/script.py
@@ -0,0 +1,41 @@
@@ -21,7 +21,7 @@ index 0000000..d82606c
+
+data = "input/iris.csv"
+
-+# make sure that the data is obtained (get will also install linked sub-ds!):
++# make sure that the data are obtained (get will also install linked sub-ds!):
+dl.get(data)
+
+# prepare the data as a pandas dataframe
diff --git a/docs/basics/_examples/DL-101-130-112 b/docs/basics/_examples/DL-101-130-112
index 42a513bcd..9951d9398 100644
--- a/docs/basics/_examples/DL-101-130-112
+++ b/docs/basics/_examples/DL-101-130-112
@@ -1,6 +1,6 @@
$ git log --oneline
-c73efce [DATALAD RUNCMD] analyze iris data with classification analysis
-789e6b4 add script for kNN classification and plotting
-9466bd3 [DATALAD] Recorded changes
-ab62c74 Apply YODA dataset setup
-8d3c887 [DATALAD] new dataset
+a65e1c3 [DATALAD RUNCMD] analyze iris data with classification analysis
+b0d252c add script for kNN classification and plotting
+a4bc6dd [DATALAD] Recorded changes
+b57de50 Apply YODA dataset setup
+f770195 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-130-116 b/docs/basics/_examples/DL-101-130-116
index ca2423833..56f915583 100644
--- a/docs/basics/_examples/DL-101-130-116
+++ b/docs/basics/_examples/DL-101-130-116
@@ -1 +1,2 @@
-$ datalad create-sibling-github -d . -r midtermproject
+
+.: github(-) [https://github.com/adswa/midtermproject.git (git)]
diff --git a/docs/basics/_examples/DL-101-132-101 b/docs/basics/_examples/DL-101-132-101
index 3c204d45f..f4abc9582 100644
--- a/docs/basics/_examples/DL-101-132-101
+++ b/docs/basics/_examples/DL-101-132-101
@@ -1,7 +1,7 @@
$ git log --oneline
-e2b9975 Provide project description
-a44265a [DATALAD RUNCMD] analyze iris data with classification analysis
-6f7ea3e add script for kNN classification and plotting
-aeed9e0 [DATALAD] Recorded changes
-855f0b7 Apply YODA dataset setup
-63e1f68 [DATALAD] new dataset
+b217c8b Provide project description
+a65e1c3 [DATALAD RUNCMD] analyze iris data with classification analysis
+b0d252c add script for kNN classification and plotting
+a4bc6dd [DATALAD] Recorded changes
+b57de50 Apply YODA dataset setup
+f770195 [DATALAD] new dataset
diff --git a/docs/basics/_examples/DL-101-132-110 b/docs/basics/_examples/DL-101-132-110
index 71279a872..0f7f472f7 100644
--- a/docs/basics/_examples/DL-101-132-110
+++ b/docs/basics/_examples/DL-101-132-110
@@ -1,4 +1,4 @@
-$ datalad save -m "finished my midterm project"
+$ datalad save -d . -m "finished my midterm project!" midterm_project
add(ok): midterm_project (file)
save(ok): . (dataset)
action summary:
diff --git a/docs/basics/_examples/DL-101-132-112 b/docs/basics/_examples/DL-101-132-112
index 8a889506e..79ae077ec 100644
--- a/docs/basics/_examples/DL-101-132-112
+++ b/docs/basics/_examples/DL-101-132-112
@@ -1,14 +1,14 @@
$ git log -p -n 1
-commit c260b371c1992bd2b9c8758c0e88ded01ef62d84
+commit c4aaeb2476206ef8e5dc6346bae179eb6875139a
Author: Elena Piscopia
-Date: Fri Nov 29 09:52:55 2019 +0100
+Date: Wed Dec 4 16:22:34 2019 +0100
- finished my midterm project
+ finished my midterm project!
diff --git a/midterm_project b/midterm_project
-index 855f0b7..e2b9975 160000
+index b57de50..b217c8b 160000
--- a/midterm_project
+++ b/midterm_project
@@ -1 +1 @@
--Subproject commit 855f0b757d8ce85f46eacbb24e77a0df3ba30ee0
-+Subproject commit e2b9975103bfcbe7ecec853b1d6771d8d19de8ae
+-Subproject commit b57de50bb54b60d348e0e7af1aab3a01c75f50a3
++Subproject commit b217c8beaa36c19459cbc4ca5b7abbdb4623b61b
diff --git a/docs/basics/_examples/DL-101-133-101 b/docs/basics/_examples/DL-101-133-101
new file mode 100644
index 000000000..2504453f3
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-101
@@ -0,0 +1,9 @@
+# we are in the midterm_project subdataset
+$ datalad containers-add midterm-software --url shub://adswa/resources:1
+add(ok): .datalad/config (file)
+save(ok): . (dataset)
+containers_add(ok): /home/me/dl-101/DataLad-101/midterm_project/.datalad/environments/midterm-software/image (file)
+action summary:
+ add (ok: 1)
+ containers_add (ok: 1)
+ save (ok: 1)
diff --git a/docs/basics/_examples/DL-101-133-102 b/docs/basics/_examples/DL-101-133-102
new file mode 100644
index 000000000..7a546acf9
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-102
@@ -0,0 +1,7 @@
+$ cat .datalad/config
+[datalad "dataset"]
+ id = d62da69a-16a9-11ea-b652-d0c637c523bc
+[datalad "containers.midterm-software"]
+ updateurl = shub://adswa/resources:1
+ image = .datalad/environments/midterm-software/image
+ cmdexec = singularity exec {img} {cmd}
diff --git a/docs/basics/_examples/DL-101-133-103 b/docs/basics/_examples/DL-101-133-103
new file mode 100644
index 000000000..4c226e915
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-103
@@ -0,0 +1,26 @@
+$ git log -n 1 -p
+commit 2344fa6676afcc92b47c7a03bbd4090b7ddabe27
+Author: Elena Piscopia
+Date: Wed Dec 4 16:22:52 2019 +0100
+
+ [DATALAD] Configure containerized environment 'midterm-software'
+
+diff --git a/.datalad/config b/.datalad/config
+index 61c5ac2..651422a 100644
+--- a/.datalad/config
++++ b/.datalad/config
+@@ -1,2 +1,6 @@
+ [datalad "dataset"]
+ id = d62da69a-16a9-11ea-b652-d0c637c523bc
++[datalad "containers.midterm-software"]
++ updateurl = shub://adswa/resources:1
++ image = .datalad/environments/midterm-software/image
++ cmdexec = singularity exec {img} {cmd}
+diff --git a/.datalad/environments/midterm-software/image b/.datalad/environments/midterm-software/image
+new file mode 120000
+index 0000000..800282a
+--- /dev/null
++++ b/.datalad/environments/midterm-software/image
+@@ -0,0 +1 @@
++../../../.git/annex/objects/zJ/8f/MD5E-s232214559--49dcb6ac1a5787636c9897c4d4df7e10/MD5E-s232214559--49dcb6ac1a5787636c9897c4d4df7e10
+\ No newline at end of file
diff --git a/docs/basics/_examples/DL-101-133-104 b/docs/basics/_examples/DL-101-133-104
new file mode 100644
index 000000000..847fad385
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-104
@@ -0,0 +1,19 @@
+$ datalad containers-run -m "rerun analysis in container" \
+ --container-name midterm-software \
+ --input "input/iris.csv" \
+ --output "prediction_report.csv" \
+ --output "pairwise_relationships.png" \
+ "python3 code/script.py"
+[INFO] Making sure inputs are available (this may take some time)
+[INFO] == Command start (output follows) =====
+[INFO] == Command exit (modification check follows) =====
+unlock(ok): pairwise_relationships.png (file)
+unlock(ok): prediction_report.csv (file)
+add(ok): pairwise_relationships.png (file)
+add(ok): prediction_report.csv (file)
+save(ok): . (dataset)
+action summary:
+ add (ok: 2)
+ get (notneeded: 2)
+ save (notneeded: 1, ok: 1)
+ unlock (ok: 2)
diff --git a/docs/basics/_examples/DL-101-133-110 b/docs/basics/_examples/DL-101-133-110
new file mode 100644
index 000000000..15b6b53f9
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-110
@@ -0,0 +1,2 @@
+$ datalad containers-list
+midterm-software -> .datalad/environments/midterm-software/image
diff --git a/docs/basics/_examples/DL-101-133-111 b/docs/basics/_examples/DL-101-133-111
new file mode 100644
index 000000000..6566c7a72
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-111
@@ -0,0 +1,45 @@
+$ git log -p -n 1
+commit 326c92512ab422651717a3869ef9d01e61b5cb61
+Author: Elena Piscopia
+Date: Wed Dec 4 16:22:57 2019 +0100
+
+ [DATALAD RUNCMD] rerun analysis in container
+
+ === Do not change lines below ===
+ {
+ "chain": [],
+ "cmd": "singularity exec .datalad/environments/midterm-software/image python3 code/script.py",
+ "dsid": "d62da69a-16a9-11ea-b652-d0c637c523bc",
+ "exit": 0,
+ "extra_inputs": [
+ ".datalad/environments/midterm-software/image"
+ ],
+ "inputs": [
+ "input/iris.csv"
+ ],
+ "outputs": [
+ "prediction_report.csv",
+ "pairwise_relationships.png"
+ ],
+ "pwd": "."
+ }
+ ^^^ Do not change lines above ^^^
+
+diff --git a/pairwise_relationships.png b/pairwise_relationships.png
+index 2f69f64..6d00014 120000
+--- a/pairwise_relationships.png
++++ b/pairwise_relationships.png
+@@ -1 +1 @@
+-.git/annex/objects/Pz/Xm/MD5E-s175662--8a9a3e225267f327e1671cf6d01b1957.png/MD5E-s175662--8a9a3e225267f327e1671cf6d01b1957.png
+\ No newline at end of file
++.git/annex/objects/z3/23/MD5E-s176597--87d8a72f5f7b1f4f191d0be1bfd15288.png/MD5E-s176597--87d8a72f5f7b1f4f191d0be1bfd15288.png
+\ No newline at end of file
+diff --git a/prediction_report.csv b/prediction_report.csv
+index 42d194b..b46a2d5 120000
+--- a/prediction_report.csv
++++ b/prediction_report.csv
+@@ -1 +1 @@
+-.git/annex/objects/8q/6M/MD5E-s345--a88cab39b1a5ec59ace322225cc88bc9.csv/MD5E-s345--a88cab39b1a5ec59ace322225cc88bc9.csv
+\ No newline at end of file
++.git/annex/objects/VF/27/MD5E-s347--7d984f53676358222aa7aa55980f205b.csv/MD5E-s347--7d984f53676358222aa7aa55980f205b.csv
+\ No newline at end of file
diff --git a/docs/basics/_examples/DL-101-133-112 b/docs/basics/_examples/DL-101-133-112
new file mode 100644
index 000000000..875f3cfa2
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-112
@@ -0,0 +1,3 @@
+$ cd ../
+$ datalad status
+ modified: midterm_project (dataset)
diff --git a/docs/basics/_examples/DL-101-133-113 b/docs/basics/_examples/DL-101-133-113
new file mode 100644
index 000000000..8bb646ba9
--- /dev/null
+++ b/docs/basics/_examples/DL-101-133-113
@@ -0,0 +1,6 @@
+$ datalad save -d . -m "add container and execute analysis within container" midterm_project
+add(ok): midterm_project (file)
+save(ok): . (dataset)
+action summary:
+ add (ok: 1)
+ save (ok: 1)
diff --git a/docs/basics/_examples/DL-101-135-101 b/docs/basics/_examples/DL-101-135-101
index b5530c61c..00bf3e7ff 100644
--- a/docs/basics/_examples/DL-101-135-101
+++ b/docs/basics/_examples/DL-101-135-101
@@ -1,2 +1,2 @@
$ datalad --version
-datalad 0.12.0rc6.dev91
+datalad 0.12.0rc6.dev97
diff --git a/docs/basics/_examples/DL-101-135-102 b/docs/basics/_examples/DL-101-135-102
index 27e99fc0d..893672be3 100644
--- a/docs/basics/_examples/DL-101-135-102
+++ b/docs/basics/_examples/DL-101-135-102
@@ -2,8 +2,8 @@ $ datalad wtf
# WTF
## configuration
## datalad
- - version: 0.12.0rc6.dev91
- - full_version: 0.12.0rc6.dev91-gde46
+ - version: 0.12.0rc6.dev97
+ - full_version: 0.12.0rc6.dev97-g9250-dirty
## dataset
- path: /home/me/dl-101/DataLad-101
- repo: AnnexRepo
@@ -11,12 +11,13 @@ $ datalad wtf
## dependencies
- tqdm: 4.32.2
- cmd:annex: 7.20190129
- - cmd:git: 2.20.1
- - cmd:bundled-git: 2.20.1
- - cmd:system-git: 2.20.1
+ - cmd:git: 2.24.0
+ - cmd:bundled-git: 2.24.0
+ - cmd:system-git: 2.24.0
- cmd:system-ssh: 7.9p1
- appdirs: 1.4.3
- boto: 2.49.0
+ - exifread: 2.1.2
- git: 2.1.11
- gitdb: 2.0.5
- humanize: 0.5.1
@@ -24,6 +25,7 @@ $ datalad wtf
- keyring: 19.0.2
- keyrings.alt: 3.1.1
- msgpack: 0.6.1
+ - mutagen: 1.43.0
- requests: 2.22.0
- scrapy: 1.7.4
- wrapt: 1.11.2
@@ -37,6 +39,53 @@ $ datalad wtf
- PATH: /home/adina/env/handbook/bin:/home/adina/Documents/freesurfer/bin:/home/adina/Documents/freesurfer/fsfast/bin:/home/adina/Documents/freesurfer/tktools:/usr/share/fsl/5.0/bin:/usr/lib/fsl/5.0:/home/adina/Documents/freesurfer/mni/bin:/usr/share/fsl/5.0/5.0/bin:/home/adina/.local/bin:/home/adina/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/home/adina/.dotfiles/bin
- GIT_PYTHON_GIT_EXECUTABLE: /usr/bin/git
## extensions
+ - webapp:
+ - load_error: None
+ - description: Generic web app support
+ - module: datalad_webapp
+ - version: 0.2
+ - entrypoints:
+ - datalad_webapp.WebApp:
+ - module: datalad_webapp
+ - class: WebApp
+ - names:
+ - webapp
+ - webapp
+ - load_error: None
+ - hirni:
+ - load_error: None
+ - description: HIRNI workflows
+ - module: datalad_hirni
+ - version: 0.0.4
+ - entrypoints:
+ - datalad_hirni.commands.import_dicoms.ImportDicoms:
+ - module: datalad_hirni.commands.import_dicoms
+ - class: ImportDicoms
+ - names:
+ - hirni-import-dcm
+ - hirni_import_dcm
+ - load_error: None
+ - datalad_hirni.commands.spec4anything.Spec4Anything:
+ - module: datalad_hirni.commands.spec4anything
+ - class: Spec4Anything
+ - names:
+ - hirni-spec4anything
+ - hirni_spec4anything
+ - load_error: None
+ - datalad_hirni.commands.dicom2spec.Dicom2Spec:
+ - module: datalad_hirni.commands.dicom2spec
+ - class: Dicom2Spec
+ - names:
+ - hirni-dicom2spec
+ - hirni_dicom2spec
+ - load_error: None
+ - datalad_hirni.commands.spec2bids.Spec2Bids:
+ - module: datalad_hirni.commands.spec2bids
+ - class: Spec2Bids
+ - names:
+ - hirni-spec2bids
+ - hirni_spec2bids
+ - load_error: None
- crawler:
- load_error: None
- description: Crawl web resources
@@ -275,7 +324,8 @@ $ datalad wtf
- load_error: None
- audio:
- module: datalad.metadata.extractors.audio
- - load_error: No module named 'mutagen' [audio.py::17]
+ - version: None
+ - load_error: None
- datacite:
- module: datalad.metadata.extractors.datacite
- version: None
@@ -290,7 +340,8 @@ $ datalad wtf
- load_error: None
- exif:
- module: datalad.metadata.extractors.exif
- - load_error: No module named 'exifread' [exif.py::16]
+ - version: None
+ - load_error: None
- frictionless_datapackage:
- module: datalad.metadata.extractors.frictionless_datapackage
- version: None
@@ -301,7 +352,8 @@ $ datalad wtf
- load_error: None
- xmp:
- module: datalad.metadata.extractors.xmp
- - load_error: No module named 'libxmp' [xmp.py::20]
+ - version: None
+ - load_error: None
## python
- version: 3.7.3
- implementation: CPython
@@ -309,8 +361,8 @@ $ datalad wtf
- type: posix
- name: Linux
- release: 4.19.0-6-amd64
- - version: #1 SMP Debian 4.19.67-2+deb10u1 (2019-09-20)
- - distribution: debian/10.1
+ - version: #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11)
+ - distribution: debian/10.2
- max_path_length: 283
- encoding:
- default: utf-8
diff --git a/docs/basics/_examples/DL-101-136-101 b/docs/basics/_examples/DL-101-136-101
index 429ad061d..80867a469 100644
--- a/docs/basics/_examples/DL-101-136-101
+++ b/docs/basics/_examples/DL-101-136-101
@@ -2,8 +2,8 @@ $ cd books/
$ mv TLCL.pdf The_Linux_Command_Line.pdf
$ ls -lah
total 20K
-drwxr-xr-x 2 adina adina 4.0K Nov 18 10:53 .
-drwxr-xr-x 7 adina adina 4.0K Nov 18 10:53 ..
-lrwxrwxrwx 1 adina adina 131 Nov 18 10:50 byte-of-python.pdf -> ../.git/annex/objects/ZZ/f1/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf
+drwxr-xr-x 2 adina adina 4.0K Dec 4 16:23 .
+drwxr-xr-x 8 adina adina 4.0K Dec 4 16:23 ..
+lrwxrwxrwx 1 adina adina 131 Dec 4 16:21 byte-of-python.pdf -> ../.git/annex/objects/ZZ/f1/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf/MD5E-s4407669--32e6b03a08a6edda12ad42eb7bb06a5c.pdf
lrwxrwxrwx 1 adina adina 133 Jun 29 17:39 progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf
lrwxrwxrwx 1 adina adina 131 Jan 28 2019 The_Linux_Command_Line.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
diff --git a/docs/basics/_examples/DL-101-136-104 b/docs/basics/_examples/DL-101-136-104
index b11a97724..083f793b0 100644
--- a/docs/basics/_examples/DL-101-136-104
+++ b/docs/basics/_examples/DL-101-136-104
@@ -1,7 +1,7 @@
$ git log -n 1 -p
-commit 4b793ed196fc072389963aa5d2d87e585a88e034
+commit d33b1e63e51e98e2c891205e39377d7fec615828
Author: Elena Piscopia
-Date: Mon Nov 18 10:53:09 2019 +0100
+Date: Wed Dec 4 16:23:02 2019 +0100
rename the book
diff --git a/docs/basics/_examples/DL-101-136-105 b/docs/basics/_examples/DL-101-136-105
index 0e1e4b6f4..e97726ad1 100644
--- a/docs/basics/_examples/DL-101-136-105
+++ b/docs/basics/_examples/DL-101-136-105
@@ -1,4 +1,3 @@
$ git reset --hard HEAD~1
$ datalad status
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-108 b/docs/basics/_examples/DL-101-136-108
index 2729fc0ed..efa77dbcc 100644
--- a/docs/basics/_examples/DL-101-136-108
+++ b/docs/basics/_examples/DL-101-136-108
@@ -1,7 +1,6 @@
$ git status
On branch master
Changes to be committed:
- (use "git reset HEAD ..." to unstage)
-
+ (use "git restore --staged ..." to unstage)
renamed: TLCL.pdf -> The_Linux_Command_Line.pdf
diff --git a/docs/basics/_examples/DL-101-136-109 b/docs/basics/_examples/DL-101-136-109
index ed232aa80..d45ccab89 100644
--- a/docs/basics/_examples/DL-101-136-109
+++ b/docs/basics/_examples/DL-101-136-109
@@ -1,4 +1,4 @@
$ git commit -m "rename book"
-[master 9892940] rename book
+[master feb1fca] rename book
1 file changed, 0 insertions(+), 0 deletions(-)
rename books/{TLCL.pdf => The_Linux_Command_Line.pdf} (100%)
diff --git a/docs/basics/_examples/DL-101-136-110 b/docs/basics/_examples/DL-101-136-110
index 0e1e4b6f4..e97726ad1 100644
--- a/docs/basics/_examples/DL-101-136-110
+++ b/docs/basics/_examples/DL-101-136-110
@@ -1,4 +1,3 @@
$ git reset --hard HEAD~1
$ datalad status
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-121 b/docs/basics/_examples/DL-101-136-121
index de56dc3fa..c2eb7fb2d 100644
--- a/docs/basics/_examples/DL-101-136-121
+++ b/docs/basics/_examples/DL-101-136-121
@@ -1,3 +1,3 @@
$ cd ../
$ ls -l TLCL.pdf
-lrwxrwxrwx 1 adina adina 131 Nov 18 10:53 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
+lrwxrwxrwx 1 adina adina 131 Dec 4 16:23 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
diff --git a/docs/basics/_examples/DL-101-136-122 b/docs/basics/_examples/DL-101-136-122
index 7fe3a9529..19fc4417a 100644
--- a/docs/basics/_examples/DL-101-136-122
+++ b/docs/basics/_examples/DL-101-136-122
@@ -7,4 +7,4 @@ action summary:
add (ok: 1)
delete (ok: 1)
save (ok: 1)
-lrwxrwxrwx 1 adina adina 128 Nov 18 10:53 TLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
+lrwxrwxrwx 1 adina adina 128 Dec 4 16:23 TLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
diff --git a/docs/basics/_examples/DL-101-136-123 b/docs/basics/_examples/DL-101-136-123
index 86b4e27f9..8b47e5350 100644
--- a/docs/basics/_examples/DL-101-136-123
+++ b/docs/basics/_examples/DL-101-136-123
@@ -1,7 +1,7 @@
$ git log -n 1 -p
-commit 3189043ce3b7998446471aff4accb624898e21a0
+commit 687fb1db82c3448073944690de9e17ab89696af1
Author: Elena Piscopia
-Date: Mon Nov 18 10:53:11 2019 +0100
+Date: Wed Dec 4 16:23:03 2019 +0100
moved book into root
diff --git a/docs/basics/_examples/DL-101-136-124 b/docs/basics/_examples/DL-101-136-124
index ee40b070e..2df35b84f 100644
--- a/docs/basics/_examples/DL-101-136-124
+++ b/docs/basics/_examples/DL-101-136-124
@@ -1,3 +1,2 @@
$ git reset --hard HEAD~1
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-132 b/docs/basics/_examples/DL-101-136-132
index 1a8b345f8..3ba831961 100644
--- a/docs/basics/_examples/DL-101-136-132
+++ b/docs/basics/_examples/DL-101-136-132
@@ -1,7 +1,7 @@
$ git log -n 1 -p
-commit 1246e8c40678edf85874b5f72940500220d3a148
+commit 8759da9a782ba607e8d9c8137176104fa988296e
Author: Elena Piscopia
-Date: Mon Nov 18 10:53:11 2019 +0100
+Date: Wed Dec 4 16:23:04 2019 +0100
add copy of TLCL.pdf
diff --git a/docs/basics/_examples/DL-101-136-133 b/docs/basics/_examples/DL-101-136-133
index 70eeac6b7..470f1f444 100644
--- a/docs/basics/_examples/DL-101-136-133
+++ b/docs/basics/_examples/DL-101-136-133
@@ -1,4 +1,4 @@
$ ls -l copyofTLCL.pdf
$ ls -l books/TLCL.pdf
-lrwxrwxrwx 1 adina adina 128 Nov 18 10:53 copyofTLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
-lrwxrwxrwx 1 adina adina 131 Nov 18 10:53 books/TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
+lrwxrwxrwx 1 adina adina 128 Dec 4 16:23 copyofTLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
+lrwxrwxrwx 1 adina adina 131 Dec 4 16:23 books/TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf
diff --git a/docs/basics/_examples/DL-101-136-134 b/docs/basics/_examples/DL-101-136-134
index 29615e42a..2df35b84f 100644
--- a/docs/basics/_examples/DL-101-136-134
+++ b/docs/basics/_examples/DL-101-136-134
@@ -1,2 +1,2 @@
$ git reset --hard HEAD~1
-HEAD is now at 587ac34 finished my midterm project!
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-140 b/docs/basics/_examples/DL-101-136-140
index 97754e5cc..e4c364f2f 100644
--- a/docs/basics/_examples/DL-101-136-140
+++ b/docs/basics/_examples/DL-101-136-140
@@ -6,7 +6,7 @@ $ cat .git/config
logallrefupdates = true
editor = nano
[annex]
- uuid = a5e9c638-cc6b-4c27-99a5-14802c8a6898
+ uuid = fdbcfeff-5296-4e58-84dc-913343e50f4d
version = 5
backends = MD5E
[submodule "recordings/longnow"]
@@ -15,7 +15,7 @@ $ cat .git/config
[remote "roommate"]
url = ../mock_user/DataLad-101
fetch = +refs/heads/*:refs/remotes/roommate/*
- annex-uuid = 050f8bfe-1ee0-4742-bcb4-b103347aaa05
+ annex-uuid = 0cfd3714-d3a7-45ab-8e70-2f741f23e8ed
annex-ignore = false
[submodule "midterm_project"]
url = /home/me/dl-101/DataLad-101/midterm_project
diff --git a/docs/basics/_examples/DL-101-136-144 b/docs/basics/_examples/DL-101-136-144
index 3a91c779c..beb798feb 100644
--- a/docs/basics/_examples/DL-101-136-144
+++ b/docs/basics/_examples/DL-101-136-144
@@ -6,7 +6,7 @@ $ cat .git/config
logallrefupdates = true
editor = nano
[annex]
- uuid = a5e9c638-cc6b-4c27-99a5-14802c8a6898
+ uuid = fdbcfeff-5296-4e58-84dc-913343e50f4d
version = 5
backends = MD5E
[submodule "recordings/longnow"]
@@ -15,7 +15,7 @@ $ cat .git/config
[remote "roommate"]
url = ../mock_user/onemoredir/DataLad-101
fetch = +refs/heads/*:refs/remotes/roommate/*
- annex-uuid = 050f8bfe-1ee0-4742-bcb4-b103347aaa05
+ annex-uuid = 0cfd3714-d3a7-45ab-8e70-2f741f23e8ed
annex-ignore = false
[submodule "midterm_project"]
url = /home/me/dl-101/DataLad-101/midterm_project
diff --git a/docs/basics/_examples/DL-101-136-146 b/docs/basics/_examples/DL-101-136-146
index 152c158bd..dc93147a5 100644
--- a/docs/basics/_examples/DL-101-136-146
+++ b/docs/basics/_examples/DL-101-136-146
@@ -1,5 +1,4 @@
$ cd ../mock_user && mv onemoredir/DataLad-101 .
$ rm -r onemoredir
$ cd ../DataLad-101 && git reset --hard master
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-152 b/docs/basics/_examples/DL-101-136-152
index bccb24948..2df35b84f 100644
--- a/docs/basics/_examples/DL-101-136-152
+++ b/docs/basics/_examples/DL-101-136-152
@@ -1,4 +1,2 @@
$ git reset --hard HEAD~1
-<<<<<<< HEAD
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-156 b/docs/basics/_examples/DL-101-136-156
index c6f48fbce..4547934c2 100644
--- a/docs/basics/_examples/DL-101-136-156
+++ b/docs/basics/_examples/DL-101-136-156
@@ -1,3 +1,3 @@
$ git reset --hard HEAD~1
warning: unable to rmdir 'longnow': Directory not empty
-HEAD is now at 587ac34 finished my midterm project!
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-164 b/docs/basics/_examples/DL-101-136-164
index d57881176..e3e402d65 100644
--- a/docs/basics/_examples/DL-101-136-164
+++ b/docs/basics/_examples/DL-101-136-164
@@ -1,3 +1,2 @@
$ git reset --hard HEAD~2
-HEAD is now at 587ac34 finished my midterm project!
-
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-136-174 b/docs/basics/_examples/DL-101-136-174
index 527366d66..f85879600 100644
--- a/docs/basics/_examples/DL-101-136-174
+++ b/docs/basics/_examples/DL-101-136-174
@@ -1,6 +1,6 @@
$ git reset --hard HEAD~1
$ ls
-HEAD is now at da61732 Added flower mosaic from wikimedia
+HEAD is now at a88c158 Added flower mosaic from wikimedia
books
code
flowers.jpg
diff --git a/docs/basics/_examples/DL-101-136-180 b/docs/basics/_examples/DL-101-136-180
index 4c6dd0fc6..e3e402d65 100644
--- a/docs/basics/_examples/DL-101-136-180
+++ b/docs/basics/_examples/DL-101-136-180
@@ -1,2 +1,2 @@
$ git reset --hard HEAD~2
-HEAD is now at 587ac34 finished my midterm project!
+HEAD is now at d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-137-101 b/docs/basics/_examples/DL-101-137-101
index fd51a8174..5e125069d 100644
--- a/docs/basics/_examples/DL-101-137-101
+++ b/docs/basics/_examples/DL-101-137-101
@@ -1,16 +1,16 @@
$ git log -15 --oneline
-587ac34 finished my midterm project!
-de7d909 [DATALAD] Recorded changes
-37d74af add note on DataLads procedures
-264d668 add note on configurations and git config
-2277fe7 Add note on adding siblings
-f015735 Merge remote-tracking branch 'refs/remotes/roommate/master'
-0a01e8a Include nesting demo from datalad website
-5e45b4e add note about datalad update
-e613db1 add note on git annex whereis
-118eed9 add note about installing from paths and recursive installations
-f42379c add note on clean datasets
-475d3de [DATALAD RUNCMD] Resize logo for slides
-6856e4f [DATALAD RUNCMD] Resize logo for slides
-72fa9f9 add additional notes on run options
-b49af2f [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
+d3ee8e9 add container and execute analysis within container
+c4aaeb2 finished my midterm project!
+ca76f3b [DATALAD] Recorded changes
+73f14ee add note on DataLads procedures
+9a795e3 add note on configurations and git config
+da9d193 Add note on adding siblings
+c15ea3e Merge remote-tracking branch 'refs/remotes/roommate/master'
+aca5177 Include nesting demo from datalad website
+1291140 add note about datalad update
+1b07d87 add note on git annex whereis
+ad17112 add note about installing from paths and recursive installations
+199587f add note on clean datasets
+dd726a6 [DATALAD RUNCMD] Resize logo for slides
+e4dd212 [DATALAD RUNCMD] Resize logo for slides
+b08d657 add additional notes on run options
diff --git a/docs/basics/_examples/DL-101-137-105 b/docs/basics/_examples/DL-101-137-105
index 66160df0f..710ee2252 100644
--- a/docs/basics/_examples/DL-101-137-105
+++ b/docs/basics/_examples/DL-101-137-105
@@ -1,7 +1,7 @@
$ git log -p -1
-commit 986ede3879a4a86a93b0b4d22ccee925c15c6230
+commit a84bc8b2d463077e33803a673d762133d8bb3e2e
Author: Elena Piscopia
-Date: Mon Nov 18 10:53:25 2019 +0100
+Date: Wed Dec 4 16:23:17 2019 +0100
[DATALAD] Recorded changes
diff --git a/docs/basics/_examples/DL-101-137-106 b/docs/basics/_examples/DL-101-137-106
index 3982396bd..c3aebf4d4 100644
--- a/docs/basics/_examples/DL-101-137-106
+++ b/docs/basics/_examples/DL-101-137-106
@@ -1,4 +1,4 @@
$ git log -n 3 --oneline
-4604d99 [DATALAD] Recorded changes
-587ac34 finished my midterm project!
-de7d909 [DATALAD] Recorded changes
+a84bc8b [DATALAD] Recorded changes
+d3ee8e9 add container and execute analysis within container
+c4aaeb2 finished my midterm project!
diff --git a/docs/basics/_examples/DL-101-137-107 b/docs/basics/_examples/DL-101-137-107
index ab6678982..53c16e35b 100644
--- a/docs/basics/_examples/DL-101-137-107
+++ b/docs/basics/_examples/DL-101-137-107
@@ -1 +1,2 @@
-$ git reset --mixed 587ac34d63c93275649cb65cd932c6a052569fdd
+
+$ git reset --mixed d3ee8e9a53e8c321e97ccea5b66fa19e7d34056a
diff --git a/docs/basics/_examples/DL-101-137-108 b/docs/basics/_examples/DL-101-137-108
index 051d98c91..fe10dd22b 100644
--- a/docs/basics/_examples/DL-101-137-108
+++ b/docs/basics/_examples/DL-101-137-108
@@ -1,3 +1,3 @@
$ git log -n 2 --oneline
-587ac34 finished my midterm project!
-de7d909 [DATALAD] Recorded changes
\ No newline at end of file
+d3ee8e9 add container and execute analysis within container
+c4aaeb2 finished my midterm project!
diff --git a/docs/basics/_examples/DL-101-137-112 b/docs/basics/_examples/DL-101-137-112
index 53e51f3e2..187b4f529 100644
--- a/docs/basics/_examples/DL-101-137-112
+++ b/docs/basics/_examples/DL-101-137-112
@@ -1,12 +1,12 @@
-$ git log -n 2
-commit 51d763ed5883bc51f6eabc36248e4ef80b9f600f
+$ git log -2
+commit b8972e080e665903f10c32c3d174211c282324e1
Author: Elena Piscopia
-Date: Mon Nov 18 08:44:46 2019 +0100
+Date: Wed Dec 4 16:23:17 2019 +0100
save my favorite Git joke
-commit 587ac34d63c93275649cb65cd932c6a052569fdd
+commit d3ee8e9a53e8c321e97ccea5b66fa19e7d34056a
Author: Elena Piscopia
-Date: Mon Nov 18 08:44:26 2019 +0100
+Date: Wed Dec 4 16:22:59 2019 +0100
- finished my midterm project!
+ add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-137-114 b/docs/basics/_examples/DL-101-137-114
index d3b1afd2b..03c7dc3be 100644
--- a/docs/basics/_examples/DL-101-137-114
+++ b/docs/basics/_examples/DL-101-137-114
@@ -1,2 +1,2 @@
$ ls -l apdffile.pdf
-lrwxrwxrwx 1 adina adina 122 Nov 18 10:53 apdffile.pdf -> .git/annex/objects/gV/gf/MD5E-s1842--40e4e7d327aa106fe64ef8b799a29d54.pdf/MD5E-s1842--40e4e7d327aa106fe64ef8b799a29d54.pdf
+lrwxrwxrwx 1 adina adina 122 Dec 4 16:23 apdffile.pdf -> .git/annex/objects/jg/Qk/MD5E-s1842--ae82655e482e95369a942ef787ffda24.pdf/MD5E-s1842--ae82655e482e95369a942ef787ffda24.pdf
diff --git a/docs/basics/_examples/DL-101-137-116 b/docs/basics/_examples/DL-101-137-116
index f2dd736eb..d1a67faa3 100644
--- a/docs/basics/_examples/DL-101-137-116
+++ b/docs/basics/_examples/DL-101-137-116
@@ -1,2 +1,2 @@
$ ls -l apdffile.pdf
--rw-r--r-- 1 adina adina 1842 Nov 18 10:53 apdffile.pdf
+-rw-r--r-- 1 adina adina 1842 Dec 4 16:23 apdffile.pdf
diff --git a/docs/basics/_examples/DL-101-137-117 b/docs/basics/_examples/DL-101-137-117
index f873dcce8..bf482fa38 100644
--- a/docs/basics/_examples/DL-101-137-117
+++ b/docs/basics/_examples/DL-101-137-117
@@ -1,4 +1,4 @@
$ git log -n 3 --oneline
-b602512 [DATALAD] Recorded changes
-51d763e save my favourite Git joke
-587ac34 finished my midterm project!
+76f65c9 [DATALAD] Recorded changes
+b8972e0 save my favorite Git joke
+d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-137-118 b/docs/basics/_examples/DL-101-137-118
index e327e1113..5e2b03128 100644
--- a/docs/basics/_examples/DL-101-137-118
+++ b/docs/basics/_examples/DL-101-137-118
@@ -1 +1,2 @@
-$ git reset --mixed 51d763ed5883bc51f6eabc36248e4ef80b9f600f
+
+$ git reset --mixed b8972e080e665903f10c32c3d174211c282324e1
diff --git a/docs/basics/_examples/DL-101-137-119 b/docs/basics/_examples/DL-101-137-119
index 008555927..931ee555d 100644
--- a/docs/basics/_examples/DL-101-137-119
+++ b/docs/basics/_examples/DL-101-137-119
@@ -1,3 +1,3 @@
$ git log -n 2 --oneline
-51d763e save my favourite Git joke
-587ac34 finished my midterm project!
+b8972e0 save my favorite Git joke
+d3ee8e9 add container and execute analysis within container
diff --git a/docs/basics/_examples/DL-101-137-121 b/docs/basics/_examples/DL-101-137-121
index 0be81d823..f08d27a55 100644
--- a/docs/basics/_examples/DL-101-137-121
+++ b/docs/basics/_examples/DL-101-137-121
@@ -1,21 +1,21 @@
$ git log -n 20 --oneline
-51d763e save my favourite Git joke
-587ac34 finished my midterm project!
-de7d909 [DATALAD] Recorded changes
-37d74af add note on DataLads procedures
-264d668 add note on configurations and git config
-2277fe7 Add note on adding siblings
-f015735 Merge remote-tracking branch 'refs/remotes/roommate/master'
-0a01e8a Include nesting demo from datalad website
-5e45b4e add note about datalad update
-e613db1 add note on git annex whereis
-118eed9 add note about installing from paths and recursive installations
-f42379c add note on clean datasets
-475d3de [DATALAD RUNCMD] Resize logo for slides
-6856e4f [DATALAD RUNCMD] Resize logo for slides
-72fa9f9 add additional notes on run options
-b49af2f [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
-f59a783 resized picture by hand
-4698deb [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
-cebdc20 add note on basic datalad run and datalad rerun
-dd71a3c add note datalad and git diff
+b8972e0 save my favorite Git joke
+d3ee8e9 add container and execute analysis within container
+c4aaeb2 finished my midterm project!
+ca76f3b [DATALAD] Recorded changes
+73f14ee add note on DataLads procedures
+9a795e3 add note on configurations and git config
+da9d193 Add note on adding siblings
+c15ea3e Merge remote-tracking branch 'refs/remotes/roommate/master'
+aca5177 Include nesting demo from datalad website
+1291140 add note about datalad update
+1b07d87 add note on git annex whereis
+ad17112 add note about installing from paths and recursive installations
+199587f add note on clean datasets
+dd726a6 [DATALAD RUNCMD] Resize logo for slides
+e4dd212 [DATALAD RUNCMD] Resize logo for slides
+b08d657 add additional notes on run options
+3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
+bd42809 resized picture by hand
+86be52e [DATALAD RUNCMD] convert -resize 400x400 recordings/longn...
+aadf74e add note on basic datalad run and datalad rerun
diff --git a/docs/basics/_examples/DL-101-137-122 b/docs/basics/_examples/DL-101-137-122
index a9f08570c..1ea969f22 100644
--- a/docs/basics/_examples/DL-101-137-122
+++ b/docs/basics/_examples/DL-101-137-122
@@ -1,14 +1,21 @@
-$ git checkout f59a78356d78525239347ecf763b6677130898af
+
+$ git checkout 3a4418dc8d74b9889da49b26e0f201e169902113
warning: unable to rmdir 'midterm_project': Directory not empty
-Note: checking out 'f59a78356d78525239347ecf763b6677130898af'.
+Note: switching to '3a4418dc8d74b9889da49b26e0f201e169902113'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
-state without impacting any branches by performing another checkout.
+state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
-do so (now or later) by using -b with the checkout command again. Example:
+do so (now or later) by using -c with the switch command. Example:
+
+ git switch -c
+
+Or undo this operation with:
+
+ git switch -
- git checkout -b
+Turn off this advice by setting config variable advice.detachedHead to false
-HEAD is now at f59a783 resized picture by hand
+HEAD is now at 3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
diff --git a/docs/basics/_examples/DL-101-137-124 b/docs/basics/_examples/DL-101-137-124
index cc8977241..8c48e3fd4 100644
--- a/docs/basics/_examples/DL-101-137-124
+++ b/docs/basics/_examples/DL-101-137-124
@@ -1,3 +1,3 @@
$ git checkout master
-Previous HEAD position was f59a783 resized picture by hand
+Previous HEAD position was 3a4418d [DATALAD RUNCMD] convert -resize 450x450 recordings/longn...
Switched to branch 'master'
diff --git a/docs/basics/_examples/DL-101-137-127 b/docs/basics/_examples/DL-101-137-127
index 932dbbb14..c08003943 100644
--- a/docs/basics/_examples/DL-101-137-127
+++ b/docs/basics/_examples/DL-101-137-127
@@ -1,4 +1,5 @@
-$ git cat-file --textconv f59a78356d78525239347ecf763b6677130898af:notes.txt
+
+$ git cat-file --textconv 3a4418dc8d74b9889da49b26e0f201e169902113:notes.txt
One can create a new dataset with 'datalad create [--description] PATH'.
The dataset is created empty
diff --git a/docs/basics/_examples/DL-101-137-132 b/docs/basics/_examples/DL-101-137-132
index 100a3bbdf..6c855c56a 100644
--- a/docs/basics/_examples/DL-101-137-132
+++ b/docs/basics/_examples/DL-101-137-132
@@ -1,3 +1,3 @@
$ git log -n 2 --oneline
-b6dd7d1 add joke evaluation to joke
-51d763e save my favourite Git joke
+26b14ab add joke evaluation to joke
+b8972e0 save my favorite Git joke
diff --git a/docs/basics/_examples/DL-101-137-133 b/docs/basics/_examples/DL-101-137-133
index 36b00e1f2..97624c928 100644
--- a/docs/basics/_examples/DL-101-137-133
+++ b/docs/basics/_examples/DL-101-137-133
@@ -1,2 +1,3 @@
-$ git reset --hard 51d763ed5883bc51f6eabc36248e4ef80b9f600f
-HEAD is now at 51d763e save my favourite Git joke
+
+$ git reset --hard b8972e080e665903f10c32c3d174211c282324e1
+HEAD is now at b8972e0 save my favorite Git joke
diff --git a/docs/basics/_examples/DL-101-137-144 b/docs/basics/_examples/DL-101-137-144
index e1fe1ca05..02c4a491b 100644
--- a/docs/basics/_examples/DL-101-137-144
+++ b/docs/basics/_examples/DL-101-137-144
@@ -1,5 +1,5 @@
-$ git revert aaa1988adfa83a703a756f911a0beffc4fefa08a
-[master 37c73e7] Revert "did a bad modification"
- Date: Mon Nov 18 08:44:48 2019 +0100
+$ git revert 795f94ab667188877575dc4db900f3d6aed0a4a2
+[master 7df383f] Revert "did a bad modification"
+ Date: Wed Dec 4 16:23:20 2019 +0100
1 file changed, 1 deletion(-)
diff --git a/docs/basics/_examples/DL-101-137-146 b/docs/basics/_examples/DL-101-137-146
index 1d143d932..a82344df5 100644
--- a/docs/basics/_examples/DL-101-137-146
+++ b/docs/basics/_examples/DL-101-137-146
@@ -1,20 +1,20 @@
$ git log -n 3
-commit 37c73e7eff6df09ce3ea9a149e64ea5e82ed5d8b
+commit 7df383fd912c9f9841c4cca0161930e14fbb3c8d
Author: Elena Piscopia
-Date: Mon Nov 18 08:44:48 2019 +0100
+Date: Wed Dec 4 16:23:20 2019 +0100
Revert "did a bad modification"
- This reverts commit aaa1988adfa83a703a756f911a0beffc4fefa08a.
+ This reverts commit 795f94ab667188877575dc4db900f3d6aed0a4a2.
-commit 696c3878120b997eb3f6b4e552de5875664ab874
+commit 35d77bee63472970f76668cb4566758044ff1f4b
Author: Elena Piscopia
-Date: Mon Nov 18 08:44:48 2019 +0100
+Date: Wed Dec 4 16:23:20 2019 +0100
add note on helpful git resource
-commit aaa1988adfa83a703a756f911a0beffc4fefa08a
+commit 795f94ab667188877575dc4db900f3d6aed0a4a2
Author: Elena Piscopia
-Date: Mon Nov 18 08:44:48 2019 +0100
+Date: Wed Dec 4 16:23:19 2019 +0100
did a bad modification
diff --git a/docs/contents.rst.inc b/docs/contents.rst.inc
index 3be76d66b..d6378e479 100644
--- a/docs/contents.rst.inc
+++ b/docs/contents.rst.inc
@@ -89,7 +89,7 @@ Make the most out of datasets
.. toctree::
:maxdepth: 1
- :caption: Organizational principles and best practices for data analyses
+ :caption: Organizational principles and best practices for reproducible data analyses
basics/101-126-intro
basics/101-127-yoda
@@ -97,16 +97,17 @@ Make the most out of datasets
basics/101-128-summary_yoda
-###########################
-Dataset nesting -- Advanced
-###########################
+################
+One step further
+################
.. toctree::
:maxdepth: 1
- :caption: Manipulating subdatasets and its impact on the superdataset(s)
+ :caption: Advanced nesting and "extended" reproducibility
basics/101-132-advancednesting
- basics/101-132-gitC
+ basics/101-133-containersrun
+ basics/101-134-summary
#############
@@ -133,6 +134,8 @@ Further options
:caption: Small pieces of advice and helpful additional options
basics/101-179-gitignore
+ basics/101-144-intro_extensions
+
#########
Use Cases
diff --git a/docs/glossary.rst b/docs/glossary.rst
index 6df8769b8..bdc6ee978 100644
--- a/docs/glossary.rst
+++ b/docs/glossary.rst
@@ -138,6 +138,11 @@ Glossary
- ``execute permissions`` grant the ability to execute a file. Any script that should be an executable
needs to get such permission.
+ pip
+ A Python package manager. Short for "Pip installs Python". ``pip install ``
+ searches the Python package index `PyPi `_ for a
+ package and installs it while resolving any potential dependencies.
+
provenance
A record that describes entities and processes that were involved in producinng or influencing
a digital resource. It provides a critical foundation for assessing authenticity, enables trust,
diff --git a/docs/intro/_examples/how-to-1 b/docs/intro/_examples/how-to-1
index 59064f2de..22bd89f0b 100644
--- a/docs/intro/_examples/how-to-1
+++ b/docs/intro/_examples/how-to-1
@@ -1,5 +1,5 @@
$ ls -l output.txt
24+0 records in
24+0 records out
-25165824 bytes (25 MB, 24 MiB) copied, 0.0195906 s, 1.3 GB/s
--rw-r--r-- 1 adina adina 25165824 Nov 18 10:53 output.txt
+25165824 bytes (25 MB, 24 MiB) copied, 0.013529 s, 1.9 GB/s
+-rw-r--r-- 1 adina adina 25165824 Nov 26 12:54 output.txt
diff --git a/docs/intro/_examples/how-to-2 b/docs/intro/_examples/how-to-2
index dcd6c3111..dff83e2d5 100644
--- a/docs/intro/_examples/how-to-2
+++ b/docs/intro/_examples/how-to-2
@@ -1,4 +1,4 @@
$ ls -lh output.txt # note that short options can be combined!
# or alternatively
$ ls -l --human-readable output.txt
--rw-r--r-- 1 adina adina 24M Nov 18 10:53 output.txt
+-rw-r--r-- 1 adina adina 24M Nov 26 12:54 output.txt