From a83f5a934a436952364bd63a3b3e298585e0cb3b Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 11:52:58 +0100 Subject: [PATCH 01/17] add some words to prevent an awkward line break The linebreak was: . gitmodules --- docs/basics/101-123-config2.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-123-config2.rst b/docs/basics/101-123-config2.rst index 3ece377d5..ccf80389e 100644 --- a/docs/basics/101-123-config2.rst +++ b/docs/basics/101-123-config2.rst @@ -148,7 +148,7 @@ There is one right in the root of your dataset: $ cat .gitmodules Based on these contents, you might have already guessed what this file -stores. ``.gitmodules`` is a configuration file that stores the mapping between +stores. The ``.gitmodules`` file is a configuration file that stores the mapping between your own dataset and any subdatasets you have installed in it. There will be an entry for each submodule (subdataset) in your dataset. The name *submodule* is Git terminology, and describes a Git repository inside of From 6a096b0a976a19a2c3841f985bb8b7e23a8e0de5 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 11:57:23 +0100 Subject: [PATCH 02/17] add a missing markup --- docs/basics/101-123-config2.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-123-config2.rst b/docs/basics/101-123-config2.rst index ccf80389e..c3fbf357b 100644 --- a/docs/basics/101-123-config2.rst +++ b/docs/basics/101-123-config2.rst @@ -257,7 +257,7 @@ Here is the directory structure: add (ok: 2) save (ok: 1) -Now, we can apply the ``datalad-recursiveinstall`` configuration to skip recursive installations for subds1 +Now, we can apply the ``datalad-recursiveinstall`` configuration to skip recursive installations for ``subds1`` .. code-block:: bash From 2dd8c3da1c51c99d0779a8e4c547c3edfb3f60ce Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 12:24:15 +0100 Subject: [PATCH 03/17] typo --- docs/basics/101-123-config2.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-123-config2.rst b/docs/basics/101-123-config2.rst index c3fbf357b..20ff9d67e 100644 --- a/docs/basics/101-123-config2.rst +++ b/docs/basics/101-123-config2.rst @@ -475,7 +475,7 @@ This has been an intense lecture, you have to admit. One definite take-away from it has been that you now know a second reason why the hidden ``.git`` and ``.datalad`` directory contents and also the contents of ``.gitmodules`` and ``.gitattributes`` should not be carelessly tampered with -- they contain all of -the repositories configurations. +the repository's configurations. But you now also know how to modify these configurations with enough care and background knowledge such that nothing should go wrong once you From 5c6e68d1df62ef27897a75253b646a8f37915f3b Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 12:26:51 +0100 Subject: [PATCH 04/17] fix sentence structure --- docs/basics/101-124-procedures.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-124-procedures.rst b/docs/basics/101-124-procedures.rst index 9185e2ffa..7f1865b9c 100644 --- a/docs/basics/101-124-procedures.rst +++ b/docs/basics/101-124-procedures.rst @@ -73,7 +73,7 @@ What makes them a particularly versatile and flexible tool is that anyone can write their own procedures. If a workflow is a standard in a team and needs to be applied often, turning it into a script can save time and effort. -To learn how to do this, read the :ref:`with a tutorial on writing own procedures `. +To learn how to do this, read the :ref:`tutorial on writing own procedures `. By pointing DataLad to the location the procedures reside in they can be applied, and by including them in a dataset they can even be shared. And even if the script is simple, it is very handy to have preconfigured From 2acf5c6542f264e8c500536cc9f7fd70b6e43543 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Wed, 1 Nov 2023 13:05:01 +0100 Subject: [PATCH 05/17] Remove superflous action summaries from command output These consume a lot of space, and are often not helpful given the simple usage patterns that dominate the handbook. This change removes any action summary that does not contain notneeded. The exception is useful, because by default notneeded results are not renderer individually. Ping #1009 Ping #1048 --- docs/conf.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index a85b801d4..ba2cf8d6a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -63,6 +63,9 @@ # should still be functional and save 30+% of line length (r'(?P[0-9a-f]{8})[0-9a-f]{32}', r'\g✂SHA1'), (r'(?P[0-9a-f]{8})[0-9a-f]{24}', r'\g✂MD5'), + # remove any action summary that contains no `notneeded`, the latter + # need to be kept, because they are not renderer individually + (r'(action summary:(\n^ \S+ \(\S+(? Date: Wed, 1 Nov 2023 13:25:56 +0100 Subject: [PATCH 06/17] add missing words --- docs/basics/101-125-summary.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/basics/101-125-summary.rst b/docs/basics/101-125-summary.rst index 8a2550245..5622f821d 100644 --- a/docs/basics/101-125-summary.rst +++ b/docs/basics/101-125-summary.rst @@ -14,7 +14,7 @@ your horizon about configurations of datasets: ``.datalad/config`` that apply to a specific dataset, but are committed and therefore distributed. More specialized scopes take precedence over more global scopes. -- Almost all configurations can be set with the :gitcmd:`config`. +- Almost all configurations can be set with the :gitcmd:`config` command. Its structure looks like this: .. code-block:: bash @@ -32,7 +32,7 @@ your horizon about configurations of datasets: in a :gitcmd:`config` command. - The ``.gitattributes`` file is the only configuration file the :gitcmd:`config` - can not write to, because it has a different layout. However, run-procedures or + command can not write to, because it has a different layout. However, run-procedures or the user can write simple rules into it that determine which files are annexed and which are stored in Git. From f53cbfe5584bfad2d766b4fcf9a8fab53d580240 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 13:47:32 +0100 Subject: [PATCH 07/17] move highlighting to correct line --- docs/basics/101-130-yodaproject.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-130-yodaproject.rst b/docs/basics/101-130-yodaproject.rst index 88e3bc1b8..84f02b68b 100644 --- a/docs/basics/101-130-yodaproject.rst +++ b/docs/basics/101-130-yodaproject.rst @@ -341,7 +341,7 @@ To compute the analysis you create the following Python script inside of ``code/ .. runrecord:: _examples/DL-101-130-107 :language: console :workdir: dl-101/DataLad-101/midterm_project - :emphasize-lines: 11-13, 23, 42 + :emphasize-lines: 11-13, 23, 43 :cast: 10_yoda :notes: Let's create code for an analysis From 11fe2513cffd6afe94d80dd166cabf620aab6e12 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Wed, 1 Nov 2023 13:49:28 +0100 Subject: [PATCH 08/17] Filter out a set of noise INFO log messages Comments are inside the diff --- docs/conf.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index ba2cf8d6a..9893832b9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -66,6 +66,17 @@ # remove any action summary that contains no `notneeded`, the latter # need to be kept, because they are not renderer individually (r'(action summary:(\n^ \S+ \(\S+(? Date: Wed, 1 Nov 2023 13:50:54 +0100 Subject: [PATCH 09/17] switch from footnote to glossary link --- docs/basics/101-130-yodaproject.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-130-yodaproject.rst b/docs/basics/101-130-yodaproject.rst index 84f02b68b..24a339575 100644 --- a/docs/basics/101-130-yodaproject.rst +++ b/docs/basics/101-130-yodaproject.rst @@ -485,7 +485,7 @@ re-execution with :dlcmd:`rerun` easy. - `seaborn `_ - `sklearn `_ - The packages can be installed via ``pip`` [#f3]_. + The packages can be installed via :term:`pip`. However, if you do not want to install any Python packages, do not execute the remaining code examples in this section -- an upcoming section on ``datalad containers-run`` will allow you to From 521e797350df13dd379c60151627a6c476e58e2a Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Wed, 1 Nov 2023 13:57:35 +0100 Subject: [PATCH 10/17] Transition handbook links to `https` This Changes the last few occurences. Closes #959 --- README.md | 2 +- artwork/OHBM_2020.svg | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 7d6ae2108..259fa50db 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![Build status](https://ci.appveyor.com/api/projects/status/v8o167109n3irf5c/branch/main?svg=true)](https://ci.appveyor.com/project/mih/book/branch/main) [![Monthly link check](https://github.com/datalad-handbook/book/actions/workflows/linkcheck.yml/badge.svg)](https://github.com/datalad-handbook/book/actions/workflows/linkcheck.yml) -[![Documentation Status](https://readthedocs.org/projects/datalad-handbook/badge/?version=latest)](http://handbook.datalad.org/en/latest/?badge=latest) +[![Documentation Status](https://readthedocs.org/projects/datalad-handbook/badge/?version=latest)](https://handbook.datalad.org/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3608611.svg)](https://doi.org/10.5281/zenodo.3608611) [![made-with-datalad](https://www.datalad.org/badges/made_with.svg)](https://datalad.org) diff --git a/artwork/OHBM_2020.svg b/artwork/OHBM_2020.svg index d60baa0aa..df2a40b61 100644 --- a/artwork/OHBM_2020.svg +++ b/artwork/OHBM_2020.svg @@ -3356,8 +3356,8 @@ id="g6756" transform="translate(0,-863.42482)"> Date: Wed, 1 Nov 2023 14:05:12 +0100 Subject: [PATCH 11/17] Also suppress push step-wise progress reporting --- docs/conf.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 9893832b9..f4f9698ae 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -77,6 +77,11 @@ (r'\n\[INFO\] Fetching updates for Dataset.*', ''), # annoying always-true test for a non-annex git remote (r'\n\[INFO\] \S+/config download failed: Not Found', ''), + # datalad push step-progress + (r'\n\[INFO\] Determine push target', ''), + (r'\n\[INFO\] Push refspecs', ''), + (r'\n\[INFO\] Transfer data', ''), + (r'\n\[INFO\] Update availability information', ''), ] # pre-crafted artificial environment to run the code examples in # start with all datalad settings From 8782ea1642ad11e89382c6f8393e91793f22b37d Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 14:08:31 +0100 Subject: [PATCH 12/17] fix sentence structure --- docs/basics/101-130-yodaproject.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/basics/101-130-yodaproject.rst b/docs/basics/101-130-yodaproject.rst index 24a339575..6d9d83c2d 100644 --- a/docs/basics/101-130-yodaproject.rst +++ b/docs/basics/101-130-yodaproject.rst @@ -674,8 +674,7 @@ configuration, or interactively). .. importantnote:: Generate a GitHub token - GitHub `deprecated user-password authentication `_ supports authentication via personal access token only. - + GitHub `deprecated user-password authentication `_ and instead supports authentication via personal access token. To ensure successful authentication, don't supply your password, but create a personal access token at `github.com/settings/tokens `_ [#f6]_ instead, and either * supply the token with the argument ``--github-login `` from the command line, From 4aa99f874c091dd1afd1e0ac08278d666adfacdd Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 14:08:59 +0100 Subject: [PATCH 13/17] remove old tool use help - the upstream documentation is better --- docs/basics/101-130-yodaproject.rst | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/basics/101-130-yodaproject.rst b/docs/basics/101-130-yodaproject.rst index 6d9d83c2d..5a6888d7b 100644 --- a/docs/basics/101-130-yodaproject.rst +++ b/docs/basics/101-130-yodaproject.rst @@ -943,8 +943,4 @@ reproduce your data science project easily from scratch (take a look into the :r .. [#f5] Alternatively, if you were to use DataLad's Python API, you could import and expose it as ``dl.`` and ``dl.get()`` the relevant files. This however, would not record them as provenance in the dataset's history. .. [#f6] Instead of using GitHub's WebUI you could also obtain a token using the command line GitHub interface (https://github.com/sociomantic-tsunami/git-hub) by running ``git hub setup`` (if no 2FA is used). - If you decide to use the command line interface, here is help on how to use it: - Clone the `GitHub repository `_ to your local computer. - Decide whether you want to build a Debian package to install, or install the single-file Python script distributed in the repository. - Make sure that all `requirements `_ for your preferred version are installed , and run either ``make deb`` followed by ``sudo dpkg -i deb/git-hub*all.deb``, or ``make install``. From c74c8d015a52b58581e04ef00160b43ed39f51d6 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Wed, 1 Nov 2023 14:19:43 +0100 Subject: [PATCH 14/17] Correct the description of hash-size impact on Windows paths The description is changed to state the correct sizes in characters (because those are immediately relevant, not the bitsize, even if directly convertable). Thanks to @NemoAndrea for reporting! Closes #977 --- docs/intro/windows.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/intro/windows.rst b/docs/intro/windows.rst index 15cb4ebf3..af9043041 100644 --- a/docs/intro/windows.rst +++ b/docs/intro/windows.rst @@ -32,9 +32,9 @@ Windows also has insufficient support for :term:`symlink`\ing and locking files In addition, Windows has a (default) `maximum path length limitation of only 260 characters `_. However, DataLad (or rather, :term:`git-annex`) relies on `file content hashing `_ to ensure file integrity. Usually, the *longer* the `hash` that is created, the more fail-safe it is. -For a general idea about the length of hashes, consider that many tools including :term:`git-annex` use ``SHA256`` (a 256 characters long hash) as their default. -As git-annex represents files with their content hash as a name, though, a secure 256 character file name is too long for Windows. -Datasets thus adjust this default to a 128 character hash [#f2]_, but still, if you place a DataLad dataset into a deeply nested directory location, you may run into issues due to hitting the path length limit [#f3]_. +For a general idea about the length of hashes, consider that many tools including :term:`git-annex` use ``SHA256`` (a 64 characters long hash) as their default. +As git-annex represents files with their content hash as their name, and places them into a directory of the same name, half of the total path length is already used up with a ``SHA256`` hash. +Datasets thus adjust this default to a 32 character hash [#f2]_, but still, if you place a DataLad dataset into a deeply nested directory location, you may run into issues due to hitting the path length limit [#f3]_. You *can* enable long paths in recent builds of Windows 10, `but it requires some tweaking `_. Windows also doesn't really come with a decent :term:`terminal`. @@ -165,7 +165,7 @@ Take a look at user forums such as `forums.linuxmint.com `_, a hash function that produces a 128 character hash value. This wouldn't be necessary on Unix-based operating systems, but is required to ensure portability of datasets to Windows computers. +.. [#f2] The path length limitation on Windows is the reason that DataLad datasets always use hashes based on `MD5 `_, a hash function that produces a 32 character hash digest value. This wouldn't be necessary on Unix-based operating systems, but is required to ensure portability of datasets to Windows computers. .. [#f3] The path length limitation certainly isn't only a problem for DataLad and its underlying tools. Many users run into a Path length related problems at least once, by accident. Downloading or copying files with long names into a folder that itself has a long name, for example, can become an unexpected issue (especially if you are not aware of the limit). Imagine transferring pictures from your friends camera into ``C:\Users\"Bob McBobface"\Desktop\Pictures\"Vacation Pictures"\2020\Saint-Remy-en-Bouzemont-Saint-Genest-et-Isson\"From Alice and Sasha"\Camera\`` -- those file names shouldn't be too long to fit in the limit. Likewise, when ``git clone``\ing a :term:`Git` repository that was created on a Unix computer and contains very long file names could fail. From ecb4f32419085f11b2b3e5b216c4a3ffc462ddb3 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 14:33:29 +0100 Subject: [PATCH 15/17] better wording --- docs/basics/101-139-hostingservices.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-139-hostingservices.rst b/docs/basics/101-139-hostingservices.rst index ab5bc89dc..4a6d4002f 100644 --- a/docs/basics/101-139-hostingservices.rst +++ b/docs/basics/101-139-hostingservices.rst @@ -357,6 +357,6 @@ Once you have set up your dataset sibling(s), you can push individual datasets w is protecting. If the private key does not have a passphrase, simply copying this file grants a person access! -.. [#f3] GitHub `deprecated user-password authentication `_ and only supports authentication via personal access token from November 13th 2020 onwards. Supplying a password instead of a token will fail to authenticate. +.. [#f3] GitHub `deprecated user-password authentication `_ in favour of authentication via personal access token. Supplying a password instead of a token will fail to authenticate. .. [#f4] The default project name ``project`` and path separator ``-`` are configurable using the dataset-level configurations ``datalad.gitlab-default-projectname`` and ``datalad.gitlab-default-pathseparator`` From 98800f7d26c38e4368a59ea9537634836215d98f Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 14:37:42 +0100 Subject: [PATCH 16/17] Add diffs --- docs/basics/_examples/DL-101-101-101 | 3 - docs/basics/_examples/DL-101-102-106 | 3 - docs/basics/_examples/DL-101-102-107 | 6 +- docs/basics/_examples/DL-101-102-110 | 3 - docs/basics/_examples/DL-101-102-111 | 4 +- docs/basics/_examples/DL-101-102-112 | 4 - docs/basics/_examples/DL-101-102-115 | 2 +- docs/basics/_examples/DL-101-102-116 | 6 +- docs/basics/_examples/DL-101-103-103 | 3 - docs/basics/_examples/DL-101-103-106 | 3 - docs/basics/_examples/DL-101-103-107 | 4 +- docs/basics/_examples/DL-101-105-102 | 10 - docs/basics/_examples/DL-101-105-115 | 3 - docs/basics/_examples/DL-101-106-101 | 18 +- docs/basics/_examples/DL-101-108-104 | 3 - 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docs/basics/_examples/DL-101-136-142 | 2 +- docs/basics/_examples/DL-101-136-144 | 2 +- docs/basics/_examples/DL-101-136-145 | 4 - docs/basics/_examples/DL-101-136-146 | 3 - docs/basics/_examples/DL-101-136-147 | 2 +- docs/basics/_examples/DL-101-136-149 | 2 +- docs/basics/_examples/DL-101-136-150 | 2 +- docs/basics/_examples/DL-101-136-152 | 4 - docs/basics/_examples/DL-101-136-153 | 2 +- docs/basics/_examples/DL-101-136-155 | 4 - docs/basics/_examples/DL-101-136-157 | 2 +- docs/basics/_examples/DL-101-136-168 | 8 +- docs/basics/_examples/DL-101-136-169 | 3 - docs/basics/_examples/DL-101-136-170 | 4 - docs/basics/_examples/DL-101-136-173 | 3 - docs/basics/_examples/DL-101-136-174 | 2 +- docs/basics/_examples/DL-101-136-177 | 3 - docs/basics/_examples/DL-101-136-180 | 2 +- docs/basics/_examples/DL-101-136-181 | 10 - docs/basics/_examples/DL-101-136-183 | 6 - docs/basics/_examples/DL-101-136-184 | 5 - docs/basics/_examples/DL-101-137-101 | 30 +-- docs/basics/_examples/DL-101-137-104 | 3 - docs/basics/_examples/DL-101-137-105 | 2 +- docs/basics/_examples/DL-101-137-106 | 6 +- docs/basics/_examples/DL-101-137-107 | 2 +- docs/basics/_examples/DL-101-137-108 | 4 +- docs/basics/_examples/DL-101-137-111 | 3 - docs/basics/_examples/DL-101-137-112 | 4 +- docs/basics/_examples/DL-101-137-113 | 3 - docs/basics/_examples/DL-101-137-114 | 2 +- docs/basics/_examples/DL-101-137-117 | 6 +- docs/basics/_examples/DL-101-137-118 | 2 +- docs/basics/_examples/DL-101-137-119 | 4 +- docs/basics/_examples/DL-101-137-121 | 38 ++-- docs/basics/_examples/DL-101-137-122 | 6 +- docs/basics/_examples/DL-101-137-124 | 2 +- docs/basics/_examples/DL-101-137-127 | 2 +- docs/basics/_examples/DL-101-137-131 | 3 - docs/basics/_examples/DL-101-137-132 | 4 +- docs/basics/_examples/DL-101-137-133 | 4 +- docs/basics/_examples/DL-101-137-141 | 3 - docs/basics/_examples/DL-101-137-143 | 3 - docs/basics/_examples/DL-101-137-144 | 4 +- docs/basics/_examples/DL-101-137-146 | 8 +- docs/basics/_examples/DL-101-139-102 | 11 - docs/basics/_examples/DL-101-139-106 | 9 +- docs/basics/_examples/DL-101-139-107 | 7 - docs/basics/_examples/DL-101-141-101 | 10 +- docs/beyond_basics/_examples/DL-101-147-103 | 5 - docs/beyond_basics/_examples/DL-101-147-104 | 4 +- docs/beyond_basics/_examples/DL-101-147-107 | 14 -- docs/beyond_basics/_examples/DL-101-147-108 | 20 +- docs/beyond_basics/_examples/DL-101-147-109 | 5 - docs/beyond_basics/_examples/DL-101-147-110 | 14 -- docs/beyond_basics/_examples/DL-101-147-112 | 26 +-- docs/beyond_basics/_examples/DL-101-147-120 | 6 - docs/beyond_basics/_examples/DL-101-147-124 | 5 - docs/beyond_basics/_examples/DL-101-147-125 | 2 +- docs/beyond_basics/_examples/DL-101-147-127 | 2 - docs/beyond_basics/_examples/DL-101-149-01 | 7 - docs/beyond_basics/_examples/DL-101-149-02 | 109 ---------- docs/beyond_basics/_examples/DL-101-149-04 | 3 - docs/beyond_basics/_examples/DL-101-149-10 | 3 - docs/beyond_basics/_examples/DL-101-149-12 | 4 +- docs/beyond_basics/_examples/DL-101-149-14 | 3 - docs/beyond_basics/_examples/DL-101-149-17 | 3 - docs/beyond_basics/_examples/DL-101-168-103 | 3 - docs/beyond_basics/_examples/DL-101-168-104 | 6 - docs/beyond_basics/_examples/DL-101-168-108 | 2 +- docs/beyond_basics/_examples/DL-101-168-113 | 2 +- docs/beyond_basics/_examples/DL-101-168-114 | 5 - docs/beyond_basics/_examples/DL-101-168-124 | 2 +- docs/beyond_basics/_examples/DL-101-168-131 | 8 - docs/beyond_basics/_examples/DL-101-168-132 | 2 - docs/beyond_basics/_examples/DL-101-168-140 | 4 - docs/beyond_basics/_examples/DL-101-168-141 | 13 +- docs/beyond_basics/_examples/DL-101-168-142 | 2 - docs/beyond_basics/_examples/DL-101-168-143 | 2 - docs/beyond_basics/_examples/DL-101-168-151 | 2 +- docs/beyond_basics/_examples/DL-101-168-154 | 4 +- docs/beyond_basics/_examples/DL-101-168-155 | 4 +- docs/beyond_basics/_examples/DL-101-168-157 | 2 +- docs/beyond_basics/_examples/DL-101-168-159 | 2 +- docs/beyond_basics/_examples/DL-101-168-160 | 2 +- docs/beyond_basics/_examples/DL-101-168-165 | 2 +- docs/beyond_basics/_examples/DL-101-168-166 | 6 +- docs/beyond_basics/_examples/DL-101-168-177 | 3 - docs/beyond_basics/_examples/DL-101-168-178 | 6 +- docs/beyond_basics/_examples/DL-101-168-179 | 6 +- docs/beyond_basics/_examples/DL-101-179-103 | 3 - docs/beyond_basics/_examples/DL-101-179-109 | 3 - docs/beyond_basics/_examples/DL-101-181-101 | 8 - docs/beyond_basics/_examples/DL-101-181-102 | 2 +- docs/beyond_basics/_examples/DL-101-181-108 | 13 +- docs/beyond_basics/_examples/DL-101-182-103 | 2 +- docs/beyond_basics/_examples/DL-101-182-105 | 8 +- docs/beyond_basics/_examples/DL-101-182-106 | 2 - docs/beyond_basics/_examples/DL-101-182-114 | 5 - 187 files changed, 423 insertions(+), 894 deletions(-) diff --git a/docs/basics/_examples/DL-101-101-101 b/docs/basics/_examples/DL-101-101-101 index 4ef899e36..51fd58921 100644 --- a/docs/basics/_examples/DL-101-101-101 +++ b/docs/basics/_examples/DL-101-101-101 @@ -4,6 +4,3 @@ $ datalad create -c text2git DataLad-101 [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101 (dataset) [VIRTUALENV/bin/python /home/a...] create(ok): /home/me/dl-101/DataLad-101 (dataset) -action summary: - create (ok: 1) - run (ok: 1) diff --git a/docs/basics/_examples/DL-101-102-106 b/docs/basics/_examples/DL-101-102-106 index 32a211f31..e691719fb 100644 --- a/docs/basics/_examples/DL-101-102-106 +++ b/docs/basics/_examples/DL-101-102-106 @@ -2,6 +2,3 @@ $ datalad save -m "add books on Python and Unix to read later" add(ok): books/TLCL.pdf (file) add(ok): books/byte-of-python.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 2) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-102-107 b/docs/basics/_examples/DL-101-102-107 index 074dbc1f4..390bf564c 100644 --- a/docs/basics/_examples/DL-101-102-107 +++ b/docs/basics/_examples/DL-101-102-107 @@ -1,5 +1,5 @@ $ git log -p -n 1 -commit d2bb1a86✂SHA1 +commit b40316a6✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -15,9 +15,9 @@ index 0000000..4c84b61 \ No newline at end of file diff --git a/books/byte-of-python.pdf b/books/byte-of-python.pdf new file mode 120000 -index 0000000..b9fcbff +index 0000000..7a6e51e --- /dev/null +++ b/books/byte-of-python.pdf @@ -0,0 +1 @@ -+../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf ++../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf \ No newline at end of file diff --git a/docs/basics/_examples/DL-101-102-110 b/docs/basics/_examples/DL-101-102-110 index f569ce228..584f52a4a 100644 --- a/docs/basics/_examples/DL-101-102-110 +++ b/docs/basics/_examples/DL-101-102-110 @@ -1,6 +1,3 @@ $ datalad save -m "add reference book about git" books/progit.pdf add(ok): books/progit.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-102-111 b/docs/basics/_examples/DL-101-102-111 index 2e7b143ff..a9126c52d 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 -8e5dc80 add reference book about git -d2bb1a8 add books on Python and Unix to read later +a875e49 add reference book about git +b40316a add books on Python and Unix to read later e0ff3a7 Instruct annex to add text files to Git 4ce681d [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-102-112 b/docs/basics/_examples/DL-101-102-112 index 6796f302e..5cc9407bc 100644 --- a/docs/basics/_examples/DL-101-102-112 +++ b/docs/basics/_examples/DL-101-102-112 @@ -7,7 +7,3 @@ $ datalad download-url \ download_url(ok): /home/me/dl-101/DataLad-101/books/bash_guide.pdf (file) add(ok): books/bash_guide.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - download_url (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-102-115 b/docs/basics/_examples/DL-101-102-115 index d4586eaef..675df6c33 100644 --- a/docs/basics/_examples/DL-101-102-115 +++ b/docs/basics/_examples/DL-101-102-115 @@ -1,5 +1,5 @@ $ git log -p -n 1 -commit bcb0ffe8✂SHA1 +commit 59ac8d32✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-102-116 b/docs/basics/_examples/DL-101-102-116 index 6a12ebe43..91218e617 100644 --- a/docs/basics/_examples/DL-101-102-116 +++ b/docs/basics/_examples/DL-101-102-116 @@ -1,6 +1,6 @@ $ git log --oneline -bcb0ffe add beginners guide on bash -8e5dc80 add reference book about git -d2bb1a8 add books on Python and Unix to read later +59ac8d3 add beginners guide on bash +a875e49 add reference book about git +b40316a add books on Python and Unix to read later e0ff3a7 Instruct annex to add text files to Git 4ce681d [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-103-103 b/docs/basics/_examples/DL-101-103-103 index c82b8d051..011069005 100644 --- a/docs/basics/_examples/DL-101-103-103 +++ b/docs/basics/_examples/DL-101-103-103 @@ -1,6 +1,3 @@ $ datalad save -m "Add notes on datalad create" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-103-106 b/docs/basics/_examples/DL-101-103-106 index 2ff261d19..50481d9c7 100644 --- a/docs/basics/_examples/DL-101-103-106 +++ b/docs/basics/_examples/DL-101-103-106 @@ -1,6 +1,3 @@ $ datalad save -m "add note on datalad save" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-103-107 b/docs/basics/_examples/DL-101-103-107 index c980506a5..005b83dee 100644 --- a/docs/basics/_examples/DL-101-103-107 +++ b/docs/basics/_examples/DL-101-103-107 @@ -1,5 +1,5 @@ $ git log -p -n 2 -commit 9783a90c✂SHA1 +commit e310b465✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -18,7 +18,7 @@ index 3a7a1fe..0142412 100644 +Note to self: Always use informative, concise commit messages. + -commit b538dae3✂SHA1 +commit 874d766f✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-105-102 b/docs/basics/_examples/DL-101-105-102 index 554c93027..055fa8518 100644 --- a/docs/basics/_examples/DL-101-105-102 +++ b/docs/basics/_examples/DL-101-105-102 @@ -1,20 +1,10 @@ $ datalad clone --dataset . \ https://github.com/datalad-datasets/longnow-podcasts.git recordings/longnow [INFO] Attempting a clone into /home/me/dl-101/DataLad-101/recordings/longnow -[INFO] Attempting to clone from https://github.com/datalad-datasets/longnow-podcasts.git to /home/me/dl-101/DataLad-101/recordings/longnow -[INFO] Start enumerating objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/DataLad-101/recordings/longnow) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-datasets/longnow-podcasts.git/config download failed: Not Found install(ok): recordings/longnow (dataset) add(ok): recordings/longnow (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 3) - install (ok: 1) - save (ok: 2) diff --git a/docs/basics/_examples/DL-101-105-115 b/docs/basics/_examples/DL-101-105-115 index 8310e781d..406561717 100644 --- a/docs/basics/_examples/DL-101-105-115 +++ b/docs/basics/_examples/DL-101-105-115 @@ -10,6 +10,3 @@ EOT $ datalad save -m "Add note on datalad clone" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-106-101 b/docs/basics/_examples/DL-101-106-101 index 474cd04a4..0628f46ee 100644 --- a/docs/basics/_examples/DL-101-106-101 +++ b/docs/basics/_examples/DL-101-106-101 @@ -1,5 +1,5 @@ $ git log -p -n 3 -commit fa63a083✂SHA1 +commit 87609a36✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -19,7 +19,7 @@ index 0142412..e34ef1f 100644 +superdataset with the '-d' option. + -commit 7c489fbf✂SHA1 +commit 3c016f73✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -44,7 +44,7 @@ index 0000000..dcc34fb @@ -0,0 +1 @@ +Subproject commit dcc34fbe✂SHA1 -commit 9783a90c✂SHA1 +commit e310b465✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -63,7 +63,7 @@ index 3a7a1fe..0142412 100644 +Note to self: Always use informative, concise commit messages. + -commit b538dae3✂SHA1 +commit 874d766f✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -79,7 +79,7 @@ index 0000000..3a7a1fe +The dataset is created empty + -commit bcb0ffe8✂SHA1 +commit 59ac8d32✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -94,7 +94,7 @@ index 0000000..00ca6bd +../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf \ No newline at end of file -commit 8e5dc808✂SHA1 +commit a875e496✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -109,7 +109,7 @@ index 0000000..c5d2ab2 +../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf \ No newline at end of file -commit d2bb1a86✂SHA1 +commit b40316a6✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -125,11 +125,11 @@ index 0000000..4c84b61 \ No newline at end of file diff --git a/books/byte-of-python.pdf b/books/byte-of-python.pdf new file mode 120000 -index 0000000..b9fcbff +index 0000000..7a6e51e --- /dev/null +++ b/books/byte-of-python.pdf @@ -0,0 +1 @@ -+../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf ++../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf \ No newline at end of file commit e0ff3a73✂SHA1 diff --git a/docs/basics/_examples/DL-101-108-104 b/docs/basics/_examples/DL-101-108-104 index f92f6b8c0..83a4af100 100644 --- a/docs/basics/_examples/DL-101-108-104 +++ b/docs/basics/_examples/DL-101-108-104 @@ -1,6 +1,3 @@ $ 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: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-108-106 b/docs/basics/_examples/DL-101-108-106 index 0acce7e09..12ac357de 100644 --- a/docs/basics/_examples/DL-101-108-106 +++ b/docs/basics/_examples/DL-101-108-106 @@ -1,5 +1,5 @@ $ git log -p -n 1 # On Windows, you may just want to type "git log". -commit f4f30396✂SHA1 +commit e37c9fc9✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-108-108 b/docs/basics/_examples/DL-101-108-108 index 0e2efcd2f..c8a1ae449 100644 --- a/docs/basics/_examples/DL-101-108-108 +++ b/docs/basics/_examples/DL-101-108-108 @@ -1,12 +1,12 @@ $ git log --oneline -f4f3039 [DATALAD RUNCMD] create a list of podcast titles -50addd7 Add short script to write a list of podcast speakers and titles -fa63a08 Add note on datalad clone -7c489fb [DATALAD] Added subdataset -9783a90 add note on datalad save -b538dae Add notes on datalad create -bcb0ffe add beginners guide on bash -8e5dc80 add reference book about git -d2bb1a8 add books on Python and Unix to read later +e37c9fc [DATALAD RUNCMD] create a list of podcast titles +e799b6b Add short script to write a list of podcast speakers and titles +87609a3 Add note on datalad clone +3c016f7 [DATALAD] Added subdataset +e310b46 add note on datalad save +874d766 Add notes on datalad create +59ac8d3 add beginners guide on bash +a875e49 add reference book about git +b40316a add books on Python and Unix to read later e0ff3a7 Instruct annex to add text files to Git 4ce681d [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-109-104 b/docs/basics/_examples/DL-101-109-104 index 33683c479..7f8a2d25e 100644 --- a/docs/basics/_examples/DL-101-109-104 +++ b/docs/basics/_examples/DL-101-109-104 @@ -2,6 +2,3 @@ $ datalad save -m "BF: list both directories content" \ code/list_titles.sh add(ok): code/list_titles.sh (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-109-105 b/docs/basics/_examples/DL-101-109-105 index f07a1f963..1d367ffff 100644 --- a/docs/basics/_examples/DL-101-109-105 +++ b/docs/basics/_examples/DL-101-109-105 @@ -1,11 +1,11 @@ $ git log -n 2 -commit 07db512b✂SHA1 +commit f7ea9f3d✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 BF: list both directories content -commit f4f30396✂SHA1 +commit e37c9fc9✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-109-106 b/docs/basics/_examples/DL-101-109-106 index 07649da23..f9cc73d49 100644 --- a/docs/basics/_examples/DL-101-109-106 +++ b/docs/basics/_examples/DL-101-109-106 @@ -1,6 +1,6 @@ -$ datalad rerun f4f30396✂SHA1 -[INFO] run commit f4f3039; (create a list of ...) +$ datalad rerun e37c9fc9✂SHA1 +[INFO] run commit e37c9fc; (create a list of ...) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101 (dataset) [bash code/list_titles.sh > recordings/po...] diff --git a/docs/basics/_examples/DL-101-109-107 b/docs/basics/_examples/DL-101-109-107 index a5323a3fc..609753961 100644 --- a/docs/basics/_examples/DL-101-109-107 +++ b/docs/basics/_examples/DL-101-109-107 @@ -1,5 +1,5 @@ $ git log -n 1 -commit f4916ccb✂SHA1 +commit 08120c38✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -8,7 +8,7 @@ Date: Tue Jun 18 16:13:00 2019 +0000 === Do not change lines below === { "chain": [ - "f4f30396✂SHA1" + "e37c9fc9✂SHA1" ], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", "dsid": "e3e70682-c209-4cac-629f-6fbed82c07cd", diff --git a/docs/basics/_examples/DL-101-109-111 b/docs/basics/_examples/DL-101-109-111 index 612cc39fb..992133d63 100644 --- a/docs/basics/_examples/DL-101-109-111 +++ b/docs/basics/_examples/DL-101-109-111 @@ -1,6 +1,3 @@ $ datalad save -m "add note datalad and git diff" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-109-112 b/docs/basics/_examples/DL-101-109-112 index 4c425af7b..6b8b1f353 100644 --- a/docs/basics/_examples/DL-101-109-112 +++ b/docs/basics/_examples/DL-101-109-112 @@ -1,5 +1,5 @@ $ git log -- recordings/podcasts.tsv -commit f4916ccb✂SHA1 +commit 08120c38✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -8,7 +8,7 @@ Date: Tue Jun 18 16:13:00 2019 +0000 === Do not change lines below === { "chain": [ - "f4f30396✂SHA1" + "e37c9fc9✂SHA1" ], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", "dsid": "e3e70682-c209-4cac-629f-6fbed82c07cd", @@ -20,7 +20,7 @@ Date: Tue Jun 18 16:13:00 2019 +0000 } ^^^ Do not change lines above ^^^ -commit f4f30396✂SHA1 +commit e37c9fc9✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-109-114 b/docs/basics/_examples/DL-101-109-114 index 1f173224d..af265f6c6 100644 --- a/docs/basics/_examples/DL-101-109-114 +++ b/docs/basics/_examples/DL-101-109-114 @@ -1,6 +1,3 @@ $ datalad save -m "add note on basic datalad run and datalad rerun" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-111-104 b/docs/basics/_examples/DL-101-111-104 index 31d7e5a9e..f2b6567b9 100644 --- a/docs/basics/_examples/DL-101-111-104 +++ b/docs/basics/_examples/DL-101-111-104 @@ -1,6 +1,3 @@ $ datalad save -m "resized picture by hand" add(ok): recordings/salt_logo_small.jpg (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-112-103 b/docs/basics/_examples/DL-101-112-103 index f536e904e..970231d4a 100644 --- a/docs/basics/_examples/DL-101-112-103 +++ b/docs/basics/_examples/DL-101-112-103 @@ -1,6 +1,3 @@ $ datalad save -m "add additional notes on run options" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-112-108 b/docs/basics/_examples/DL-101-112-108 index d9bce4123..a30e768c1 100644 --- a/docs/basics/_examples/DL-101-112-108 +++ b/docs/basics/_examples/DL-101-112-108 @@ -1,6 +1,3 @@ $ datalad save -m "add note on clean datasets" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-112-109 b/docs/basics/_examples/DL-101-112-109 index 2b8ba061d..8742724be 100644 --- a/docs/basics/_examples/DL-101-112-109 +++ b/docs/basics/_examples/DL-101-112-109 @@ -1,5 +1,5 @@ $ git log -p -n 2 -commit b5fc1296✂SHA1 +commit 41fdaab8✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -20,7 +20,7 @@ index 6a465f0..e2829b2 100644 +those changes done to the files listed with --output flags. + -commit d5845d33✂SHA1 +commit fd4a25e6✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-114-101 b/docs/basics/_examples/DL-101-114-101 index 17b5c0aca..2c060e0e4 100644 --- a/docs/basics/_examples/DL-101-114-101 +++ b/docs/basics/_examples/DL-101-114-101 @@ -1,23 +1,23 @@ $ git log --reverse --oneline 4ce681d [DATALAD] new dataset e0ff3a7 Instruct annex to add text files to Git -d2bb1a8 add books on Python and Unix to read later -8e5dc80 add reference book about git -bcb0ffe add beginners guide on bash -b538dae Add notes on datalad create -9783a90 add note on datalad save -7c489fb [DATALAD] Added subdataset -fa63a08 Add note on datalad clone -50addd7 Add short script to write a list of podcast speakers and titles -f4f3039 [DATALAD RUNCMD] create a list of podcast titles -07db512 BF: list both directories content -f4916cc [DATALAD RUNCMD] create a list of podcast titles -572fd65 add note datalad and git diff -4009576 add note on basic datalad run and datalad rerun -be503c3 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -9369462 resized picture by hand -a4044db [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -af9ca10 add additional notes on run options -d24531d [DATALAD RUNCMD] Resize logo for slides -d5845d3 [DATALAD RUNCMD] Resize logo for slides -b5fc129 add note on clean datasets +b40316a add books on Python and Unix to read later +a875e49 add reference book about git +59ac8d3 add beginners guide on bash +874d766 Add notes on datalad create +e310b46 add note on datalad save +3c016f7 [DATALAD] Added subdataset +87609a3 Add note on datalad clone +e799b6b Add short script to write a list of podcast speakers and titles +e37c9fc [DATALAD RUNCMD] create a list of podcast titles +f7ea9f3 BF: list both directories content +08120c3 [DATALAD RUNCMD] create a list of podcast titles +cdedbc3 add note datalad and git diff +4b7a0a0 add note on basic datalad run and datalad rerun +6686234 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +5227d93 resized picture by hand +d0c060f [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +87b4f80 add additional notes on run options +08f2efb [DATALAD RUNCMD] Resize logo for slides +fd4a25e [DATALAD RUNCMD] Resize logo for slides +41fdaab add note on clean datasets diff --git a/docs/basics/_examples/DL-101-115-101 b/docs/basics/_examples/DL-101-115-101 index 31a129c09..97ff6464f 100644 --- a/docs/basics/_examples/DL-101-115-101 +++ b/docs/basics/_examples/DL-101-115-101 @@ -3,7 +3,7 @@ $ cd books $ tree . ├── bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -├── byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +├── byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf ├── progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf └── TLCL.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-115-103 b/docs/basics/_examples/DL-101-115-103 index f5b77a2f9..2787c9078 100644 --- a/docs/basics/_examples/DL-101-115-103 +++ b/docs/basics/_examples/DL-101-115-103 @@ -1,6 +1,6 @@ $ ls -lh total 16K lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf lrwxrwxrwx 1 elena elena 133 2019-06-18 16:13 progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 TLCL.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-116-102 b/docs/basics/_examples/DL-101-116-102 index c1040715b..3ea1bd6bc 100644 --- a/docs/basics/_examples/DL-101-116-102 +++ b/docs/basics/_examples/DL-101-116-102 @@ -1,6 +1,4 @@ $ cd mock_user $ datalad clone --description "DataLad-101 in mock_user" ../DataLad-101 [INFO] Attempting a clone into /home/me/dl-101/mock_user/DataLad-101 -[INFO] Attempting to clone from ../DataLad-101 to /home/me/dl-101/mock_user/DataLad-101 -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/mock_user/DataLad-101) install(ok): /home/me/dl-101/mock_user/DataLad-101 (dataset) diff --git a/docs/basics/_examples/DL-101-116-103 b/docs/basics/_examples/DL-101-116-103 index 2da69fa4b..d59cda51a 100644 --- a/docs/basics/_examples/DL-101-116-103 +++ b/docs/basics/_examples/DL-101-116-103 @@ -3,7 +3,7 @@ $ tree . ├── books │   ├── bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -│   ├── byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +│   ├── byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf │   ├── progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf │   └── TLCL.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf ├── code diff --git a/docs/basics/_examples/DL-101-116-107 b/docs/basics/_examples/DL-101-116-107 index b269fa131..482e55c94 100644 --- a/docs/basics/_examples/DL-101-116-107 +++ b/docs/basics/_examples/DL-101-116-107 @@ -1,10 +1,4 @@ $ datalad get -n recordings/longnow [INFO] Attempting a clone into /home/me/dl-101/mock_user/DataLad-101/recordings/longnow -[INFO] Attempting to clone from https://github.com/datalad-datasets/longnow-podcasts.git to /home/me/dl-101/mock_user/DataLad-101/recordings/longnow -[INFO] Start enumerating objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/mock_user/DataLad-101/recordings/longnow) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-datasets/longnow-podcasts.git/config download failed: Not Found install(ok): /home/me/dl-101/mock_user/DataLad-101/recordings/longnow (dataset) [Installed subdataset in order to get /home/me/dl-101/mock_user/DataLad-101/recordings/longnow] diff --git a/docs/basics/_examples/DL-101-116-108 b/docs/basics/_examples/DL-101-116-108 index 7875f7be6..a24121184 100644 --- a/docs/basics/_examples/DL-101-116-108 +++ b/docs/basics/_examples/DL-101-116-108 @@ -2,7 +2,7 @@ $ tree . ├── books │   ├── bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -│   ├── byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +│   ├── byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf │   ├── progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf │   └── TLCL.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf ├── code diff --git a/docs/basics/_examples/DL-101-116-110 b/docs/basics/_examples/DL-101-116-110 index 32fd7a749..b77a7515f 100644 --- a/docs/basics/_examples/DL-101-116-110 +++ b/docs/basics/_examples/DL-101-116-110 @@ -1,6 +1,3 @@ $ datalad save -m "add note about cloning from paths and recursive datalad get" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-117-107 b/docs/basics/_examples/DL-101-117-107 index ec9f20957..10f70ac4d 100644 --- a/docs/basics/_examples/DL-101-117-107 +++ b/docs/basics/_examples/DL-101-117-107 @@ -1,6 +1,3 @@ $ datalad save -m "add note on git annex whereis" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-118-102 b/docs/basics/_examples/DL-101-118-102 index 044354540..40f77da26 100644 --- a/docs/basics/_examples/DL-101-118-102 +++ b/docs/basics/_examples/DL-101-118-102 @@ -1,12 +1,12 @@ # lets view the history $ git log --oneline -n 10 -b5fc129 add note on clean datasets -d5845d3 [DATALAD RUNCMD] Resize logo for slides -d24531d [DATALAD RUNCMD] Resize logo for slides -af9ca10 add additional notes on run options -a4044db [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -9369462 resized picture by hand -be503c3 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -4009576 add note on basic datalad run and datalad rerun -572fd65 add note datalad and git diff -f4916cc [DATALAD RUNCMD] create a list of podcast titles +41fdaab add note on clean datasets +fd4a25e [DATALAD RUNCMD] Resize logo for slides +08f2efb [DATALAD RUNCMD] Resize logo for slides +87b4f80 add additional notes on run options +d0c060f [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +5227d93 resized picture by hand +6686234 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +4b7a0a0 add note on basic datalad run and datalad rerun +cdedbc3 add note datalad and git diff +08120c3 [DATALAD RUNCMD] create a list of podcast titles diff --git a/docs/basics/_examples/DL-101-118-103 b/docs/basics/_examples/DL-101-118-103 index b9534c8bf..2eb5ac639 100644 --- a/docs/basics/_examples/DL-101-118-103 +++ b/docs/basics/_examples/DL-101-118-103 @@ -1,6 +1,6 @@ -$ datalad rerun d5845d33✂SHA1 -[INFO] run commit d5845d3; (Resize logo for s...) +$ datalad rerun fd4a25e6✂SHA1 +[INFO] run commit fd4a25e; (Resize logo for s...) [INFO] Making sure inputs are available (this may take some time) get(ok): recordings/longnow/.datalad/feed_metadata/logo_salt.jpg (file) [from web...] run.remove(ok): recordings/salt_logo_small.jpg (file) [Removed file] diff --git a/docs/basics/_examples/DL-101-119-102 b/docs/basics/_examples/DL-101-119-102 index f5b131274..c227b704b 100644 --- a/docs/basics/_examples/DL-101-119-102 +++ b/docs/basics/_examples/DL-101-119-102 @@ -1,12 +1,5 @@ $ datalad update --how merge [INFO] Fetching updates for Dataset(/home/me/dl-101/mock_user/DataLad-101) -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects merge(ok): . (dataset) [Merged origin/main] update.annex_merge(ok): . (dataset) [Merged annex branch] update(ok): . (dataset) -action summary: - merge (ok: 1) - update (ok: 1) - update.annex_merge (ok: 1) diff --git a/docs/basics/_examples/DL-101-119-105 b/docs/basics/_examples/DL-101-119-105 index 6a5592426..342e631eb 100644 --- a/docs/basics/_examples/DL-101-119-105 +++ b/docs/basics/_examples/DL-101-119-105 @@ -3,6 +3,3 @@ $ datalad save -m "add note about datalad update" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-121-101 b/docs/basics/_examples/DL-101-121-101 index 974e60dac..1b68e4328 100644 --- a/docs/basics/_examples/DL-101-121-101 +++ b/docs/basics/_examples/DL-101-121-101 @@ -11,7 +11,3 @@ $ datalad download-url \ download_url(ok): /home/me/dl-101/mock_user/DataLad-101/code/nested_repos.sh (file) add(ok): code/nested_repos.sh (file) save(ok): . (dataset) -action summary: - add (ok: 1) - download_url (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-121-103 b/docs/basics/_examples/DL-101-121-103 index 5e9044a95..e4cf735f2 100644 --- a/docs/basics/_examples/DL-101-121-103 +++ b/docs/basics/_examples/DL-101-121-103 @@ -1,5 +1,5 @@ $ git log -n 1 -p -commit 28a99fb2✂SHA1 +commit 5b6e19a5✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-121-106 b/docs/basics/_examples/DL-101-121-106 index b507cd971..5db41d76b 100644 --- a/docs/basics/_examples/DL-101-121-106 +++ b/docs/basics/_examples/DL-101-121-106 @@ -1,6 +1,3 @@ $ datalad update -s roommate [INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-121-110 b/docs/basics/_examples/DL-101-121-110 index b2bfe17fd..14b1e5102 100644 --- a/docs/basics/_examples/DL-101-121-110 +++ b/docs/basics/_examples/DL-101-121-110 @@ -3,7 +3,3 @@ $ datalad update --how merge -s roommate merge(ok): . (dataset) [Merged roommate/main] update.annex_merge(ok): . (dataset) [Merged annex branch] update(ok): . (dataset) -action summary: - merge (ok: 1) - update (ok: 1) - update.annex_merge (ok: 1) diff --git a/docs/basics/_examples/DL-101-121-112 b/docs/basics/_examples/DL-101-121-112 index 25e9bffa5..a1c282b8c 100644 --- a/docs/basics/_examples/DL-101-121-112 +++ b/docs/basics/_examples/DL-101-121-112 @@ -1,28 +1,28 @@ $ git log --oneline -0fbbe8c Merge remote-tracking branch 'roommate/main' -81bf4d3 add note about datalad update -28a99fb Include nesting demo from datalad website -26595f2 add note on git annex whereis -afa2884 add note about cloning from paths and recursive datalad get -b5fc129 add note on clean datasets -d5845d3 [DATALAD RUNCMD] Resize logo for slides -d24531d [DATALAD RUNCMD] Resize logo for slides -af9ca10 add additional notes on run options -a4044db [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -9369462 resized picture by hand -be503c3 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -4009576 add note on basic datalad run and datalad rerun -572fd65 add note datalad and git diff -f4916cc [DATALAD RUNCMD] create a list of podcast titles -07db512 BF: list both directories content -f4f3039 [DATALAD RUNCMD] create a list of podcast titles -50addd7 Add short script to write a list of podcast speakers and titles -fa63a08 Add note on datalad clone -7c489fb [DATALAD] Added subdataset -9783a90 add note on datalad save -b538dae Add notes on datalad create -bcb0ffe add beginners guide on bash -8e5dc80 add reference book about git -d2bb1a8 add books on Python and Unix to read later +6ae8e71 Merge remote-tracking branch 'roommate/main' +4bb5d39 add note about datalad update +5b6e19a Include nesting demo from datalad website +adb4b5d add note on git annex whereis +1e73592 add note about cloning from paths and recursive datalad get +41fdaab add note on clean datasets +fd4a25e [DATALAD RUNCMD] Resize logo for slides +08f2efb [DATALAD RUNCMD] Resize logo for slides +87b4f80 add additional notes on run options +d0c060f [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +5227d93 resized picture by hand +6686234 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +4b7a0a0 add note on basic datalad run and datalad rerun +cdedbc3 add note datalad and git diff +08120c3 [DATALAD RUNCMD] create a list of podcast titles +f7ea9f3 BF: list both directories content +e37c9fc [DATALAD RUNCMD] create a list of podcast titles +e799b6b Add short script to write a list of podcast speakers and titles +87609a3 Add note on datalad clone +3c016f7 [DATALAD] Added subdataset +e310b46 add note on datalad save +874d766 Add notes on datalad create +59ac8d3 add beginners guide on bash +a875e49 add reference book about git +b40316a add books on Python and Unix to read later e0ff3a7 Instruct annex to add text files to Git 4ce681d [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-121-113 b/docs/basics/_examples/DL-101-121-113 index a83667cde..45191a5ba 100644 --- a/docs/basics/_examples/DL-101-121-113 +++ b/docs/basics/_examples/DL-101-121-113 @@ -12,6 +12,3 @@ EOT $ datalad save -m "Add note on adding siblings" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-123-111 b/docs/basics/_examples/DL-101-123-111 index a0d16a364..559e2cd95 100644 --- a/docs/basics/_examples/DL-101-123-111 +++ b/docs/basics/_examples/DL-101-123-111 @@ -1,6 +1,3 @@ $ datalad save -m "add note on configurations and git config" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-124-105 b/docs/basics/_examples/DL-101-124-105 index 8365c9705..55d40c289 100644 --- a/docs/basics/_examples/DL-101-124-105 +++ b/docs/basics/_examples/DL-101-124-105 @@ -1,6 +1,3 @@ $ datalad save -m "add custom procedure" add(ok): .datalad/procedures/example.py (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-124-106 b/docs/basics/_examples/DL-101-124-106 index 354f7fbc6..789f0bf6c 100644 --- a/docs/basics/_examples/DL-101-124-106 +++ b/docs/basics/_examples/DL-101-124-106 @@ -5,8 +5,5 @@ add(ok): example2 (file) add(ok): somedir/example (file) add(ok): .gitattributes (file) save(ok): . (dataset) -action summary: - add (ok: 3) - save (ok: 1) [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/procs/somedataset (dataset) [VIRTUALENV/bin/python /home/m...] diff --git a/docs/basics/_examples/DL-101-124-109 b/docs/basics/_examples/DL-101-124-109 index 99b7d0e6c..a55d4d61e 100644 --- a/docs/basics/_examples/DL-101-124-109 +++ b/docs/basics/_examples/DL-101-124-109 @@ -2,6 +2,3 @@ $ git config -f .datalad/config datalad.procedures.example.help "A toy example" $ datalad save -m "add help description" add(ok): .datalad/config (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-124-112 b/docs/basics/_examples/DL-101-124-112 index 7f8f8aac2..aec19687a 100644 --- a/docs/basics/_examples/DL-101-124-112 +++ b/docs/basics/_examples/DL-101-124-112 @@ -1,6 +1,3 @@ $ datalad save -m "add note on DataLad's procedures" add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-102 b/docs/basics/_examples/DL-101-130-102 index 86374ea5c..08d14c34c 100644 --- a/docs/basics/_examples/DL-101-130-102 +++ b/docs/basics/_examples/DL-101-130-102 @@ -4,7 +4,3 @@ $ datalad download-url https://gist.githubusercontent.com/netj/8836201/raw/6f930 download_url(ok): /home/me/dl-101/iris_data/iris.csv (file) add(ok): iris.csv (file) save(ok): . (dataset) -action summary: - add (ok: 1) - download_url (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-103 b/docs/basics/_examples/DL-101-130-103 index 67d91f384..2bfa3ecb5 100644 --- a/docs/basics/_examples/DL-101-130-103 +++ b/docs/basics/_examples/DL-101-130-103 @@ -8,8 +8,3 @@ add(ok): midterm_project (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): midterm_project (dataset) -action summary: - add (ok: 2) - create (ok: 1) - run (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-105 b/docs/basics/_examples/DL-101-130-105 index 01dc655a9..f995014b1 100644 --- a/docs/basics/_examples/DL-101-130-105 +++ b/docs/basics/_examples/DL-101-130-105 @@ -4,22 +4,10 @@ $ datalad clone -d . \ https://github.com/datalad-handbook/iris_data.git \ input/ [INFO] Attempting a clone into /home/me/dl-101/DataLad-101/midterm_project/input -[INFO] Attempting to clone from https://github.com/datalad-handbook/iris_data.git to /home/me/dl-101/DataLad-101/midterm_project/input -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/DataLad-101/midterm_project/input) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-handbook/iris_data.git/config download failed: Not Found install(ok): input (dataset) add(ok): input (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 3) - install (ok: 1) - save (ok: 2) diff --git a/docs/basics/_examples/DL-101-130-109 b/docs/basics/_examples/DL-101-130-109 index ce510c376..e554b9ec6 100644 --- a/docs/basics/_examples/DL-101-130-109 +++ b/docs/basics/_examples/DL-101-130-109 @@ -3,6 +3,3 @@ $ datalad save -m "add script for kNN classification and plotting" \ code/script.py add(ok): code/script.py (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-110 b/docs/basics/_examples/DL-101-130-110 index 8b6e5a2be..2963538e0 100644 --- a/docs/basics/_examples/DL-101-130-110 +++ b/docs/basics/_examples/DL-101-130-110 @@ -1,5 +1,5 @@ $ git show ready4analysis -commit 5081206e✂SHA1 +commit ca0c7477✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -7,10 +7,10 @@ Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/code/script.py b/code/script.py new file mode 100644 -index 0000000..4f5833b +index 0000000..c7a6ea9 --- /dev/null +++ b/code/script.py -@@ -0,0 +1,42 @@ +@@ -0,0 +1,43 @@ + +import argparse +import pandas as pd diff --git a/docs/basics/_examples/DL-101-130-111 b/docs/basics/_examples/DL-101-130-111 index cc5119a5c..7101c9db7 100644 --- a/docs/basics/_examples/DL-101-130-111 +++ b/docs/basics/_examples/DL-101-130-111 @@ -6,8 +6,6 @@ $ datalad run -m "analyze iris data with classification analysis" \ [INFO] Making sure inputs are available (this may take some time) get(ok): input/iris.csv (file) [from web...] [INFO] == Command start (output follows) ===== -VIRTUALENV/lib/python3.8/site-packages/seaborn/axisgrid.py:118: UserWarning: The figure layout has changed to tight - self._figure.tight_layout(*args, **kwargs) [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101/midterm_project (dataset) [python3 code/script.py input/iris.csv pa...] add(ok): pairwise_relationships.png (file) diff --git a/docs/basics/_examples/DL-101-130-112 b/docs/basics/_examples/DL-101-130-112 index 8675e4265..2a666a99a 100644 --- a/docs/basics/_examples/DL-101-130-112 +++ b/docs/basics/_examples/DL-101-130-112 @@ -1,6 +1,6 @@ $ git log --oneline -7469b34 [DATALAD RUNCMD] analyze iris data with classification analysis -5081206 add script for kNN classification and plotting +9aadac7 [DATALAD RUNCMD] analyze iris data with classification analysis +ca0c747 add script for kNN classification and plotting 4f945ed [DATALAD] Added subdataset 18f4a98 Apply YODA dataset setup bf231d5 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-130-115 b/docs/basics/_examples/DL-101-130-115 index ac8ec70eb..9a8fdf769 100644 --- a/docs/basics/_examples/DL-101-130-115 +++ b/docs/basics/_examples/DL-101-130-115 @@ -1,6 +1,3 @@ $ datalad save -m "Provide project description" README.md add(ok): README.md (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-118 b/docs/basics/_examples/DL-101-130-118 index e71026d28..ede9e474d 100644 --- a/docs/basics/_examples/DL-101-130-118 +++ b/docs/basics/_examples/DL-101-130-118 @@ -1,17 +1,7 @@ $ datalad push --to github [INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data copy(ok): pairwise_relationships.png (file) [to github...] copy(ok): prediction_report.csv (file) [to github...] -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects publish(ok): . (dataset) [refs/heads/git-annex->github:refs/heads/git-annex ✂FROM✂..✂TO✂] publish(ok): . (dataset) [refs/heads/main->github:refs/heads/main [new branch]] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) -action summary: - copy (ok: 2) - publish (ok: 2) diff --git a/docs/basics/_examples/DL-101-130-119 b/docs/basics/_examples/DL-101-130-119 index b8048386f..e1c3eb6bd 100644 --- a/docs/basics/_examples/DL-101-130-119 +++ b/docs/basics/_examples/DL-101-130-119 @@ -1,13 +1,5 @@ $ cd ../../ $ datalad clone "https://github.com/adswa/midtermproject.git" [INFO] Attempting a clone into /home/me/dl-101/midtermproject -[INFO] Attempting to clone from https://github.com/adswa/midtermproject.git to /home/me/dl-101/midtermproject -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/midtermproject) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/adswa/midtermproject.git/config download failed: Not Found install(ok): /home/me/dl-101/midtermproject (dataset) diff --git a/docs/basics/_examples/DL-101-130-120 b/docs/basics/_examples/DL-101-130-120 index f714405ee..7cf37d2e8 100644 --- a/docs/basics/_examples/DL-101-130-120 +++ b/docs/basics/_examples/DL-101-130-120 @@ -1,17 +1,6 @@ $ cd midtermproject $ datalad get input/iris.csv [INFO] Attempting a clone into /home/me/dl-101/midtermproject/input -[INFO] Attempting to clone from https://github.com/datalad-handbook/iris_data.git to /home/me/dl-101/midtermproject/input -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/midtermproject/input) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-handbook/iris_data.git/config download failed: Not Found install(ok): /home/me/dl-101/midtermproject/input (dataset) [Installed subdataset in order to get /home/me/dl-101/midtermproject/input/iris.csv] get(ok): input/iris.csv (file) [from web...] -action summary: - get (ok: 1) - install (ok: 1) diff --git a/docs/basics/_examples/DL-101-130-121 b/docs/basics/_examples/DL-101-130-121 index e66dc3cdf..df8709f57 100644 --- a/docs/basics/_examples/DL-101-130-121 +++ b/docs/basics/_examples/DL-101-130-121 @@ -1,5 +1,3 @@ $ datalad get prediction_report.csv pairwise_relationships.png -get(error): prediction_report.csv (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): pairwise_relationships.png (file) [not available; (Note that these git remotes have annex-ignore set: origin)] -action summary: - get (error: 2) +get(error): prediction_report.csv (file) [not available; (Note that these git remotes have annex-ignore set: origin)] diff --git a/docs/basics/_examples/DL-101-130-122 b/docs/basics/_examples/DL-101-130-122 index 21283647b..6c17b5d01 100644 --- a/docs/basics/_examples/DL-101-130-122 +++ b/docs/basics/_examples/DL-101-130-122 @@ -7,8 +7,6 @@ run.remove(ok): prediction_report.csv (file) [Removed file] [INFO] == Command start (output follows) ===== action summary: get (notneeded: 2) -VIRTUALENV/lib/python3.8/site-packages/seaborn/axisgrid.py:118: UserWarning: The figure layout has changed to tight - self._figure.tight_layout(*args, **kwargs) [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/midtermproject (dataset) [python3 code/script.py] add(ok): pairwise_relationships.png (file) diff --git a/docs/basics/_examples/DL-101-132-101 b/docs/basics/_examples/DL-101-132-101 index 9de903070..20489d2d6 100644 --- a/docs/basics/_examples/DL-101-132-101 +++ b/docs/basics/_examples/DL-101-132-101 @@ -1,7 +1,7 @@ $ git log --oneline -1ffc282 Provide project description -7469b34 [DATALAD RUNCMD] analyze iris data with classification analysis -5081206 add script for kNN classification and plotting +6fc0d0f Provide project description +9aadac7 [DATALAD RUNCMD] analyze iris data with classification analysis +ca0c747 add script for kNN classification and plotting 4f945ed [DATALAD] Added subdataset 18f4a98 Apply YODA dataset setup bf231d5 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-132-108a b/docs/basics/_examples/DL-101-132-108a index d5bd7a22a..8d5b13987 100644 --- a/docs/basics/_examples/DL-101-132-108a +++ b/docs/basics/_examples/DL-101-132-108a @@ -1,10 +1,10 @@ $ datalad -f json_pp status -d . midterm_project { "action": "status", - "gitshasum": "209997cc✂SHA1", + "gitshasum": "6fc0d0f5✂SHA1", "parentds": "/home/me/dl-101/DataLad-101", "path": "/home/me/dl-101/DataLad-101/midterm_project", - "prev_gitshasum": "85e526a9✂SHA1", + "prev_gitshasum": "18f4a981✂SHA1", "refds": "/home/me/dl-101/DataLad-101", "state": "modified", "status": "ok", diff --git a/docs/basics/_examples/DL-101-132-110 b/docs/basics/_examples/DL-101-132-110 index e3fd3fc71..c480a1308 100644 --- a/docs/basics/_examples/DL-101-132-110 +++ b/docs/basics/_examples/DL-101-132-110 @@ -2,6 +2,3 @@ $ datalad save -d . -m "finished my midterm project" midterm_project add(ok): midterm_project (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 2) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-132-112 b/docs/basics/_examples/DL-101-132-112 index 77e87c150..13f15d348 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 bfcdc773✂SHA1 +commit c5c90178✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 finished my midterm project diff --git a/midterm_project b/midterm_project -index 18f4a98..1ffc282 160000 +index 18f4a98..6fc0d0f 160000 --- a/midterm_project +++ b/midterm_project @@ -1 +1 @@ -Subproject commit 18f4a981✂SHA1 -+Subproject commit 1ffc2821✂SHA1 ++Subproject commit 6fc0d0f5✂SHA1 diff --git a/docs/basics/_examples/DL-101-133-101 b/docs/basics/_examples/DL-101-133-101 index 321cf7c9e..add09aef1 100644 --- a/docs/basics/_examples/DL-101-133-101 +++ b/docs/basics/_examples/DL-101-133-101 @@ -3,13 +3,6 @@ $ datalad containers-add midterm-software --url shub://adswa/resources:2 [INFO] Initializing special remote datalad add(ok): .datalad/config (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 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-101-133-103 b/docs/basics/_examples/DL-101-133-103 index 93fa4a830..8546fa4e6 100644 --- a/docs/basics/_examples/DL-101-133-103 +++ b/docs/basics/_examples/DL-101-133-103 @@ -1,5 +1,5 @@ $ git log -n 1 -p -commit 537f5815✂SHA1 +commit 54aad5de✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-133-104 b/docs/basics/_examples/DL-101-133-104 index 3569b3ce4..b7fe0aeaf 100644 --- a/docs/basics/_examples/DL-101-133-104 +++ b/docs/basics/_examples/DL-101-133-104 @@ -2,6 +2,3 @@ $ git config -f .datalad/config datalad.containers.midterm-software.cmdexec 'sin $ datalad save -m "Modify the container call format to bind-mount the working directory" add(ok): .datalad/config (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-133-111 b/docs/basics/_examples/DL-101-133-111 index d120cc26f..8d5c7027b 100644 --- a/docs/basics/_examples/DL-101-133-111 +++ b/docs/basics/_examples/DL-101-133-111 @@ -1,5 +1,5 @@ $ git log -p -n 1 -commit 264f46ee✂SHA1 +commit 4f00ad07✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -26,11 +26,11 @@ Date: Tue Jun 18 16:13:00 2019 +0000 ^^^ Do not change lines above ^^^ diff --git a/pairwise_relationships.png b/pairwise_relationships.png -index d1a536a..963d5a8 120000 +index a24e6b9..963d5a8 120000 --- a/pairwise_relationships.png +++ b/pairwise_relationships.png @@ -1 +1 @@ --.git/annex/objects/gX/Mf/✂/MD5E-s260804--b017ecdb✂MD5.png +-.git/annex/objects/G3/Mg/✂/MD5E-s260649--127313ad✂MD5.png \ No newline at end of file +.git/annex/objects/q1/gp/✂/MD5E-s261062--025dc493✂MD5.png \ No newline at end of file diff --git a/docs/basics/_examples/DL-101-133-113 b/docs/basics/_examples/DL-101-133-113 index f895aab76..316575743 100644 --- a/docs/basics/_examples/DL-101-133-113 +++ b/docs/basics/_examples/DL-101-133-113 @@ -2,6 +2,3 @@ $ datalad save -d . -m "add container and execute analysis within container" mid add(ok): midterm_project (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 2) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-135-102 b/docs/basics/_examples/DL-101-135-102 index b6d8d6f4f..5087434e4 100644 --- a/docs/basics/_examples/DL-101-135-102 +++ b/docs/basics/_examples/DL-101-135-102 @@ -12,44 +12,44 @@ $ datalad wtf ## dataset - branches: - git-annex@✂GITSHA✂ - - master@442a384 - - sct_computational_reproducibility@442a384 + - main@39e55c8 + - sct_computational_reproducibility@39e55c8 - sct_create_a_dataset@e0ff3a7 - - sct_datalad_rerun@4009576 - - sct_input_and_output@a4044db - - sct_install_datasets@fa63a08 - - sct_keeping_track@f4f3039 - - sct_looking_without_touching@afa2884 - - sct_modify_content@9783a90 - - sct_more_on_DYI_configurations@b21ea30 - - sct_more_on_dataset_nesting@b4e773b - - sct_networking@b232c62 - - sct_populate_a_dataset@bcb0ffe - - sct_retrace_and_reenact@26595f2 - - sct_stay_up_to_date@81bf4d3 - - sct_where_is_waldo@26595f2 - - sct_yoda_project@6134fb1 + - sct_datalad_rerun@4b7a0a0 + - sct_input_and_output@d0c060f + - sct_install_datasets@87609a3 + - sct_keeping_track@e37c9fc + - sct_looking_without_touching@1e73592 + - sct_modify_content@e310b46 + - sct_more_on_DYI_configurations@c2400da + - sct_more_on_dataset_nesting@c5c9017 + - sct_networking@e202e94 + - sct_populate_a_dataset@59ac8d3 + - sct_retrace_and_reenact@adb4b5d + - sct_stay_up_to_date@4bb5d39 + - sct_where_is_waldo@adb4b5d + - sct_yoda_project@0edd3ea - id: e3e70682-c209-4cac-629f-6fbed82c07cd - path: /home/me/dl-101/DataLad-101 - repo: AnnexRepo ## dependencies - - annexremote: 1.6.0 + - annexremote: 1.6.4 - boto: 2.49.0 - cmd:7z: 16.02 - - cmd:annex: 10.20230627-g85aadcfa1 + - cmd:annex: 10.20230926-g44a7b4c9✂SHA1 - cmd:bundled-git: UNKNOWN - cmd:git: 2.40.1 - cmd:ssh: 8.2p1 - cmd:system-git: 2.40.1 - cmd:system-ssh: 8.2p1 - - git: 3.1.32 - - gitdb: 4.0.10 - - humanize: 4.7.0 - - iso8601: 2.0.0 + - git: 3.1.40 + - gitdb: 4.0.11 + - humanize: 4.8.0 + - iso8601: 2.1.0 - keyring: 24.2.0 - keyrings.alt: 5.0.0 - - msgpack: 1.0.5 - - platformdirs: 3.10.0 + - msgpack: 1.0.7 + - platformdirs: 3.11.0 - requests: 2.31.0 ## environment - GIT_AUTHOR_DATE: 2019-06-18T16:13:00 @@ -67,14 +67,68 @@ $ datalad wtf - catalog: - description: DataLad Catalog command suite - entrypoints: + - datalad_catalog.add.Add: + - class: Add + - module: datalad_catalog.add + - names: + - catalog-add + - catalog_add - datalad_catalog.catalog.Catalog: - class: Catalog - module: datalad_catalog.catalog - names: - catalog - catalog + - datalad_catalog.create.Create: + - class: Create + - module: datalad_catalog.create + - names: + - catalog-create + - catalog_create + - datalad_catalog.get.Get: + - class: Get + - module: datalad_catalog.get + - names: + - catalog-get + - catalog_get + - datalad_catalog.remove.Remove: + - class: Remove + - module: datalad_catalog.remove + - names: + - catalog-remove + - catalog_remove + - datalad_catalog.serve.Serve: + - class: Serve + - module: datalad_catalog.serve + - names: + - catalog-serve + - catalog_serve + - datalad_catalog.set.Set: + - class: Set + - module: datalad_catalog.set + - names: + - catalog-set + - catalog_set + - datalad_catalog.translate.MetaTranslate: + - class: MetaTranslate + - module: datalad_catalog.translate + - names: + - catalog-translate + - catalog_translate + - datalad_catalog.validate.Validate: + - class: Validate + - module: datalad_catalog.validate + - names: + - catalog-validate + - catalog_validate + - datalad_catalog.workflow.Workflow: + - class: Workflow + - module: datalad_catalog.workflow + - names: + - catalog-workflow + - catalog_workflow - module: datalad_catalog - - version: v0.2.2 + - version: v1.0.1 - container: - description: Containerized environments - entrypoints: @@ -103,7 +157,7 @@ $ datalad wtf - containers-run - containers_run - module: datalad_container - - version: 1.2.2 + - version: 1.2.3 - deprecated: - description: Deprecated functionality - entrypoints: @@ -181,7 +235,36 @@ $ datalad wtf - meta-filter - meta_filter - module: datalad_metalad - - version: 0.4.17 + - version: 0.4.18 + - next: + - description: What is next in DataLad + - entrypoints: + - datalad_next.commands.create_sibling_webdav.CreateSiblingWebDAV: + - class: CreateSiblingWebDAV + - module: datalad_next.commands.create_sibling_webdav + - names: + - create-sibling-webdav + - datalad_next.commands.credentials.Credentials: + - class: Credentials + - module: datalad_next.commands.credentials + - names: + - datalad_next.commands.download.Download: + - class: Download + - module: datalad_next.commands.download + - names: + - download + - datalad_next.commands.ls_file_collection.LsFileCollection: + - class: LsFileCollection + - module: datalad_next.commands.ls_file_collection + - names: + - ls-file-collection + - datalad_next.commands.tree.TreeCommand: + - class: TreeCommand + - module: datalad_next.commands.tree + - names: + - tree + - module: datalad_next + - version: 1.0.2 ## git-annex - build flags: - Assistant @@ -200,7 +283,7 @@ $ datalad wtf - dependency versions: - aws-0.22.1 - bloomfilter-2.0.1.0 - - cryptonite-0.29 + - crypton-0.33 - DAV-1.3.4 - feed-1.3.2.1 - ghc-9.0.2 @@ -297,126 +380,118 @@ $ datalad wtf - 8 - 9 - 10 - - version: 10.20230627-g85aadcfa1 + - version: 10.20230926-g44a7b4c9✂SHA1 ## location - path: /home/me/dl-101/DataLad-101 - type: dataset ## metadata.extractors - annex: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.annex + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.annex - audio: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.audio + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.audio - container_inspect: - - distribution: datalad-container 1.2.2 + - distribution: datalad-container 1.2.3 - doc: Populates metadata singularity/apptainer version and `inspect` output. - generation: 4 - load_error: TypeError(get_version() takes 0 positional arguments but 1 was given) - module: datalad_container.extractors.metalad_container - datacite: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.datacite + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.datacite - datacite_gin: - - distribution: datalad-catalog 0.2.2 + - distribution: datalad-catalog 1.0.1 - doc: Inherits from metalad's DatasetMetadataExtractor class - generation: 4 - module: datalad_catalog.extractors.datacite_gin - version: 0.0.1 - datalad_core: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.datalad_core + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.datalad_core - datalad_rfc822: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.datalad_rfc822 + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.datalad_rfc822 - exif: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.exif + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.exif - external_dataset: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.external_dataset - external_file: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.external_file - frictionless_datapackage: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.frictionless_datapackage + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.frictionless_datapackage - image: - - distribution: datalad-metalad 0.4.17 - - generation: 2 - - module: datalad_metalad.extractors.legacy.image + - distribution: datalad-deprecated 0.3.0 + - module: datalad_deprecated.metadata.extractors.image - metalad_annex: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 3 - module: datalad_metalad.extractors.annex - metalad_core: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 3 - module: datalad_metalad.extractors.core - metalad_custom: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 3 - module: datalad_metalad.extractors.custom - metalad_example_dataset: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.metalad_example_dataset - version: 0.0.1 - metalad_example_file: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.metalad_example_file - version: 0.0.1 - metalad_external_dataset: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.external_dataset - metalad_external_file: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 4 - module: datalad_metalad.extractors.external_file - metalad_genericjson_dataset: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - doc: Generic JSON dataset-level extractor class Inherits from metalad's DatasetMetadataExtractor class - generation: 4 - module: datalad_metalad.extractors.genericjson_dataset - version: 0.0.1 - metalad_genericjson_file: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - doc: Main 'custom' file-level extractor class Inherits from metalad's FileMetadataExtractor class - generation: 4 - module: datalad_metalad.extractors.genericjson_file - version: 0.0.1 - metalad_runprov: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 3 - module: datalad_metalad.extractors.runprov - metalad_studyminimeta: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - generation: 3 - module: datalad_metalad.extractors.studyminimeta.main - xmp: - - distribution: datalad-metalad 0.4.17 - - load_error: ExempiLoadError(Exempi library not found.) - - module: datalad_metalad.extractors.legacy.xmp + - distribution: datalad-deprecated 0.3.0 + - load_error: ImportError(libxmp is not usable due to Exempi library not found.) + - module: datalad_deprecated.metadata.extractors.xmp ## metadata.filters - metalad_demofilter: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - doc: Create a "histogram"-like summary of the key values of all specified name_tuple across all metadata that is yielded by the metadata iterables. Histograms bins are determined by the metadata format and "name" within the format. The "name" is a flattened JSON key hierarchy. The set of metadata yielded by the iterables is determined by the metadata urls and the recursion flag that are passed to "datalad meta-filter". - module: datalad_metalad.filters.demofilter - version: 1.0 ## metadata.indexers - metalad_studyminimeta: - - distribution: datalad-metalad 0.4.17 + - distribution: datalad-metalad 0.4.18 - doc: Indexer for metadata that was extracted from studyminimeta metadata (usually contained in ".studyminimeta.yaml"-files). - module: datalad_metalad.indexers.studyminimeta ## python @@ -446,6 +521,6 @@ $ datalad wtf - type: ext4 - max_path_length: 283 - name: Linux - - release: 5.15.0-1034-azure + - release: 5.15.0-1042-azure - type: posix - - version: #41~20.04.1-Ubuntu SMP Sat Feb 11 17:02:42 UTC 2023 + - version: #49~20.04.1-Ubuntu SMP Wed Jul 12 12:44:56 UTC 2023 diff --git a/docs/basics/_examples/DL-101-136-101 b/docs/basics/_examples/DL-101-136-101 index e80e526a1..21fff222b 100644 --- a/docs/basics/_examples/DL-101-136-101 +++ b/docs/basics/_examples/DL-101-136-101 @@ -3,6 +3,6 @@ $ mv TLCL.pdf The_Linux_Command_Line.pdf $ ls -lh The_Linux_Command_Line.pdf total 16K lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf lrwxrwxrwx 1 elena elena 133 2019-06-18 16:13 progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf lrwxrwxrwx 1 elena elena 131 2019-06-18 16:13 The_Linux_Command_Line.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-136-103 b/docs/basics/_examples/DL-101-136-103 index 7eba712de..6bbe720f5 100644 --- a/docs/basics/_examples/DL-101-136-103 +++ b/docs/basics/_examples/DL-101-136-103 @@ -2,7 +2,3 @@ $ datalad save -m "rename the book" delete(ok): books/TLCL.pdf (symlink) add(ok): books/The_Linux_Command_Line.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - delete (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-104 b/docs/basics/_examples/DL-101-136-104 index 8a2bb94a8..5176185be 100644 --- a/docs/basics/_examples/DL-101-136-104 +++ b/docs/basics/_examples/DL-101-136-104 @@ -1,5 +1,5 @@ $ git log -n 1 -p -commit 6d1d9bc3✂SHA1 +commit d05e0ded✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-136-105 b/docs/basics/_examples/DL-101-136-105 index a61b2961e..e248ad745 100644 --- a/docs/basics/_examples/DL-101-136-105 +++ b/docs/basics/_examples/DL-101-136-105 @@ -1,4 +1,4 @@ $ git reset --hard HEAD~1 $ datalad status -HEAD is now at 88db2a0 add container and execute analysis within container +HEAD is now at 39e55c8 add container and execute analysis within container nothing to save, working tree clean diff --git a/docs/basics/_examples/DL-101-136-109 b/docs/basics/_examples/DL-101-136-109 index 483910c6b..7dd3171f5 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" -[main ee16aca] rename book +[main 515fcc2] 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 a61b2961e..e248ad745 100644 --- a/docs/basics/_examples/DL-101-136-110 +++ b/docs/basics/_examples/DL-101-136-110 @@ -1,4 +1,4 @@ $ git reset --hard HEAD~1 $ datalad status -HEAD is now at 88db2a0 add container and execute analysis within container +HEAD is now at 39e55c8 add container and execute analysis within container nothing to save, working tree clean diff --git a/docs/basics/_examples/DL-101-136-122 b/docs/basics/_examples/DL-101-136-122 index de1ea725a..31114f0a9 100644 --- a/docs/basics/_examples/DL-101-136-122 +++ b/docs/basics/_examples/DL-101-136-122 @@ -3,8 +3,4 @@ $ ls -l TLCL.pdf delete(ok): books/TLCL.pdf (symlink) add(ok): TLCL.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - delete (ok: 1) - save (ok: 1) lrwxrwxrwx 1 elena elena 128 2019-06-18 16:13 TLCL.pdf -> .git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-136-123 b/docs/basics/_examples/DL-101-136-123 index 1bbc103b0..810c4c053 100644 --- a/docs/basics/_examples/DL-101-136-123 +++ b/docs/basics/_examples/DL-101-136-123 @@ -1,5 +1,5 @@ $ git log -n 1 -p -commit fc12a6c2✂SHA1 +commit b315f5c4✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-136-124 b/docs/basics/_examples/DL-101-136-124 index 23c0d3e13..6280a149a 100644 --- a/docs/basics/_examples/DL-101-136-124 +++ b/docs/basics/_examples/DL-101-136-124 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at 88db2a0 add container and execute analysis within container +HEAD is now at 39e55c8 add container and execute analysis within container diff --git a/docs/basics/_examples/DL-101-136-128 b/docs/basics/_examples/DL-101-136-128 index e59a79f68..617831bce 100644 --- a/docs/basics/_examples/DL-101-136-128 +++ b/docs/basics/_examples/DL-101-136-128 @@ -1,6 +1,6 @@ $ cd midterm_project $ git log notes.txt -commit c4701000✂SHA1 +commit 1e273c59✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-136-129 b/docs/basics/_examples/DL-101-136-129 index 309948e79..4e3b21824 100644 --- a/docs/basics/_examples/DL-101-136-129 +++ b/docs/basics/_examples/DL-101-136-129 @@ -4,5 +4,5 @@ $ git reset --hard HEAD~ # in DataLad-101 $ cd ../ $ git reset --hard HEAD~ -HEAD is now at 264f46e [DATALAD RUNCMD] rerun analysis in container -HEAD is now at 88db2a0 add container and execute analysis within container +HEAD is now at 4f00ad0 [DATALAD RUNCMD] rerun analysis in container +HEAD is now at 39e55c8 add container and execute analysis within container diff --git a/docs/basics/_examples/DL-101-136-133 b/docs/basics/_examples/DL-101-136-133 index 6eda7916a..ba4c1a79a 100644 --- a/docs/basics/_examples/DL-101-136-133 +++ b/docs/basics/_examples/DL-101-136-133 @@ -1,5 +1,5 @@ $ git reset --hard HEAD~ $ cd ../ $ git reset --hard HEAD~ -HEAD is now at 264f46e [DATALAD RUNCMD] rerun analysis in container -HEAD is now at 88db2a0 add container and execute analysis within container +HEAD is now at 4f00ad0 [DATALAD RUNCMD] rerun analysis in container +HEAD is now at 39e55c8 add container and execute analysis within container diff --git a/docs/basics/_examples/DL-101-136-141 b/docs/basics/_examples/DL-101-136-141 index 8a4cb194f..36afd8c91 100644 --- a/docs/basics/_examples/DL-101-136-141 +++ b/docs/basics/_examples/DL-101-136-141 @@ -1,6 +1,3 @@ $ datalad save -m "add copy of TLCL.pdf" add(ok): copyofTLCL.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-142 b/docs/basics/_examples/DL-101-136-142 index 0ac74e770..ecc8a9c43 100644 --- a/docs/basics/_examples/DL-101-136-142 +++ b/docs/basics/_examples/DL-101-136-142 @@ -1,5 +1,5 @@ $ git log -n 1 -p -commit fbe4aac9✂SHA1 +commit ebbe6b93✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-136-144 b/docs/basics/_examples/DL-101-136-144 index 3e3e4fc1b..a1a3f24e2 100644 --- a/docs/basics/_examples/DL-101-136-144 +++ b/docs/basics/_examples/DL-101-136-144 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at a7188cd move book back from midterm_project +HEAD is now at de2d23c move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-145 b/docs/basics/_examples/DL-101-136-145 index 200d74345..fecc35796 100644 --- a/docs/basics/_examples/DL-101-136-145 +++ b/docs/basics/_examples/DL-101-136-145 @@ -3,7 +3,3 @@ $ datalad copy-file notes.txt midterm_project -d midterm_project copy_file(ok): /home/me/dl-101/DataLad-101/notes.txt add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - copy_file (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-146 b/docs/basics/_examples/DL-101-136-146 index 036537149..facb5ac90 100644 --- a/docs/basics/_examples/DL-101-136-146 +++ b/docs/basics/_examples/DL-101-136-146 @@ -1,6 +1,3 @@ $ datalad copy-file books/bash_guide.pdf midterm_project -d midterm_project copy_file(ok): /home/me/dl-101/DataLad-101/books/bash_guide.pdf [/home/me/dl-101/DataLad-101/midterm_project/bash_guide.pdf] save(ok): . (dataset) -action summary: - copy_file (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-147 b/docs/basics/_examples/DL-101-136-147 index abb1793b7..3c758c909 100644 --- a/docs/basics/_examples/DL-101-136-147 +++ b/docs/basics/_examples/DL-101-136-147 @@ -7,7 +7,7 @@ midterm_project │   └── script.py ├── input │   └── iris.csv -> .git/annex/objects/qz/Jg/✂/MD5E-s3975--341a3b52✂MD5.csv -├── notes.txt -> .git/annex/objects/Km/p3/✂/MD5E-s5082--f5d5883f✂MD5.txt +├── notes.txt -> .git/annex/objects/p1/jm/✂/MD5E-s5080--73ec6967✂MD5.txt ├── pairwise_relationships.png -> .git/annex/objects/q1/gp/✂/MD5E-s261062--025dc493✂MD5.png ├── prediction_report.csv -> .git/annex/objects/8q/6M/✂/MD5E-s345--a88cab39✂MD5.csv └── README.md diff --git a/docs/basics/_examples/DL-101-136-149 b/docs/basics/_examples/DL-101-136-149 index f21ea6bbd..34535884a 100644 --- a/docs/basics/_examples/DL-101-136-149 +++ b/docs/basics/_examples/DL-101-136-149 @@ -1,6 +1,6 @@ $ cd midterm_project $ git log notes.txt -commit e43a90dd✂SHA1 +commit 5b8d330f✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-136-150 b/docs/basics/_examples/DL-101-136-150 index aafd9f8b9..b6672d175 100644 --- a/docs/basics/_examples/DL-101-136-150 +++ b/docs/basics/_examples/DL-101-136-150 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~2 -HEAD is now at ccbba1e move book back from midterm_project +HEAD is now at b2b6855 move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-152 b/docs/basics/_examples/DL-101-136-152 index 48663d9c8..945f691bc 100644 --- a/docs/basics/_examples/DL-101-136-152 +++ b/docs/basics/_examples/DL-101-136-152 @@ -8,7 +8,3 @@ add(ok): readings/bash_guide.pdf (file) add(ok): readings/byte-of-python.pdf (file) add(ok): readings/progit.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 4) - delete (ok: 4) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-153 b/docs/basics/_examples/DL-101-136-153 index 3e3e4fc1b..a1a3f24e2 100644 --- a/docs/basics/_examples/DL-101-136-153 +++ b/docs/basics/_examples/DL-101-136-153 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at a7188cd move book back from midterm_project +HEAD is now at de2d23c move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-155 b/docs/basics/_examples/DL-101-136-155 index 11e38aa1f..2ec83f7fa 100644 --- a/docs/basics/_examples/DL-101-136-155 +++ b/docs/basics/_examples/DL-101-136-155 @@ -3,7 +3,3 @@ delete(ok): recordings/longnow (dataset) add(ok): longnow (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 2) - delete (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-157 b/docs/basics/_examples/DL-101-136-157 index 67af87417..c94edeeff 100644 --- a/docs/basics/_examples/DL-101-136-157 +++ b/docs/basics/_examples/DL-101-136-157 @@ -1,3 +1,3 @@ $ git reset --hard HEAD~1 warning: unable to rmdir 'longnow': Directory not empty -HEAD is now at a7188cd move book back from midterm_project +HEAD is now at de2d23c move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-168 b/docs/basics/_examples/DL-101-136-168 index f0930a9a1..a7a213c59 100644 --- a/docs/basics/_examples/DL-101-136-168 +++ b/docs/basics/_examples/DL-101-136-168 @@ -1,5 +1,5 @@ $ git log -p -n 1 -commit a7188cde✂SHA1 +commit de2d23c8✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 @@ -14,9 +14,9 @@ index 0000000..4c84b61 +../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf \ No newline at end of file diff --git a/midterm_project b/midterm_project -index cbfdcb5..ccbba1e 160000 +index 4698466..b2b6855 160000 --- a/midterm_project +++ b/midterm_project @@ -1 +1 @@ --Subproject commit cbfdcb5d✂SHA1 -+Subproject commit ccbba1ec✂SHA1 +-Subproject commit 46984663✂SHA1 ++Subproject commit b2b68556✂SHA1 diff --git a/docs/basics/_examples/DL-101-136-169 b/docs/basics/_examples/DL-101-136-169 index 99dadcf93..629465d0e 100644 --- a/docs/basics/_examples/DL-101-136-169 +++ b/docs/basics/_examples/DL-101-136-169 @@ -2,6 +2,3 @@ $ datalad save --to-git -m "save cropped logos to Git" recordings/*jpg add(ok): recordings/interval_logo_small.jpg (file) add(ok): recordings/salt_logo_small.jpg (file) save(ok): . (dataset) -action summary: - add (ok: 2) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-170 b/docs/basics/_examples/DL-101-136-170 index 1f7bfccae..65ddc776d 100644 --- a/docs/basics/_examples/DL-101-136-170 +++ b/docs/basics/_examples/DL-101-136-170 @@ -7,8 +7,4 @@ $ ls -l flowers.jpg download_url(ok): /home/me/dl-101/DataLad-101/flowers.jpg (file) add(ok): flowers.jpg (file) save(ok): . (dataset) -action summary: - add (ok: 1) - download_url (ok: 1) - save (ok: 1) lrwxrwxrwx 1 elena elena 128 2019-06-18 16:13 2013 flowers.jpg -> .git/annex/objects/7q/9Z/✂/MD5E-s4487679--3898ef0e✂MD5.jpg diff --git a/docs/basics/_examples/DL-101-136-173 b/docs/basics/_examples/DL-101-136-173 index 253ba0fdd..633a9b1bf 100644 --- a/docs/basics/_examples/DL-101-136-173 +++ b/docs/basics/_examples/DL-101-136-173 @@ -1,6 +1,3 @@ $ datalad save -m "removed file again" delete(ok): flowers.jpg (symlink) save(ok): . (dataset) -action summary: - delete (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-174 b/docs/basics/_examples/DL-101-136-174 index fb5cb42da..a79865673 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 06f5f47 Added flower mosaic from wikimedia +HEAD is now at 682d11f Added flower mosaic from wikimedia books code flowers.jpg diff --git a/docs/basics/_examples/DL-101-136-177 b/docs/basics/_examples/DL-101-136-177 index 291209a32..79f9420b9 100644 --- a/docs/basics/_examples/DL-101-136-177 +++ b/docs/basics/_examples/DL-101-136-177 @@ -2,6 +2,3 @@ $ dd if=/dev/zero | head -c 18520 > a.pdf $ datalad save -m "add some file" a.pdf add(ok): a.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-180 b/docs/basics/_examples/DL-101-136-180 index 304ee03a1..fed9290ac 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 650c95c save cropped logos to Git +HEAD is now at c278f6a save cropped logos to Git diff --git a/docs/basics/_examples/DL-101-136-181 b/docs/basics/_examples/DL-101-136-181 index 083a0d9a1..0f9104dbc 100644 --- a/docs/basics/_examples/DL-101-136-181 +++ b/docs/basics/_examples/DL-101-136-181 @@ -3,20 +3,10 @@ $ datalad clone -d . \ https://github.com/datalad-datasets/disneyanimation-cloud.git \ cloud [INFO] Attempting a clone into /home/me/dl-101/DataLad-101/cloud -[INFO] Attempting to clone from https://github.com/datalad-datasets/disneyanimation-cloud.git to /home/me/dl-101/DataLad-101/cloud -[INFO] Start enumerating objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/DataLad-101/cloud) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-datasets/disneyanimation-cloud.git/config download failed: Not Found install(ok): cloud (dataset) add(ok): cloud (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 3) - install (ok: 1) - save (ok: 2) diff --git a/docs/basics/_examples/DL-101-136-183 b/docs/basics/_examples/DL-101-136-183 index 624265dd4..446424376 100644 --- a/docs/basics/_examples/DL-101-136-183 +++ b/docs/basics/_examples/DL-101-136-183 @@ -1,10 +1,4 @@ $ datalad get -n cloud [INFO] Attempting a clone into /home/me/dl-101/DataLad-101/cloud -[INFO] Attempting to clone from https://github.com/datalad-datasets/disneyanimation-cloud.git to /home/me/dl-101/DataLad-101/cloud -[INFO] Start enumerating objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/DataLad-101/cloud) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-datasets/disneyanimation-cloud.git/config download failed: Not Found install(ok): /home/me/dl-101/DataLad-101/cloud (dataset) [Installed subdataset in order to get /home/me/dl-101/DataLad-101/cloud] diff --git a/docs/basics/_examples/DL-101-136-184 b/docs/basics/_examples/DL-101-136-184 index ba3181278..9496bb3a7 100644 --- a/docs/basics/_examples/DL-101-136-184 +++ b/docs/basics/_examples/DL-101-136-184 @@ -4,8 +4,3 @@ uninstall(ok): cloud (dataset) remove(ok): cloud (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 1) - remove (ok: 1) - save (ok: 1) - uninstall (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-101 b/docs/basics/_examples/DL-101-137-101 index b8581506d..8f15d62ae 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 -5206254 remove obsolete subds -39948ba [DATALAD] Added subdataset -650c95c save cropped logos to Git -a7188cd move book back from midterm_project -b83cc48 move book into midterm_project -88db2a0 add container and execute analysis within container -bfcdc77 finished my midterm project -6134fb1 [DATALAD] Recorded changes -4be94ca add note on DataLad's procedures -b21ea30 add note on configurations and git config -b232c62 Add note on adding siblings -0fbbe8c Merge remote-tracking branch 'roommate/main' -81bf4d3 add note about datalad update -28a99fb Include nesting demo from datalad website -26595f2 add note on git annex whereis +996f459 remove obsolete subds +15acb2a [DATALAD] Added subdataset +c278f6a save cropped logos to Git +de2d23c move book back from midterm_project +a648756 move book into midterm_project +39e55c8 add container and execute analysis within container +c5c9017 finished my midterm project +0edd3ea [DATALAD] Recorded changes +08684a4 add note on DataLad's procedures +c2400da add note on configurations and git config +e202e94 Add note on adding siblings +6ae8e71 Merge remote-tracking branch 'roommate/main' +4bb5d39 add note about datalad update +5b6e19a Include nesting demo from datalad website +adb4b5d add note on git annex whereis diff --git a/docs/basics/_examples/DL-101-137-104 b/docs/basics/_examples/DL-101-137-104 index 36b1dcbd0..25f36fead 100644 --- a/docs/basics/_examples/DL-101-137-104 +++ b/docs/basics/_examples/DL-101-137-104 @@ -3,6 +3,3 @@ add(ok): Gitjoke1.txt (file) add(ok): Gitjoke2.txt (file) add(ok): Gitjoke3.txt (file) save(ok): . (dataset) -action summary: - add (ok: 3) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-105 b/docs/basics/_examples/DL-101-137-105 index d9fa04360..e62e308cd 100644 --- a/docs/basics/_examples/DL-101-137-105 +++ b/docs/basics/_examples/DL-101-137-105 @@ -1,5 +1,5 @@ $ git log -p -1 -commit 88310a7c✂SHA1 +commit 58e40d9a✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-137-106 b/docs/basics/_examples/DL-101-137-106 index 30e7133c7..d366f1f9f 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 -88310a7 [DATALAD] Recorded changes -5206254 remove obsolete subds -39948ba [DATALAD] Added subdataset +58e40d9 [DATALAD] Recorded changes +996f459 remove obsolete subds +15acb2a [DATALAD] Added subdataset diff --git a/docs/basics/_examples/DL-101-137-107 b/docs/basics/_examples/DL-101-137-107 index 6ba93aaa9..d45117b9e 100644 --- a/docs/basics/_examples/DL-101-137-107 +++ b/docs/basics/_examples/DL-101-137-107 @@ -1,2 +1,2 @@ -$ git reset --mixed 52062545✂SHA1 +$ git reset --mixed 996f459a✂SHA1 diff --git a/docs/basics/_examples/DL-101-137-108 b/docs/basics/_examples/DL-101-137-108 index a8aac0116..6297a471f 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 -5206254 remove obsolete subds -39948ba [DATALAD] Added subdataset +996f459 remove obsolete subds +15acb2a [DATALAD] Added subdataset diff --git a/docs/basics/_examples/DL-101-137-111 b/docs/basics/_examples/DL-101-137-111 index 5d6dd4344..ea8fba97c 100644 --- a/docs/basics/_examples/DL-101-137-111 +++ b/docs/basics/_examples/DL-101-137-111 @@ -1,6 +1,3 @@ $ datalad save -m "save my favorite Git joke" Gitjoke2.txt add(ok): Gitjoke2.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-112 b/docs/basics/_examples/DL-101-137-112 index 02be3694b..2b509a04d 100644 --- a/docs/basics/_examples/DL-101-137-112 +++ b/docs/basics/_examples/DL-101-137-112 @@ -1,11 +1,11 @@ $ git log -2 -commit c48923fb✂SHA1 +commit 4bdb06cf✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 save my favorite Git joke -commit 52062545✂SHA1 +commit 996f459a✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-137-113 b/docs/basics/_examples/DL-101-137-113 index 271c8c29d..ceb20ca94 100644 --- a/docs/basics/_examples/DL-101-137-113 +++ b/docs/basics/_examples/DL-101-137-113 @@ -6,6 +6,3 @@ add(ok): Gitjoke1.txt (file) add(ok): Gitjoke3.txt (file) add(ok): apdffile.pdf (file) save(ok): . (dataset) -action summary: - add (ok: 3) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-114 b/docs/basics/_examples/DL-101-137-114 index 0c69a18e0..c0cea3fa7 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 elena elena 122 2019-06-18 16:13 apdffile.pdf -> .git/annex/objects/4w/78/✂/MD5E-s1216--2a96ec70✂MD5.pdf +lrwxrwxrwx 1 elena elena 122 2019-06-18 16:13 apdffile.pdf -> .git/annex/objects/W8/PK/✂/MD5E-s1216--8bddf647✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-137-117 b/docs/basics/_examples/DL-101-137-117 index ac2288e6c..27d3a0bab 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 -2ebdb40 [DATALAD] Recorded changes -c48923f save my favorite Git joke -5206254 remove obsolete subds +98eb974 [DATALAD] Recorded changes +4bdb06c save my favorite Git joke +996f459 remove obsolete subds diff --git a/docs/basics/_examples/DL-101-137-118 b/docs/basics/_examples/DL-101-137-118 index 00f793efa..77aa3942a 100644 --- a/docs/basics/_examples/DL-101-137-118 +++ b/docs/basics/_examples/DL-101-137-118 @@ -1,2 +1,2 @@ -$ git reset --mixed c48923fb✂SHA1 +$ git reset --mixed 4bdb06cf✂SHA1 diff --git a/docs/basics/_examples/DL-101-137-119 b/docs/basics/_examples/DL-101-137-119 index 99da0a741..9f3ac6762 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 -c48923f save my favorite Git joke -5206254 remove obsolete subds +4bdb06c save my favorite Git joke +996f459 remove obsolete subds diff --git a/docs/basics/_examples/DL-101-137-121 b/docs/basics/_examples/DL-101-137-121 index e76a1420a..6589293d9 100644 --- a/docs/basics/_examples/DL-101-137-121 +++ b/docs/basics/_examples/DL-101-137-121 @@ -1,21 +1,17 @@ -$ git log -n 20 --oneline -c48923f save my favorite Git joke -5206254 remove obsolete subds -39948ba [DATALAD] Added subdataset -650c95c save cropped logos to Git -a7188cd move book back from midterm_project -b83cc48 move book into midterm_project -88db2a0 add container and execute analysis within container -bfcdc77 finished my midterm project -6134fb1 [DATALAD] Recorded changes -4be94ca add note on DataLad's procedures -b21ea30 add note on configurations and git config -b232c62 Add note on adding siblings -0fbbe8c Merge remote-tracking branch 'roommate/main' -81bf4d3 add note about datalad update -28a99fb Include nesting demo from datalad website -26595f2 add note on git annex whereis -afa2884 add note about cloning from paths and recursive datalad get -b5fc129 add note on clean datasets -d5845d3 [DATALAD RUNCMD] Resize logo for slides -d24531d [DATALAD RUNCMD] Resize logo for slides +$ git log -n 16 --oneline +4bdb06c save my favorite Git joke +996f459 remove obsolete subds +15acb2a [DATALAD] Added subdataset +c278f6a save cropped logos to Git +de2d23c move book back from midterm_project +a648756 move book into midterm_project +39e55c8 add container and execute analysis within container +c5c9017 finished my midterm project +0edd3ea [DATALAD] Recorded changes +08684a4 add note on DataLad's procedures +c2400da add note on configurations and git config +e202e94 Add note on adding siblings +6ae8e71 Merge remote-tracking branch 'roommate/main' +4bb5d39 add note about datalad update +5b6e19a Include nesting demo from datalad website +adb4b5d add note on git annex whereis diff --git a/docs/basics/_examples/DL-101-137-122 b/docs/basics/_examples/DL-101-137-122 index 64e6c878e..9dbd8b51e 100644 --- a/docs/basics/_examples/DL-101-137-122 +++ b/docs/basics/_examples/DL-101-137-122 @@ -1,7 +1,7 @@ -$ git checkout afa2884e✂SHA1 +$ git checkout 1e73592e✂SHA1 warning: unable to rmdir 'midterm_project': Directory not empty -Note: switching to 'afa2884e✂SHA1'. +Note: switching to '1e73592e✂SHA1'. 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 @@ -18,4 +18,4 @@ Or undo this operation with: Turn off this advice by setting config variable advice.detachedHead to false -HEAD is now at afa2884 add note about cloning from paths and recursive datalad get +HEAD is now at 1e73592 add note about cloning from paths and recursive datalad get diff --git a/docs/basics/_examples/DL-101-137-124 b/docs/basics/_examples/DL-101-137-124 index d51b0bce3..cf7282e88 100644 --- a/docs/basics/_examples/DL-101-137-124 +++ b/docs/basics/_examples/DL-101-137-124 @@ -1,3 +1,3 @@ $ git checkout main -Previous HEAD position was afa2884 add note about cloning from paths and recursive datalad get +Previous HEAD position was 1e73592 add note about cloning from paths and recursive datalad get Switched to branch 'main' diff --git a/docs/basics/_examples/DL-101-137-127 b/docs/basics/_examples/DL-101-137-127 index 9662e0cbe..b95167dc8 100644 --- a/docs/basics/_examples/DL-101-137-127 +++ b/docs/basics/_examples/DL-101-137-127 @@ -1,5 +1,5 @@ -$ git cat-file --textconv afa2884e✂SHA1:notes.txt +$ git cat-file --textconv 1e73592e✂SHA1: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-101-137-131 b/docs/basics/_examples/DL-101-137-131 index 2218281a6..6a75090c2 100644 --- a/docs/basics/_examples/DL-101-137-131 +++ b/docs/basics/_examples/DL-101-137-131 @@ -1,6 +1,3 @@ $ datalad save -m "add joke evaluation to joke" Gitjoke2.txt add(ok): Gitjoke2.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-132 b/docs/basics/_examples/DL-101-137-132 index c034e9468..a3b48afd3 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 -e22faf1 add joke evaluation to joke -c48923f save my favorite Git joke +a4ab359 add joke evaluation to joke +4bdb06c save my favorite Git joke diff --git a/docs/basics/_examples/DL-101-137-133 b/docs/basics/_examples/DL-101-137-133 index 72142b4ff..16eee22ee 100644 --- a/docs/basics/_examples/DL-101-137-133 +++ b/docs/basics/_examples/DL-101-137-133 @@ -1,3 +1,3 @@ -$ git reset --hard c48923fb✂SHA1 -HEAD is now at c48923f save my favorite Git joke +$ git reset --hard 4bdb06cf✂SHA1 +HEAD is now at 4bdb06c save my favorite Git joke diff --git a/docs/basics/_examples/DL-101-137-141 b/docs/basics/_examples/DL-101-137-141 index eca4d1164..92ab4734c 100644 --- a/docs/basics/_examples/DL-101-137-141 +++ b/docs/basics/_examples/DL-101-137-141 @@ -1,6 +1,3 @@ $ datalad save -m "did a bad modification" Gitjoke2.txt add(ok): Gitjoke2.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-143 b/docs/basics/_examples/DL-101-137-143 index 05fce358c..9416c8fac 100644 --- a/docs/basics/_examples/DL-101-137-143 +++ b/docs/basics/_examples/DL-101-137-143 @@ -1,6 +1,3 @@ $ datalad save -m "add note on helpful git resource" notes.txt add(ok): notes.txt (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/basics/_examples/DL-101-137-144 b/docs/basics/_examples/DL-101-137-144 index 482c3bf08..bd0361b52 100644 --- a/docs/basics/_examples/DL-101-137-144 +++ b/docs/basics/_examples/DL-101-137-144 @@ -1,5 +1,5 @@ -$ git revert 73b49af9✂SHA1 -[main 33ad93e] Revert "did a bad modification" +$ git revert 713e79d3✂SHA1 +[main 6d3d93b] Revert "did a bad modification" Date: Tue Jun 18 16:13:00 2019 +0000 1 file changed, 1 deletion(-) diff --git a/docs/basics/_examples/DL-101-137-146 b/docs/basics/_examples/DL-101-137-146 index 96f15f596..2b9ba0314 100644 --- a/docs/basics/_examples/DL-101-137-146 +++ b/docs/basics/_examples/DL-101-137-146 @@ -1,19 +1,19 @@ $ git log -n 3 -commit 33ad93e4✂SHA1 +commit 6d3d93b9✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 Revert "did a bad modification" - This reverts commit 73b49af9✂SHA1. + This reverts commit 713e79d3✂SHA1. -commit 4e8f18ea✂SHA1 +commit 04536a1e✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 add note on helpful git resource -commit 73b49af9✂SHA1 +commit 713e79d3✂SHA1 Author: Elena Piscopia Date: Tue Jun 18 16:13:00 2019 +0000 diff --git a/docs/basics/_examples/DL-101-139-102 b/docs/basics/_examples/DL-101-139-102 index 3d8ecb445..038caea78 100644 --- a/docs/basics/_examples/DL-101-139-102 +++ b/docs/basics/_examples/DL-101-139-102 @@ -1,20 +1,9 @@ $ datalad push --to gin [INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data copy(ok): books/TLCL.pdf (file) [to gin...] copy(ok): books/bash_guide.pdf (file) [to gin...] copy(ok): books/byte-of-python.pdf (file) [to gin...] copy(ok): books/progit.pdf (file) [to gin...] -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -[INFO] Start resolving deltas publish(ok): . (dataset) [refs/heads/git-annex->gin:refs/heads/git-annex ✂FROM✂..✂TO✂] publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main [new branch]] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) -action summary: - copy (ok: 4) - publish (ok: 2) diff --git a/docs/basics/_examples/DL-101-139-106 b/docs/basics/_examples/DL-101-139-106 index 4605ff36c..d22a45da3 100644 --- a/docs/basics/_examples/DL-101-139-106 +++ b/docs/basics/_examples/DL-101-139-106 @@ -1,13 +1,6 @@ $ datalad push --to gin [INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main 33ad93e..4191b5f] +publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main 6d3d93b..344b0ec] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) action summary: publish (notneeded: 1, ok: 1) diff --git a/docs/basics/_examples/DL-101-139-107 b/docs/basics/_examples/DL-101-139-107 index a56411e8d..4fb9280e1 100644 --- a/docs/basics/_examples/DL-101-139-107 +++ b/docs/basics/_examples/DL-101-139-107 @@ -1,10 +1,3 @@ $ datalad clone https://gin.g-node.org/adswa/DataLad-101 [INFO] Attempting a clone into /home/me/dl-101/clone_of_dl-101/DataLad-101 -[INFO] Attempting to clone from https://gin.g-node.org/adswa/DataLad-101 to /home/me/dl-101/clone_of_dl-101/DataLad-101 -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/dl-101/clone_of_dl-101/DataLad-101) install(ok): /home/me/dl-101/clone_of_dl-101/DataLad-101 (dataset) diff --git a/docs/basics/_examples/DL-101-141-101 b/docs/basics/_examples/DL-101-141-101 index 2992fad69..e0b0bb945 100644 --- a/docs/basics/_examples/DL-101-141-101 +++ b/docs/basics/_examples/DL-101-141-101 @@ -1,18 +1,10 @@ $ datalad push --to roommate [INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data copy(ok): books/TLCL.pdf (file) [to roommate...] copy(ok): books/bash_guide.pdf (file) [to roommate...] copy(ok): books/byte-of-python.pdf (file) [to roommate...] -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -[INFO] Start resolving deltas [INFO] Finished -publish(ok): . (dataset) [refs/heads/git-annex->roommate:refs/heads/git-annex FROM..TO ✂FROM✂..✂TO✂] +publish(ok): . (dataset) [refs/heads/git-annex->roommate:refs/heads/git-annex ✂FROM✂..✂TO✂] publish(error): . (dataset) [refs/heads/main->roommate:refs/heads/main [remote rejected] (branch is currently checked out)] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) action summary: diff --git a/docs/beyond_basics/_examples/DL-101-147-103 b/docs/beyond_basics/_examples/DL-101-147-103 index a2eaad85d..88cd40438 100644 --- a/docs/beyond_basics/_examples/DL-101-147-103 +++ b/docs/beyond_basics/_examples/DL-101-147-103 @@ -2,13 +2,8 @@ $ datalad create-sibling-ria -s ria-backup --alias dl-101 --new-store-ok "ria+file:///home/me/myriastore" [INFO] Creating a new RIA store at /home/me/myriastore [INFO] create siblings 'ria-backup' and 'ria-backup-storage' ... -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) update(ok): . (dataset) update(ok): . (dataset) [INFO] Configure additional publication dependency on "ria-backup-storage" configure-sibling(ok): . (sibling) create-sibling-ria(ok): /home/me/dl-101/DataLad-101 (dataset) -action summary: - configure-sibling (ok: 1) - create-sibling-ria (ok: 1) - update (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-147-104 b/docs/beyond_basics/_examples/DL-101-147-104 index 3319cf236..96edc7f9e 100644 --- a/docs/beyond_basics/_examples/DL-101-147-104 +++ b/docs/beyond_basics/_examples/DL-101-147-104 @@ -1,6 +1,6 @@ $ datalad siblings .: here(+) [git] -.: gin(+) [/home/me/pushes/DataLad-101 (git)] .: ria-backup-storage(+) [ora] -.: ria-backup(-) [/home/me/myriastore/e3e/70682-c209-4cac-629f-6fbed82c07cd (git)] +.: gin(+) [/home/me/pushes/DataLad-101 (git)] .: roommate(+) [../mock_user/DataLad-101 (git)] +.: ria-backup(-) [/home/me/myriastore/e3e/70682-c209-4cac-629f-6fbed82c07cd (git)] diff --git a/docs/beyond_basics/_examples/DL-101-147-107 b/docs/beyond_basics/_examples/DL-101-147-107 index 697c9824d..501574ec4 100644 --- a/docs/beyond_basics/_examples/DL-101-147-107 +++ b/docs/beyond_basics/_examples/DL-101-147-107 @@ -1,24 +1,10 @@ $ datalad push --to ria-backup [INFO] Determine push target -[INFO] Push refspecs -[INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data copy(ok): books/TLCL.pdf (file) [to ria-backup-storage...] copy(ok): books/bash_guide.pdf (file) [to ria-backup-storage...] copy(ok): books/byte-of-python.pdf (file) [to ria-backup-storage...] copy(ok): books/progit.pdf (file) [to ria-backup-storage...] -[INFO] Transfer data -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -[INFO] Start resolving deltas publish(ok): . (dataset) [refs/heads/main->ria-backup:refs/heads/main [new branch]] publish(ok): . (dataset) [refs/heads/git-annex->ria-backup:refs/heads/git-annex [new branch]] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) -action summary: - copy (ok: 4) - publish (ok: 2) diff --git a/docs/beyond_basics/_examples/DL-101-147-108 b/docs/beyond_basics/_examples/DL-101-147-108 index db406a736..51eb74326 100644 --- a/docs/beyond_basics/_examples/DL-101-147-108 +++ b/docs/beyond_basics/_examples/DL-101-147-108 @@ -14,14 +14,14 @@ $ tree /home/me/myriastore │   │   │   └── 3M │   │   │   └── MD5E-s2120211--06d1efcb✂MD5.pdf │   │   │   └── MD5E-s2120211--06d1efcb✂MD5.pdf -│   │   ├── P5 -│   │   │   └── qK -│   │   │   └── MD5E-s2693891--e61afe4b✂MD5.pdf -│   │   │   └── MD5E-s2693891--e61afe4b✂MD5.pdf -│   │   └── WF -│   │   └── Gq -│   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf -│   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   ├── WF +│   │   │   └── Gq +│   │   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   └── xF +│   │   └── 42 +│   │   └── MD5E-s4161086--c832fc13✂MD5.pdf +│   │   └── MD5E-s4161086--c832fc13✂MD5.pdf │   ├── archives │   ├── branches │   ├── config @@ -47,8 +47,8 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-0c77bdff✂SHA1.idx -│   │   └── pack-0c77bdff✂SHA1.pack +│   │   ├── pack-94b1d055✂SHA1.idx +│   │   └── pack-94b1d055✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-147-109 b/docs/beyond_basics/_examples/DL-101-147-109 index ea8e26d21..576b9d8a0 100644 --- a/docs/beyond_basics/_examples/DL-101-147-109 +++ b/docs/beyond_basics/_examples/DL-101-147-109 @@ -2,13 +2,8 @@ $ cd midterm_project $ datalad create-sibling-ria -s ria-backup ria+file:///home/me/myriastore [INFO] Creating a new RIA store at /home/me/myriastore [INFO] create siblings 'ria-backup' and 'ria-backup-storage' ... -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101/midterm_project) update(ok): . (dataset) update(ok): . (dataset) [INFO] Configure additional publication dependency on "ria-backup-storage" configure-sibling(ok): . (sibling) create-sibling-ria(ok): /home/me/dl-101/DataLad-101/midterm_project (dataset) -action summary: - configure-sibling (ok: 1) - create-sibling-ria (ok: 1) - update (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-147-110 b/docs/beyond_basics/_examples/DL-101-147-110 index 024982551..0ef0e795d 100644 --- a/docs/beyond_basics/_examples/DL-101-147-110 +++ b/docs/beyond_basics/_examples/DL-101-147-110 @@ -1,23 +1,9 @@ $ datalad push --to ria-backup [INFO] Determine push target -[INFO] Push refspecs -[INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data copy(ok): .datalad/environments/midterm-software/image (file) [to ria-backup-storage...] copy(ok): pairwise_relationships.png (file) [to ria-backup-storage...] copy(ok): prediction_report.csv (file) [to ria-backup-storage...] -[INFO] Transfer data -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -[INFO] Start resolving deltas publish(ok): . (dataset) [refs/heads/main->ria-backup:refs/heads/main [new branch]] publish(ok): . (dataset) [refs/heads/git-annex->ria-backup:refs/heads/git-annex [new branch]] [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) [INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) -action summary: - copy (ok: 3) - publish (ok: 2) diff --git a/docs/beyond_basics/_examples/DL-101-147-112 b/docs/beyond_basics/_examples/DL-101-147-112 index 7a65fd91f..6e79a2cbf 100644 --- a/docs/beyond_basics/_examples/DL-101-147-112 +++ b/docs/beyond_basics/_examples/DL-101-147-112 @@ -43,9 +43,9 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-57578b5f✂SHA1.idx -│   │   └── pack-57578b5f✂SHA1.pack -│   ├── ora-remote-4b80e0df-e4a4-47d4-b59d-8e00641bf193 +│   │   ├── pack-8a336fbd✂SHA1.idx +│   │   └── pack-8a336fbd✂SHA1.pack +│   ├── ora-remote-5762bcab-e464-4ccd-898f-77e45c8dab51 │   │   └── transfer │   ├── refs │   │   ├── heads @@ -65,14 +65,14 @@ $ tree /home/me/myriastore │   │   │   └── 3M │   │   │   └── MD5E-s2120211--06d1efcb✂MD5.pdf │   │   │   └── MD5E-s2120211--06d1efcb✂MD5.pdf -│   │   ├── P5 -│   │   │   └── qK -│   │   │   └── MD5E-s2693891--e61afe4b✂MD5.pdf -│   │   │   └── MD5E-s2693891--e61afe4b✂MD5.pdf -│   │   └── WF -│   │   └── Gq -│   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf -│   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   ├── WF +│   │   │   └── Gq +│   │   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   │   └── MD5E-s1198170--0ab2c121✂MD5.pdf +│   │   └── xF +│   │   └── 42 +│   │   └── MD5E-s4161086--c832fc13✂MD5.pdf +│   │   └── MD5E-s4161086--c832fc13✂MD5.pdf │   ├── archives │   ├── branches │   ├── config @@ -98,8 +98,8 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-0c77bdff✂SHA1.idx -│   │   └── pack-0c77bdff✂SHA1.pack +│   │   ├── pack-94b1d055✂SHA1.idx +│   │   └── pack-94b1d055✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-147-120 b/docs/beyond_basics/_examples/DL-101-147-120 index 6cabf8c33..76cc00f45 100644 --- a/docs/beyond_basics/_examples/DL-101-147-120 +++ b/docs/beyond_basics/_examples/DL-101-147-120 @@ -1,11 +1,5 @@ $ datalad clone ria+file:///home/me/myriastore#e3e70682-c209-4cac-629f-6fbed82c07cd myclone -[INFO] Attempting a clone into /home/me/beyond_basics/myclone -[INFO] Attempting to clone from file:///home/me/myriastore/e3e/70682-c209-4cac-629f-6fbed82c07cd to /home/me/beyond_basics/myclone -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/myclone) [INFO] Configure additional publication dependency on "ria-backup-storage" configure-sibling(ok): . (sibling) install(ok): /home/me/beyond_basics/myclone (dataset) -action summary: - configure-sibling (ok: 1) - install (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-147-124 b/docs/beyond_basics/_examples/DL-101-147-124 index 8d7b4ce10..e48f08cd3 100644 --- a/docs/beyond_basics/_examples/DL-101-147-124 +++ b/docs/beyond_basics/_examples/DL-101-147-124 @@ -1,10 +1,5 @@ datalad clone ria+file:///home/me/myriastore#~midterm_project [INFO] Attempting a clone into /home/me/beyond_basics/midterm_project -[INFO] Attempting to clone from file:///home/me/myriastore/alias/midterm_project to /home/me/beyond_basics/midterm_project -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/midterm_project) [INFO] Configure additional publication dependency on "ria-backup-storage" configure-sibling(ok): . (sibling) install(ok): /home/me/beyond_basics/midterm_project (dataset) -action summary: - configure-sibling (ok: 1) - install (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-147-125 b/docs/beyond_basics/_examples/DL-101-147-125 index d288be864..0ea9898b3 100644 --- a/docs/beyond_basics/_examples/DL-101-147-125 +++ b/docs/beyond_basics/_examples/DL-101-147-125 @@ -3,7 +3,7 @@ $ tree . ├── books │   ├── bash_guide.pdf -> ../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf -│   ├── byte-of-python.pdf -> ../.git/annex/objects/P5/qK/✂/MD5E-s2693891--e61afe4b✂MD5.pdf +│   ├── byte-of-python.pdf -> ../.git/annex/objects/xF/42/✂/MD5E-s4161086--c832fc13✂MD5.pdf │   ├── progit.pdf -> ../.git/annex/objects/G6/Gj/✂/MD5E-s12465653--05cd7ed5✂MD5.pdf │   └── TLCL.pdf -> ../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf ├── code diff --git a/docs/beyond_basics/_examples/DL-101-147-127 b/docs/beyond_basics/_examples/DL-101-147-127 index cd794a7a3..19b895677 100644 --- a/docs/beyond_basics/_examples/DL-101-147-127 +++ b/docs/beyond_basics/_examples/DL-101-147-127 @@ -1,6 +1,4 @@ $ datalad get -n midterm_project [INFO] Attempting a clone into /home/me/beyond_basics/myclone/midterm_project -[INFO] Attempting to clone from file:///home/me/myriastore/d95/bafc8-f2a4-d27b-dcf4-bb99f4bea973 to /home/me/beyond_basics/myclone/midterm_project -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/myclone/midterm_project) [INFO] Configure additional publication dependency on "ria-backup-storage" install(ok): /home/me/beyond_basics/myclone/midterm_project (dataset) [Installed subdataset in order to get /home/me/beyond_basics/myclone/midterm_project] diff --git a/docs/beyond_basics/_examples/DL-101-149-01 b/docs/beyond_basics/_examples/DL-101-149-01 index 36becbcd5..287c3f110 100644 --- a/docs/beyond_basics/_examples/DL-101-149-01 +++ b/docs/beyond_basics/_examples/DL-101-149-01 @@ -1,10 +1,3 @@ $ datalad clone https://github.com/datalad-datasets/human-connectome-project-openaccess.git hcp [INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp -[INFO] Attempting to clone from https://github.com/datalad-datasets/human-connectome-project-openaccess.git to /home/me/beyond_basics/HPC/hcp -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp) install(ok): /home/me/beyond_basics/HPC/hcp (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-149-02 b/docs/beyond_basics/_examples/DL-101-149-02 index 31f367295..ef8ec44de 100644 --- a/docs/beyond_basics/_examples/DL-101-149-02 +++ b/docs/beyond_basics/_examples/DL-101-149-02 @@ -1,157 +1,48 @@ $ cd hcp $ datalad get -n -r HCP1200/130* [INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130013 -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130013 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130013) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130013] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130013 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130013/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/876/c9c98-2aa7-11ea-85a1-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130013/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130013/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130013/T1w -[INFO] Attempting to clone from http://store.datalad.org/8b5/6089e-2aa7-11ea-85a1-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130013/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130013/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130013/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/8e0/91aae-2aa7-11ea-85a1-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130013/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130013/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130114 -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130114 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130114) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130114] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130114 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130114/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/a71/ab0e4-2aa6-11ea-a248-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130114/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130114/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w -[INFO] Attempting to clone from http://store.datalad.org/aa1/d4284-2aa6-11ea-a248-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130114/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/ac8/7ba5e-2aa6-11ea-a248-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130114/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130114/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130316 -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130316 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130316) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130316 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130316] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130316 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130316/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/439/61042-38ff-11ea-be90-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130316/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130316/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130316/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130316/T1w -[INFO] Attempting to clone from http://store.datalad.org/452/2bbea-38ff-11ea-be90-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130316/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130316/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130316/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130316/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/46a/1cd80-38ff-11ea-be90-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130316/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130316/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130316/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130417 -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130417 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130417) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130417 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130417] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130417 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130417/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/e8f/5ce4e-2aa2-11ea-a418-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130417/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130417/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130417/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130417/T1w -[INFO] Attempting to clone from http://store.datalad.org/eb1/55924-2aa2-11ea-a418-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130417/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130417/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130417/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130417/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/ed2/969bc-2aa2-11ea-a418-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130417/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130417/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130417/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130518 -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130518 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130518) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130518 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130518] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130518 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130518/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/63f/8a1aa-2aa0-11ea-bf71-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130518/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130518/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130518/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130518/T1w -[INFO] Attempting to clone from http://store.datalad.org/658/7d860-2aa0-11ea-bf71-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130518/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130518/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130518/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130518/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/674/822f4-2aa0-11ea-bf71-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130518/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130518/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130518/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130619 -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130619 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130619) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130619 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130619] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130619 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130619/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/032/2a332-2a9e-11ea-a1e6-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130619/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130619/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130619/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130619/T1w -[INFO] Attempting to clone from http://store.datalad.org/04a/bbcde-2a9e-11ea-a1e6-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130619/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130619/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130619/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130619/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/064/8fd7c-2a9e-11ea-a1e6-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130619/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130619/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130619/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130720 -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130720 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130720) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130720 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130720] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130720 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130720/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/700/ffce2-2a99-11ea-b8dd-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130720/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130720/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130720/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130720/T1w -[INFO] Attempting to clone from http://store.datalad.org/722/fef3c-2a99-11ea-b8dd-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130720/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130720/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130720/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130720/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/76a/4579c-2a99-11ea-b8dd-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130720/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130720/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130720/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130821 -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130821 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130821) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130821 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130821] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130821 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130821/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/c4c/0f862-2a95-11ea-b221-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130821/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130821/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130821/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130821/T1w -[INFO] Attempting to clone from http://store.datalad.org/c7c/23094-2a95-11ea-b221-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130821/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130821/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130821/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130821/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/cb9/ea382-2a95-11ea-b221-002590496000 to /home/me/beyond_basics/HPC/hcp/HCP1200/130821/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130821/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130821/unprocessed (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130922 -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130922 -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130922) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130922 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130922] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130922 -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130922/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/1d8/e51cc-2a93-11ea-bc67-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130922/MNINonLinear -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130922/MNINonLinear) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130922/MNINonLinear (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130922/T1w -[INFO] Attempting to clone from http://store.datalad.org/239/fe7a6-2a93-11ea-bc67-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130922/T1w -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130922/T1w) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130922/T1w (dataset) -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130922/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/25e/ee1ba-2a93-11ea-bc67-0025904abcb0 to /home/me/beyond_basics/HPC/hcp/HCP1200/130922/unprocessed -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/HPC/hcp/HCP1200/130922/unprocessed) install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130922/unprocessed (dataset) -action summary: - install (ok: 36) diff --git a/docs/beyond_basics/_examples/DL-101-149-04 b/docs/beyond_basics/_examples/DL-101-149-04 index c642828cc..4de4d60bf 100644 --- a/docs/beyond_basics/_examples/DL-101-149-04 +++ b/docs/beyond_basics/_examples/DL-101-149-04 @@ -3,6 +3,3 @@ $ datalad copy-file \ -d dataset-to-copy-to copy_file(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013/T1w/Diffusion/bvals [/home/me/beyond_basics/HPC/dataset-to-copy-to/bvals] save(ok): . (dataset) -action summary: - copy_file (ok: 1) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-149-10 b/docs/beyond_basics/_examples/DL-101-149-10 index fffa3dc92..97cdf8a62 100644 --- a/docs/beyond_basics/_examples/DL-101-149-10 +++ b/docs/beyond_basics/_examples/DL-101-149-10 @@ -17,6 +17,3 @@ copy_file(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w/Diffusion/eddyl copy_file(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w/Diffusion/grad_dev.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/130114/T1w/Diffusion/grad_dev.nii.gz] copy_file(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130114/T1w/Diffusion/nodif_brain_mask.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/130114/T1w/Diffusion/nodif_brain_mask.nii.gz] save(ok): . (dataset) -action summary: - copy_file (ok: 13) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-149-12 b/docs/beyond_basics/_examples/DL-101-149-12 index 7e4f233fb..df4159134 100644 --- a/docs/beyond_basics/_examples/DL-101-149-12 +++ b/docs/beyond_basics/_examples/DL-101-149-12 @@ -1,7 +1,5 @@ $ cd dataset-to-copy-to $ datalad get bvals anothercopyofbvecs 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters +get(ok): 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters (file) [from datalad...] get(ok): bvals (file) [from datalad...] get(ok): anothercopyofbvecs (file) [from datalad...] -get(ok): 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters (file) [from datalad...] -action summary: - get (ok: 3) diff --git a/docs/beyond_basics/_examples/DL-101-149-14 b/docs/beyond_basics/_examples/DL-101-149-14 index 16c946de5..af503e68f 100644 --- a/docs/beyond_basics/_examples/DL-101-149-14 +++ b/docs/beyond_basics/_examples/DL-101-149-14 @@ -8,6 +8,3 @@ copy_file(ok): HCP1200/130013/T1w/T1w_acpc_dc.nii.gz [/home/me/beyond_basics/HPC copy_file(ok): HCP1200/130013/T1w/T1wDividedByT2w.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/T1wDividedByT2w.nii.gz] copy_file(ok): HCP1200/130013/T1w/T1w_acpc_dc_restore.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/T1w_acpc_dc_restore.nii.gz] save(ok): . (dataset) -action summary: - copy_file (ok: 6) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-149-17 b/docs/beyond_basics/_examples/DL-101-149-17 index e3b8dc087..593ce0f76 100644 --- a/docs/beyond_basics/_examples/DL-101-149-17 +++ b/docs/beyond_basics/_examples/DL-101-149-17 @@ -9,6 +9,3 @@ copy_file(ok): HCP1200/130518/T1w/T1w_acpc_dc.nii.gz [/home/me/beyond_basics/HPC copy_file(ok): HCP1200/130518/T1w/T1wDividedByT2w.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/130518/T1w/T1wDividedByT2w.nii.gz] copy_file(ok): HCP1200/130518/T1w/T1w_acpc_dc_restore.nii.gz [/home/me/beyond_basics/HPC/dataset-to-copy-to/130518/T1w/T1w_acpc_dc_restore.nii.gz] save(ok): . (dataset) -action summary: - copy_file (ok: 7) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-168-103 b/docs/beyond_basics/_examples/DL-101-168-103 index 8edb5ac16..57a96cc55 100644 --- a/docs/beyond_basics/_examples/DL-101-168-103 +++ b/docs/beyond_basics/_examples/DL-101-168-103 @@ -11,6 +11,3 @@ run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [VIRTUALENV/bin/python /home/a.. [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [VIRTUALENV/bin/python /home/a...] create(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) -action summary: - create (ok: 1) - run (ok: 2) diff --git a/docs/beyond_basics/_examples/DL-101-168-104 b/docs/beyond_basics/_examples/DL-101-168-104 index 22e347159..8f801de4a 100644 --- a/docs/beyond_basics/_examples/DL-101-168-104 +++ b/docs/beyond_basics/_examples/DL-101-168-104 @@ -5,15 +5,9 @@ $ datalad download-url -m "download scripts for ML analysis" \ -O 'code/' [INFO] Downloading 'https://raw.githubusercontent.com/datalad-handbook/data-version-control/master/src/train.py' into '/home/me/DVCvsDL/DVC-DataLad/code/' download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/train.py (file) -[INFO] Downloading 'https://raw.githubusercontent.com/datalad-handbook/data-version-control/master/src/prepare.py' into '/home/me/DVCvsDL/DVC-DataLad/code/' download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/prepare.py (file) -[INFO] Downloading 'https://raw.githubusercontent.com/datalad-handbook/data-version-control/master/src/evaluate.py' into '/home/me/DVCvsDL/DVC-DataLad/code/' download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/evaluate.py (file) add(ok): code/evaluate.py (file) add(ok): code/prepare.py (file) add(ok): code/train.py (file) save(ok): . (dataset) -action summary: - add (ok: 3) - download_url (ok: 3) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-168-108 b/docs/beyond_basics/_examples/DL-101-168-108 index fbf6cd70d..3b6d27bd1 100644 --- a/docs/beyond_basics/_examples/DL-101-168-108 +++ b/docs/beyond_basics/_examples/DL-101-168-108 @@ -1,6 +1,6 @@ ### DVC $ git commit -m "initialize dvc" -[master 87e41ba] initialize dvc +[master ae6d2e1] initialize dvc 3 files changed, 6 insertions(+) create mode 100644 .dvc/.gitignore create mode 100644 .dvc/config diff --git a/docs/beyond_basics/_examples/DL-101-168-113 b/docs/beyond_basics/_examples/DL-101-168-113 index 11044b7cc..70637c166 100644 --- a/docs/beyond_basics/_examples/DL-101-168-113 +++ b/docs/beyond_basics/_examples/DL-101-168-113 @@ -1,6 +1,6 @@ ### DVC $ git commit -m "control data with DVC" -[master befe6b7] control data with DVC +[master 9420e0e] control data with DVC 3 files changed, 14 insertions(+) create mode 100644 data/raw/train.dvc create mode 100644 data/raw/val.dvc diff --git a/docs/beyond_basics/_examples/DL-101-168-114 b/docs/beyond_basics/_examples/DL-101-168-114 index ad7891b4f..6f811ed5f 100644 --- a/docs/beyond_basics/_examples/DL-101-168-114 +++ b/docs/beyond_basics/_examples/DL-101-168-114 @@ -15,8 +15,3 @@ save(ok): . (dataset) [INFO] Finished adding /home/me/DVCvsDL/DVC-DataLad/data/raw/imagenette2-160.tgz: Files processed: 2701, renamed: 2701, +annex: 2701 [INFO] Finished extraction add-archive-content(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) -action summary: - add (ok: 1) - add-archive-content (ok: 1) - download_url (ok: 1) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-168-124 b/docs/beyond_basics/_examples/DL-101-168-124 index db0767a3a..0ebd206d8 100644 --- a/docs/beyond_basics/_examples/DL-101-168-124 +++ b/docs/beyond_basics/_examples/DL-101-168-124 @@ -1,5 +1,5 @@ ### DVC $ git add .dvc/config $ git commit -m "add local remote" -[master b4f8467] add local remote +[master e8ef28d] add local remote 1 file changed, 4 insertions(+) diff --git a/docs/beyond_basics/_examples/DL-101-168-131 b/docs/beyond_basics/_examples/DL-101-168-131 index d5046576a..4620c70ec 100644 --- a/docs/beyond_basics/_examples/DL-101-168-131 +++ b/docs/beyond_basics/_examples/DL-101-168-131 @@ -3,13 +3,5 @@ $ datalad clone https://github.com/datalad-handbook/DVC-DataLad.git DVC-DataLad-2 $ cd DVC-DataLad-2 [INFO] Attempting a clone into /home/me/DVCvsDL/DVC-DataLad-2 -[INFO] Attempting to clone from https://github.com/datalad-handbook/DVC-DataLad.git to /home/me/DVCvsDL/DVC-DataLad-2 -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/DVCvsDL/DVC-DataLad-2) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-handbook/DVC-DataLad.git/config download failed: Not Found install(ok): /home/me/DVCvsDL/DVC-DataLad-2 (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-168-132 b/docs/beyond_basics/_examples/DL-101-168-132 index fdcf7ad49..92390db61 100644 --- a/docs/beyond_basics/_examples/DL-101-168-132 +++ b/docs/beyond_basics/_examples/DL-101-168-132 @@ -3,5 +3,3 @@ $ datalad get data/raw/val [INFO] To obtain some keys we need to fetch an archive of size 15.1 MB [INFO] datalad-archives special remote is using an extraction cache under /home/me/DVCvsDL/DVC-DataLad-2/.git/datalad/tmp/archives/8f2938add6. Remove it with DataLad's 'clean' command to save disk space. get(ok): data/raw/val (directory) -action summary: - get (ok: 790) diff --git a/docs/beyond_basics/_examples/DL-101-168-140 b/docs/beyond_basics/_examples/DL-101-168-140 index 015d67e84..e2735c7f2 100644 --- a/docs/beyond_basics/_examples/DL-101-168-140 +++ b/docs/beyond_basics/_examples/DL-101-168-140 @@ -2,10 +2,6 @@ $ cd DVC-DataLad $ datalad create-sibling --name mysibling ../datalad-sibling [INFO] Considering to create a target dataset /home/me/DVCvsDL/DVC-DataLad at /home/me/DVCvsDL/datalad-sibling of localhost -[INFO] Fetching updates for Dataset(/home/me/DVCvsDL/DVC-DataLad) -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects update(ok): . (dataset) [INFO] Adjusting remote git configuration [INFO] Running post-update hooks in all created siblings diff --git a/docs/beyond_basics/_examples/DL-101-168-141 b/docs/beyond_basics/_examples/DL-101-168-141 index 9a9c3ca76..bc20011b7 100644 --- a/docs/beyond_basics/_examples/DL-101-168-141 +++ b/docs/beyond_basics/_examples/DL-101-168-141 @@ -1,17 +1,6 @@ ### DVC-DataLad $ datalad push --to mysibling [INFO] Determine push target -[INFO] Push refspecs -[INFO] Transfer data -[INFO] Update availability information -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start writing objects -[INFO] Start resolving deltas [INFO] Finished push of Dataset(/home/me/DVCvsDL/DVC-DataLad) -publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex 68c6f019..2ea4ae6f] +publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex eed90ebd..3e75bdaa] publish(ok): . (dataset) [refs/heads/main->mysibling:refs/heads/main [new branch]] -action summary: - copy (ok: 2701) - publish (ok: 2) diff --git a/docs/beyond_basics/_examples/DL-101-168-142 b/docs/beyond_basics/_examples/DL-101-168-142 index 154e8f284..b4f00362c 100644 --- a/docs/beyond_basics/_examples/DL-101-168-142 +++ b/docs/beyond_basics/_examples/DL-101-168-142 @@ -1,5 +1,3 @@ ### DVC-DataLad $ datalad drop data/raw/val drop(ok): data/raw/val (directory) -action summary: - drop (ok: 790) diff --git a/docs/beyond_basics/_examples/DL-101-168-143 b/docs/beyond_basics/_examples/DL-101-168-143 index b8f5ce9b6..aeadbd9b8 100644 --- a/docs/beyond_basics/_examples/DL-101-168-143 +++ b/docs/beyond_basics/_examples/DL-101-168-143 @@ -1,5 +1,3 @@ ### DVC-DataLad $ datalad get data/raw/val get(ok): data/raw/val (directory) -action summary: - get (ok: 790) diff --git a/docs/beyond_basics/_examples/DL-101-168-151 b/docs/beyond_basics/_examples/DL-101-168-151 index 5780e3f37..9a854cc10 100644 --- a/docs/beyond_basics/_examples/DL-101-168-151 +++ b/docs/beyond_basics/_examples/DL-101-168-151 @@ -12,7 +12,7 @@ Updating lock file 'dvc.lock' To track the changes with git, run: - git add data/prepared/.gitignore dvc.lock dvc.yaml + git add data/prepared/.gitignore dvc.yaml dvc.lock To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-154 b/docs/beyond_basics/_examples/DL-101-168-154 index db99d4f65..d1d471b15 100644 --- a/docs/beyond_basics/_examples/DL-101-168-154 +++ b/docs/beyond_basics/_examples/DL-101-168-154 @@ -17,9 +17,9 @@ stages: outs: - path: data/prepared/test.csv hash: md5 - md5: 536fe137✂MD5 + md5: 0b90b0e8✂MD5 size: 62023 - path: data/prepared/train.csv hash: md5 - md5: 0bad47e2✂MD5 + md5: 360a73ac✂MD5 size: 155128 diff --git a/docs/beyond_basics/_examples/DL-101-168-155 b/docs/beyond_basics/_examples/DL-101-168-155 index d27027f6a..1e5fc1fa0 100644 --- a/docs/beyond_basics/_examples/DL-101-168-155 +++ b/docs/beyond_basics/_examples/DL-101-168-155 @@ -6,13 +6,13 @@ $ dvc stage add -n train \ Added stage 'train' in 'dvc.yaml' Running stage 'train': > python src/train.py -VIRTUALENV/lib/python3.11/site-packages/sklearn/linear_model/_stochastic_gradient.py:702: ConvergenceWarning: Maximum number of iteration reached before convergence. Consider increasing max_iter to improve the fit. +VIRTUALENV/lib/python3.8/site-packages/sklearn/linear_model/_stochastic_gradient.py:713: ConvergenceWarning: Maximum number of iteration reached before convergence. Consider increasing max_iter to improve the fit. warnings.warn( Updating lock file 'dvc.lock' To track the changes with git, run: - git add dvc.yaml dvc.lock model/.gitignore + git add dvc.lock model/.gitignore dvc.yaml To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-157 b/docs/beyond_basics/_examples/DL-101-168-157 index 9e850d10b..2c64d85e2 100644 --- a/docs/beyond_basics/_examples/DL-101-168-157 +++ b/docs/beyond_basics/_examples/DL-101-168-157 @@ -10,7 +10,7 @@ Updating lock file 'dvc.lock' To track the changes with git, run: - git add dvc.lock dvc.yaml + git add dvc.yaml dvc.lock To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-159 b/docs/beyond_basics/_examples/DL-101-168-159 index d0049baa7..bcb834b0d 100644 --- a/docs/beyond_basics/_examples/DL-101-168-159 +++ b/docs/beyond_basics/_examples/DL-101-168-159 @@ -1,4 +1,4 @@ ### DVC $ dvc metrics show Path accuracy -metrics/accuracy.json 0.67934 +metrics/accuracy.json 0.75919 diff --git a/docs/beyond_basics/_examples/DL-101-168-160 b/docs/beyond_basics/_examples/DL-101-168-160 index 9dac50cb9..f25ace59c 100644 --- a/docs/beyond_basics/_examples/DL-101-168-160 +++ b/docs/beyond_basics/_examples/DL-101-168-160 @@ -6,7 +6,7 @@ $ git push --set-upstream origin sgd-pipeline $ git tag -a sgd -m "Trained SGD as DVC pipeline." $ git push origin --tags $ dvc push -[sgd-pipeline 21a7688] Add SGD pipeline +[sgd-pipeline 9238080] Add SGD pipeline 5 files changed, 83 insertions(+) create mode 100644 dvc.lock create mode 100644 dvc.yaml diff --git a/docs/beyond_basics/_examples/DL-101-168-165 b/docs/beyond_basics/_examples/DL-101-168-165 index 1b79d5129..fda480c70 100644 --- a/docs/beyond_basics/_examples/DL-101-168-165 +++ b/docs/beyond_basics/_examples/DL-101-168-165 @@ -6,7 +6,7 @@ $ git push --set-upstream origin random-forest $ git tag -a randomforest -m "Random Forest classifier with 80.99% accuracy." $ git push origin --tags $ dvc push -[random-forest 6eb389f] Train Random Forest classifier +[random-forest 64a8207] Train Random Forest classifier 3 files changed, 11 insertions(+), 17 deletions(-) To /home/me/pushes/data-version-control * [new branch] random-forest -> random-forest diff --git a/docs/beyond_basics/_examples/DL-101-168-166 b/docs/beyond_basics/_examples/DL-101-168-166 index ffd4938d7..84c6c0eca 100644 --- a/docs/beyond_basics/_examples/DL-101-168-166 +++ b/docs/beyond_basics/_examples/DL-101-168-166 @@ -1,6 +1,6 @@ ### DVC $ dvc metrics show -T Revision Path accuracy -workspace metrics/accuracy.json 0.80735 -randomforest metrics/accuracy.json 0.80735 -sgd metrics/accuracy.json 0.67934 +workspace metrics/accuracy.json 0.82129 +randomforest metrics/accuracy.json 0.82129 +sgd metrics/accuracy.json 0.75919 diff --git a/docs/beyond_basics/_examples/DL-101-168-177 b/docs/beyond_basics/_examples/DL-101-168-177 index 53fd49e76..bf7905c97 100644 --- a/docs/beyond_basics/_examples/DL-101-168-177 +++ b/docs/beyond_basics/_examples/DL-101-168-177 @@ -1,6 +1,3 @@ $ datalad save -m "Switch to random forest classification" code/train.py add(ok): code/train.py (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-168-178 b/docs/beyond_basics/_examples/DL-101-168-178 index 11844244d..4ebad9f17 100644 --- a/docs/beyond_basics/_examples/DL-101-168-178 +++ b/docs/beyond_basics/_examples/DL-101-168-178 @@ -1,6 +1,6 @@ $ datalad rerun --branch="randomforest" -m "Recompute classification with random forest classifier" ready-for-analysis..SGD -[INFO] checkout commit de525c5; -[INFO] run commit 941ab2f; (Train an SGD clas...) +[INFO] checkout commit 97457b0; +[INFO] run commit c8eb8dc; (Train an SGD clas...) [INFO] Making sure inputs are available (this may take some time) [INFO] Unlocking files unlock(ok): model/model.joblib (file) @@ -11,7 +11,7 @@ unlock(ok): model/model.joblib (file) run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [python code/train.py] add(ok): model/model.joblib (file) save(ok): . (dataset) -[INFO] run commit 178d7c6; (Evaluate SGD clas...) +[INFO] run commit b0793d4; (Evaluate SGD clas...) [INFO] Making sure inputs are available (this may take some time) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/beyond_basics/_examples/DL-101-168-179 b/docs/beyond_basics/_examples/DL-101-168-179 index 56784e3c9..468cd9faf 100644 --- a/docs/beyond_basics/_examples/DL-101-168-179 +++ b/docs/beyond_basics/_examples/DL-101-168-179 @@ -1,10 +1,10 @@ $ git diff SGD -- metrics/accuracy.json diff --git a/metrics/accuracy.json b/metrics/accuracy.json -index b8423003..41634f21 100644 +index 1058d868..9279f676 100644 --- a/metrics/accuracy.json +++ b/metrics/accuracy.json @@ -1 +1 @@ --{"accuracy": 0.770595690747782} +-{"accuracy": 0.7718631178707225} \ No newline at end of file -+{"accuracy": 0.8086185044359949} ++{"accuracy": 0.8149556400506971} \ No newline at end of file diff --git a/docs/beyond_basics/_examples/DL-101-179-103 b/docs/beyond_basics/_examples/DL-101-179-103 index 28cd8561b..0ce7d0b9f 100644 --- a/docs/beyond_basics/_examples/DL-101-179-103 +++ b/docs/beyond_basics/_examples/DL-101-179-103 @@ -1,6 +1,3 @@ $ datalad save -m "add something to ignore" .gitignore add(ok): .gitignore (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-179-109 b/docs/beyond_basics/_examples/DL-101-179-109 index a83dfcb03..f7f6357a1 100644 --- a/docs/beyond_basics/_examples/DL-101-179-109 +++ b/docs/beyond_basics/_examples/DL-101-179-109 @@ -2,6 +2,3 @@ $ git config -f .gitmodules --replace-all submodule.midterm_project.url https:// $ datalad save -m "SERVICE COMMIT - IGNORE. This commit only serves to appropriately reference the subdataset in the public showroom dataset" add(ok): .gitmodules (file) save(ok): . (dataset) -action summary: - add (ok: 1) - save (ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-181-101 b/docs/beyond_basics/_examples/DL-101-181-101 index bd0f7967c..9bbb6f10f 100644 --- a/docs/beyond_basics/_examples/DL-101-181-101 +++ b/docs/beyond_basics/_examples/DL-101-181-101 @@ -1,13 +1,5 @@ $ datalad clone https://github.com/datalad-handbook/cozy-screensavers.git $ cd cozy-screensavers [INFO] Attempting a clone into /home/me/beyond_basics/meta/cozy-screensavers -[INFO] Attempting to clone from https://github.com/datalad-handbook/cozy-screensavers.git to /home/me/beyond_basics/meta/cozy-screensavers -[INFO] Start enumerating objects -[INFO] Start counting objects -[INFO] Start compressing objects -[INFO] Start receiving objects -[INFO] Start resolving deltas -[INFO] Completed clone attempts for Dataset(/home/me/beyond_basics/meta/cozy-screensavers) [INFO] Remote origin not usable by git-annex; setting annex-ignore -[INFO] https://github.com/datalad-handbook/cozy-screensavers.git/config download failed: Not Found install(ok): /home/me/beyond_basics/meta/cozy-screensavers (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-181-102 b/docs/beyond_basics/_examples/DL-101-181-102 index dd214c69e..4103fd7c3 100644 --- a/docs/beyond_basics/_examples/DL-101-181-102 +++ b/docs/beyond_basics/_examples/DL-101-181-102 @@ -1,5 +1,5 @@ $ tree . -└── zen.jpg -> .git/annex/objects/PV/X5/✂/MD5E-s5217743--ad8f6e78✂MD5.jpg +└── zen.jpg -> .git/annex/objects/Fx/fM/✂/MD5E-s3351765--e4c0b8d7✂MD5.jpg 0 directories, 1 file diff --git a/docs/beyond_basics/_examples/DL-101-181-108 b/docs/beyond_basics/_examples/DL-101-181-108 index 7f40e084b..fa135186e 100644 --- a/docs/beyond_basics/_examples/DL-101-181-108 +++ b/docs/beyond_basics/_examples/DL-101-181-108 @@ -5,11 +5,11 @@ $ datalad meta-extract -d . metalad_core | jq { "type": "dataset", "dataset_id": "2d540a9d-2ef7-4b5f-8931-7c92f483f0c7", - "dataset_version": "19f2d98d✂SHA1", + "dataset_version": "66aa4e8a✂SHA1", "extractor_name": "metalad_core", "extractor_version": "1", "extraction_parameter": {}, - "extraction_time": 1691514094.1297715, + "extraction_time": 1698845024.5401418, "agent_name": "Elena Piscopia", "agent_email": "elena@example.net", "extracted_metadata": { @@ -25,16 +25,19 @@ $ datalad meta-extract -d . metalad_core | jq "email": "adina.wagner@t-online.de" }, { - "@id": "19f2d98d✂SHA1", + "@id": "66aa4e8a✂SHA1", "identifier": "2d540a9d-2ef7-4b5f-8931-7c92f483f0c7", "@type": "Dataset", - "version": "0-2-g19f2d98", + "version": "0-3-g66aa4e8", "dateCreated": "2023-02-13T07:48:15+01:00", - "dateModified": "2023-02-13T07:55:38+01:00", + "dateModified": "2023-11-01T13:08:02+01:00", "hasContributor": { "@id": "d3765bf6✂MD5" }, "distribution": [ + { + "@id": "4aef00ff-3027-4364-911a-98905cdbdf8d" + }, { "@id": "b8938507-77c0-4479-84a6-cbeb41214ca6" }, diff --git a/docs/beyond_basics/_examples/DL-101-182-103 b/docs/beyond_basics/_examples/DL-101-182-103 index 85273030e..20042dd5f 100644 --- a/docs/beyond_basics/_examples/DL-101-182-103 +++ b/docs/beyond_basics/_examples/DL-101-182-103 @@ -1,11 +1,11 @@ $ tree -L 1 data-cat data-cat -├── README.md ├── artwork ├── assets ├── config.json ├── index.html ├── metadata +├── README.md ├── schema └── templates diff --git a/docs/beyond_basics/_examples/DL-101-182-105 b/docs/beyond_basics/_examples/DL-101-182-105 index d016d195a..064703b8d 100644 --- a/docs/beyond_basics/_examples/DL-101-182-105 +++ b/docs/beyond_basics/_examples/DL-101-182-105 @@ -1,6 +1,4 @@ $ datalad catalog-validate --metadata toy_metadata.jsonl -catalog_validate(ok): /private/tmp/me/catalog -catalog_validate(ok): /private/tmp/me/catalog -catalog_validate(ok): /private/tmp/me/catalog -action summary: - catalog_validate (ok: 3) +catalog_validate(ok): /home/me/catalog +catalog_validate(ok): /home/me/catalog +catalog_validate(ok): /home/me/catalog diff --git a/docs/beyond_basics/_examples/DL-101-182-106 b/docs/beyond_basics/_examples/DL-101-182-106 index 9947e599a..4ab3131df 100644 --- a/docs/beyond_basics/_examples/DL-101-182-106 +++ b/docs/beyond_basics/_examples/DL-101-182-106 @@ -2,5 +2,3 @@ $ datalad catalog-add --catalog data-cat --metadata toy_metadata.jsonl catalog_add(ok): data-cat [Metadata record successfully added to catalog (dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): data-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): data-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] -action summary: - catalog_add (ok: 3) diff --git a/docs/beyond_basics/_examples/DL-101-182-114 b/docs/beyond_basics/_examples/DL-101-182-114 index 1bbf53809..6a87776c4 100644 --- a/docs/beyond_basics/_examples/DL-101-182-114 +++ b/docs/beyond_basics/_examples/DL-101-182-114 @@ -4,12 +4,7 @@ catalog_create(ok): custom-cat [Catalog successfully created at: custom-cat] catalog_add(ok): custom-cat [Metadata record successfully added to catalog (dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): custom-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): custom-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] -action summary: - catalog_add (ok: 3) catalog_add(ok): custom-cat [Metadata record successfully added to catalog (dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): custom-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] catalog_add(ok): custom-cat [Metadata record successfully updated in catalog (filetree of dataset: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1)] -action summary: - catalog_add (ok: 3) - catalog_create (ok: 1) catalog_set(ok): custom-cat [Home page successfully set to: dataset_id=5df8eb3a-95c5-11ea-b4b9-a0369f287950, dataset_version=dae38cf9✂SHA1.] From 661f9dff1e013a620e29f87005f49aa3747ac1d0 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Wed, 1 Nov 2023 15:52:42 +0100 Subject: [PATCH 17/17] british english -> american english --- docs/basics/101-139-hostingservices.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/basics/101-139-hostingservices.rst b/docs/basics/101-139-hostingservices.rst index 4a6d4002f..366e46312 100644 --- a/docs/basics/101-139-hostingservices.rst +++ b/docs/basics/101-139-hostingservices.rst @@ -357,6 +357,6 @@ Once you have set up your dataset sibling(s), you can push individual datasets w is protecting. If the private key does not have a passphrase, simply copying this file grants a person access! -.. [#f3] GitHub `deprecated user-password authentication `_ in favour of authentication via personal access token. Supplying a password instead of a token will fail to authenticate. +.. [#f3] GitHub `deprecated user-password authentication `_ in favor of authentication via personal access token. Supplying a password instead of a token will fail to authenticate. .. [#f4] The default project name ``project`` and path separator ``-`` are configurable using the dataset-level configurations ``datalad.gitlab-default-projectname`` and ``datalad.gitlab-default-pathseparator``