From a29b85e924d3f27ee5363b3c9ecdd99406ebbc0f Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Mon, 18 May 2020 14:47:46 +0200 Subject: [PATCH 1/7] update submodule: updated funding logos --- docs/artwork | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/artwork b/docs/artwork index 353182cac..78576751f 160000 --- a/docs/artwork +++ b/docs/artwork @@ -1 +1 @@ -Subproject commit 353182cac33aac42c62168dd4c3246bf9985186f +Subproject commit 78576751ffc0c301a7fe3b6be02d9254b4a6c8b1 From 0441a6af0a471fd78ab068dd52a4404e49a3431e Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Mon, 18 May 2020 15:07:35 +0200 Subject: [PATCH 2/7] Rename chapter: 12 -> 11, for sequental chapter numbers --- docs/beyond_basics/basics-scaling.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/beyond_basics/basics-scaling.rst b/docs/beyond_basics/basics-scaling.rst index 10628d9e6..0b00945f0 100644 --- a/docs/beyond_basics/basics-scaling.rst +++ b/docs/beyond_basics/basics-scaling.rst @@ -1,7 +1,7 @@ .. _chapter_gobig: -**XII - Go big or go home** ---------------------------- +**XI - Go big or go home** +-------------------------- .. figure:: ../artwork/src/gobig.svg From d76ba6175c28dcb6b7b88ed3575dbbbe1d37f2f0 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Sun, 24 May 2020 12:18:06 +0200 Subject: [PATCH 3/7] update submodule: improved funding overview --- docs/artwork | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/artwork b/docs/artwork index 78576751f..a0a6f4b59 160000 --- a/docs/artwork +++ b/docs/artwork @@ -1 +1 @@ -Subproject commit 78576751ffc0c301a7fe3b6be02d9254b4a6c8b1 +Subproject commit a0a6f4b59080dcf9fe70e31da39259167846ecbb From ae2c44d91c8718cfcc751feb29e647d90725ad7e Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Tue, 23 Jun 2020 20:56:30 +0200 Subject: [PATCH 4/7] BF: fix download link for byte of python --- docs/basics/101-102-populate.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/basics/101-102-populate.rst b/docs/basics/101-102-populate.rst index 2f115880d..cdebdc943 100644 --- a/docs/basics/101-102-populate.rst +++ b/docs/basics/101-102-populate.rst @@ -32,7 +32,7 @@ Below is a short list of optional readings. We decide to download them (they are all free, in total about 15 MB), and save them in ``DataLad-101/books``. - Additional reading about the command line: `The Linux Command Line `_ -- An intro to Python: `A byte of Python `_ +- An intro to Python: `A byte of Python `_ You can either visit the links and save them in ``books/``, or run the following commands [#f2]_ to download the books right from the terminal: @@ -40,7 +40,7 @@ or run the following commands [#f2]_ to download the books right from the termin .. runrecord:: _examples/DL-101-102-103 :language: console :workdir: dl-101/DataLad-101 - :realcommand: cd books && wget -nv https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download -O TLCL.pdf && wget -nv https://edisciplinas.usp.br/pluginfile.php/3252353/mod_resource/content/1/b_Swaroop_Byte_of_python.pdf -O byte-of-python.pdf && cd ../ + :realcommand: cd books && wget -nv https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download -O TLCL.pdf && wget -nv https://github.com/swaroopch/byte-of-python/releases/download/v14558db59a326ba99eda0da6c4548c48ccb4cd0f/byte-of-python.pdf -O byte-of-python.pdf && cd ../ :cast: 01_dataset_basics :notes: We use wget to download a few books from the web. CAVE: longish realcommand! From 9abbb73e4f93fdc38730c7cd8cfcda589137c07b Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Tue, 23 Jun 2020 21:10:24 +0200 Subject: [PATCH 5/7] update examples --- docs/basics/_examples/DL-101-101-103 | 8 +-- docs/basics/_examples/DL-101-102-103 | 4 +- docs/basics/_examples/DL-101-102-107 | 8 +-- docs/basics/_examples/DL-101-102-108 | 2 +- docs/basics/_examples/DL-101-102-111 | 8 +-- docs/basics/_examples/DL-101-102-115 | 4 +- docs/basics/_examples/DL-101-102-116 | 10 ++-- docs/basics/_examples/DL-101-103-107 | 8 +-- docs/basics/_examples/DL-101-105-107 | 2 - docs/basics/_examples/DL-101-105-109 | 6 +-- docs/basics/_examples/DL-101-105-113 | 2 - docs/basics/_examples/DL-101-106-101 | 49 +++++++++--------- docs/basics/_examples/DL-101-108-106 | 6 +-- docs/basics/_examples/DL-101-108-108 | 22 ++++---- docs/basics/_examples/DL-101-109-105 | 10 ++-- docs/basics/_examples/DL-101-109-106 | 2 +- docs/basics/_examples/DL-101-109-107 | 8 +-- docs/basics/_examples/DL-101-109-112 | 14 +++--- docs/basics/_examples/DL-101-110-102 | 5 +- docs/basics/_examples/DL-101-110-104 | 5 +- docs/basics/_examples/DL-101-112-109 | 10 ++-- docs/basics/_examples/DL-101-114-101 | 44 ++++++++-------- docs/basics/_examples/DL-101-115-101 | 2 +- docs/basics/_examples/DL-101-115-103 | 6 +-- docs/basics/_examples/DL-101-116-102 | 4 +- docs/basics/_examples/DL-101-116-103 | 2 +- docs/basics/_examples/DL-101-116-105 | 2 +- docs/basics/_examples/DL-101-116-106 | 2 +- docs/basics/_examples/DL-101-116-107 | 7 +-- docs/basics/_examples/DL-101-116-108 | 2 +- docs/basics/_examples/DL-101-117-101 | 2 +- docs/basics/_examples/DL-101-118-102 | 44 ++++++++-------- docs/basics/_examples/DL-101-118-103 | 2 +- docs/basics/_examples/DL-101-119-102 | 10 +++- docs/basics/_examples/DL-101-121-103 | 4 +- docs/basics/_examples/DL-101-121-106 | 5 +- docs/basics/_examples/DL-101-121-110 | 7 ++- docs/basics/_examples/DL-101-121-112 | 54 ++++++++++---------- docs/basics/_examples/DL-101-122-101 | 4 +- docs/basics/_examples/DL-101-122-103 | 4 +- docs/basics/_examples/DL-101-123-101 | 2 +- docs/basics/_examples/DL-101-123-104 | 1 - docs/basics/_examples/DL-101-123-105 | 2 +- docs/basics/_examples/DL-101-123-108 | 5 +- docs/basics/_examples/DL-101-124-101 | 2 +- docs/basics/_examples/DL-101-130-105 | 6 +-- docs/basics/_examples/DL-101-130-110 | 4 +- docs/basics/_examples/DL-101-130-112 | 10 ++-- docs/basics/_examples/DL-101-130-117 | 3 -- docs/basics/_examples/DL-101-130-118 | 10 +++- docs/basics/_examples/DL-101-130-119 | 6 +-- docs/basics/_examples/DL-101-130-120 | 6 +-- docs/basics/_examples/DL-101-132-101 | 12 ++--- docs/basics/_examples/DL-101-132-112 | 10 ++-- docs/basics/_examples/DL-101-133-102 | 2 +- docs/basics/_examples/DL-101-133-103 | 8 +-- docs/basics/_examples/DL-101-133-111 | 6 +-- docs/basics/_examples/DL-101-135-101 | 2 +- docs/basics/_examples/DL-101-135-102 | 43 +++++----------- docs/basics/_examples/DL-101-135-103 | 49 ++++++++++-------- docs/basics/_examples/DL-101-136-101 | 6 +-- docs/basics/_examples/DL-101-136-104 | 4 +- docs/basics/_examples/DL-101-136-105 | 2 +- docs/basics/_examples/DL-101-136-109 | 2 +- docs/basics/_examples/DL-101-136-110 | 2 +- docs/basics/_examples/DL-101-136-121 | 2 +- docs/basics/_examples/DL-101-136-122 | 2 +- docs/basics/_examples/DL-101-136-123 | 4 +- docs/basics/_examples/DL-101-136-124 | 2 +- docs/basics/_examples/DL-101-136-128 | 4 +- docs/basics/_examples/DL-101-136-129 | 4 +- docs/basics/_examples/DL-101-136-132 | 4 +- docs/basics/_examples/DL-101-136-133 | 2 +- docs/basics/_examples/DL-101-136-134 | 2 +- docs/basics/_examples/DL-101-136-137 | 2 +- docs/basics/_examples/DL-101-136-139 | 4 +- docs/basics/_examples/DL-101-136-140 | 4 +- docs/basics/_examples/DL-101-136-142 | 15 +++--- docs/basics/_examples/DL-101-136-144 | 4 +- docs/basics/_examples/DL-101-136-145 | 2 +- docs/basics/_examples/DL-101-136-146 | 2 +- docs/basics/_examples/DL-101-136-148 | 4 +- docs/basics/_examples/DL-101-136-152 | 2 +- docs/basics/_examples/DL-101-136-156 | 2 +- docs/basics/_examples/DL-101-136-160 | 11 ++-- docs/basics/_examples/DL-101-136-163 | 9 +++- docs/basics/_examples/DL-101-136-164 | 2 +- docs/basics/_examples/DL-101-136-174 | 2 +- docs/basics/_examples/DL-101-136-180 | 2 +- docs/basics/_examples/DL-101-136-184 | 4 +- docs/basics/_examples/DL-101-136-187 | 2 +- docs/basics/_examples/DL-101-137-101 | 30 +++++------ docs/basics/_examples/DL-101-137-105 | 4 +- docs/basics/_examples/DL-101-137-106 | 6 +-- docs/basics/_examples/DL-101-137-112 | 10 ++-- docs/basics/_examples/DL-101-137-114 | 2 +- docs/basics/_examples/DL-101-137-116 | 2 +- docs/basics/_examples/DL-101-137-117 | 6 +-- docs/basics/_examples/DL-101-137-119 | 4 +- docs/basics/_examples/DL-101-137-121 | 40 +++++++-------- docs/basics/_examples/DL-101-137-122 | 6 +-- docs/basics/_examples/DL-101-137-123 | 19 +++++++ docs/basics/_examples/DL-101-137-127 | 21 +++++++- docs/basics/_examples/DL-101-137-132 | 4 +- docs/basics/_examples/DL-101-137-133 | 4 +- docs/basics/_examples/DL-101-137-144 | 6 +-- docs/basics/_examples/DL-101-137-146 | 14 +++--- docs/basics/_examples/DL-101-139-102 | 14 +++++- docs/basics/_examples/DL-101-139-104 | 4 +- docs/basics/_examples/DL-101-139-106 | 9 +++- docs/basics/_examples/DL-101-139-107 | 4 +- docs/basics/_examples/DL-101-141-101 | 3 ++ docs/beyond_basics/_examples/DL-101-179-107 | 4 +- docs/beyond_basics/_examples/DL-101-179-108 | 4 +- docs/intro/_examples/how-to-1 | 4 +- docs/intro/_examples/how-to-2 | 2 +- docs/usecases/_examples/HCP-12 | 2 +- docs/usecases/_examples/HCP-2 | 56 +-------------------- docs/usecases/_examples/collab-103 | 13 +++-- docs/usecases/_examples/collab-107 | 4 +- docs/usecases/_examples/collab-110 | 10 +++- docs/usecases/_examples/dataset | 10 +++- docs/usecases/_examples/dataset4 | 6 ++- docs/usecases/_examples/prov-103 | 2 +- docs/usecases/_examples/prov-106 | 6 +-- docs/usecases/_examples/prov-109 | 2 +- docs/usecases/_examples/prov-110 | 2 +- docs/usecases/_examples/prov-111 | 2 +- docs/usecases/_examples/prov-113 | 16 +++--- docs/usecases/_examples/prov-115 | 12 ++--- docs/usecases/_examples/repro-102 | 11 +++- docs/usecases/_examples/repro-103 | 11 +++- docs/usecases/_examples/repro-106 | 2 + docs/usecases/_examples/repro-110 | 6 +-- docs/usecases/_examples/repro-117 | 16 +++++- 135 files changed, 587 insertions(+), 532 deletions(-) delete mode 100644 docs/basics/_examples/DL-101-130-117 diff --git a/docs/basics/_examples/DL-101-101-103 b/docs/basics/_examples/DL-101-101-103 index 73d485955..7538dc4f3 100644 --- a/docs/basics/_examples/DL-101-101-103 +++ b/docs/basics/_examples/DL-101-101-103 @@ -1,12 +1,12 @@ $ git log -commit c74e2b7951db566d5ccce7faeb2f86584d4d6321 +commit a50e5c92a7fbe805284a4d85c8986155bf5fe60d Author: Elena Piscopia -Date: Mon Feb 17 08:48:47 2020 +0100 +Date: Tue Jun 23 21:02:42 2020 +0200 Instruct annex to add text files to Git -commit dbaf9fae9f69b9bfea1a6b7e2f374335f41702c1 +commit c76005349f18dd0fe3eacad01deb433bee4e9f27 Author: Elena Piscopia -Date: Mon Feb 17 08:48:46 2020 +0100 +Date: Tue Jun 23 21:02:41 2020 +0200 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-102-103 b/docs/basics/_examples/DL-101-102-103 index d9af80d91..8e62697c2 100644 --- a/docs/basics/_examples/DL-101-102-103 +++ b/docs/basics/_examples/DL-101-102-103 @@ -3,5 +3,5 @@ $ wget https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01 $ wget https://edisciplinas.usp.br/pluginfile.php/3252353/mod_resource/content/1/b_Swaroop_Byte_of_python.pdf -O byte-of-python.pdf # get back into the root of the dataset $ cd ../ -2020-02-17 08:48:50 URL:https://netix.dl.sourceforge.net/project/linuxcommand/TLCL/19.01/TLCL-19.01.pdf [2120211/2120211] -> "TLCL.pdf" [1] -2020-02-17 08:49:11 URL:https://edisciplinas.usp.br/pluginfile.php/3252353/mod_resource/content/1/b_Swaroop_Byte_of_python.pdf [4242644/4242644] -> "byte-of-python.pdf" [1] +2020-06-23 21:02:46 URL:https://netcologne.dl.sourceforge.net/project/linuxcommand/TLCL/19.01/TLCL-19.01.pdf [2120211/2120211] -> "TLCL.pdf" [1] +2020-06-23 21:02:48 URL:https://github-production-release-asset-2e65be.s3.amazonaws.com/6501727/56225300-af61-11ea-8d7f-be2b68e479be?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200623%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200623T190246Z&X-Amz-Expires=300&X-Amz-Signature=66de4cc92435e7b0cb3d44919e65b530174156cb3d18d3fe7aaa99ac257ac3a2&X-Amz-SignedHeaders=host&actor_id=0&repo_id=6501727&response-content-disposition=attachment%3B%20filename%3Dbyte-of-python.pdf&response-content-type=application%2Foctet-stream [4208954/4208954] -> "byte-of-python.pdf" [1] diff --git a/docs/basics/_examples/DL-101-102-107 b/docs/basics/_examples/DL-101-102-107 index 37fbb566b..9b9451ab7 100644 --- a/docs/basics/_examples/DL-101-102-107 +++ b/docs/basics/_examples/DL-101-102-107 @@ -1,7 +1,7 @@ $ git log -p -n 1 -commit 44aa3e27dfd88183567f22a6a835e042171391f0 +commit da1610a8597da3cbcb16c0b4afefcb9df12de97a Author: Elena Piscopia -Date: Mon Feb 17 08:49:12 2020 +0100 +Date: Tue Jun 23 21:02:49 2020 +0200 add books on Python and Unix to read later @@ -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..58c0629 +index 0000000..adaec61 --- /dev/null +++ b/books/byte-of-python.pdf @@ -0,0 +1 @@ -+../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf ++../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf \ No newline at end of file diff --git a/docs/basics/_examples/DL-101-102-108 b/docs/basics/_examples/DL-101-102-108 index e88bab173..89fe709a6 100644 --- a/docs/basics/_examples/DL-101-102-108 +++ b/docs/basics/_examples/DL-101-102-108 @@ -1,4 +1,4 @@ $ cd books $ wget https://github.com/progit/progit2/releases/download/2.1.154/progit.pdf $ cd ../ -2020-02-17 08:49:16 URL:https://github-production-release-asset-2e65be.s3.amazonaws.com/15400220/57552a00-9a49-11e9-9144-d9607ed4c2db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200217%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200217T074913Z&X-Amz-Expires=300&X-Amz-Signature=d570838402c46cfaec8c625167c0df0a6f8aae6eaa1fef4b1791da7325e5d8a8&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dprogit.pdf&response-content-type=application%2Foctet-stream [12465653/12465653] -> "progit.pdf" [1] +2020-06-23 21:02:53 URL:https://github-production-release-asset-2e65be.s3.amazonaws.com/15400220/57552a00-9a49-11e9-9144-d9607ed4c2db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200623%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200623T190249Z&X-Amz-Expires=300&X-Amz-Signature=cbfc8b0998bb231993983a990007850d6c20c22374e3c93f515d59b4d30d0c71&X-Amz-SignedHeaders=host&actor_id=0&repo_id=15400220&response-content-disposition=attachment%3B%20filename%3Dprogit.pdf&response-content-type=application%2Foctet-stream [12465653/12465653] -> "progit.pdf" [1] diff --git a/docs/basics/_examples/DL-101-102-111 b/docs/basics/_examples/DL-101-102-111 index 6be028f63..7e111764b 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 -393f24f add reference book about git -44aa3e2 add books on Python and Unix to read later -c74e2b7 Instruct annex to add text files to Git -dbaf9fa [DATALAD] new dataset +769bbe9 add reference book about git +da1610a add books on Python and Unix to read later +a50e5c9 Instruct annex to add text files to Git +c760053 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-102-115 b/docs/basics/_examples/DL-101-102-115 index 0a1cb8668..9d6b8ca90 100644 --- a/docs/basics/_examples/DL-101-102-115 +++ b/docs/basics/_examples/DL-101-102-115 @@ -1,7 +1,7 @@ $ git log -p -n 1 -commit 8d3b831c9850ec783870c26d516db78ac4a5d1d1 +commit 2821a5aa03bb68633db1382fe73251f1ab0b9c83 Author: Elena Piscopia -Date: Mon Feb 17 08:49:26 2020 +0100 +Date: Tue Jun 23 21:02:59 2020 +0200 add beginners guide on bash diff --git a/docs/basics/_examples/DL-101-102-116 b/docs/basics/_examples/DL-101-102-116 index 62eb37410..236712d30 100644 --- a/docs/basics/_examples/DL-101-102-116 +++ b/docs/basics/_examples/DL-101-102-116 @@ -1,6 +1,6 @@ $ git log --oneline -8d3b831 add beginners guide on bash -393f24f add reference book about git -44aa3e2 add books on Python and Unix to read later -c74e2b7 Instruct annex to add text files to Git -dbaf9fa [DATALAD] new dataset +2821a5a add beginners guide on bash +769bbe9 add reference book about git +da1610a add books on Python and Unix to read later +a50e5c9 Instruct annex to add text files to Git +c760053 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-103-107 b/docs/basics/_examples/DL-101-103-107 index 151869a3e..30435a172 100644 --- a/docs/basics/_examples/DL-101-103-107 +++ b/docs/basics/_examples/DL-101-103-107 @@ -1,7 +1,7 @@ $ git log -p -n 2 -commit 12ced25277c47d5f52946937ef28df87e61b3d42 +commit 5a857d09e484cc86dfe7eae1ece09e686db3a956 Author: Elena Piscopia -Date: Mon Feb 17 08:49:29 2020 +0100 +Date: Tue Jun 23 21:03:01 2020 +0200 add note on datalad save @@ -18,9 +18,9 @@ index 3a7a1fe..bfa64d7 100644 +Always use informative, concise commit messages. + -commit 63d50c8818d6982bd158b14e34e1601db03c6a6e +commit 46bcde7044e54cb3129c07d5e07cf66819c5971a Author: Elena Piscopia -Date: Mon Feb 17 08:49:28 2020 +0100 +Date: Tue Jun 23 21:03:01 2020 +0200 Add notes on datalad create diff --git a/docs/basics/_examples/DL-101-105-107 b/docs/basics/_examples/DL-101-105-107 index 6a0ee4e49..e1b56a131 100644 --- a/docs/basics/_examples/DL-101-105-107 +++ b/docs/basics/_examples/DL-101-105-107 @@ -1,4 +1,2 @@ $ datalad get Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 get(ok): Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 (file) [from web...] -Tried to get 1 file that had no content yet. Successfully obtained 1. -/home/me/dl-101/DataLad-101/recordings/longnow/Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 [file] ... ok diff --git a/docs/basics/_examples/DL-101-105-109 b/docs/basics/_examples/DL-101-105-109 index b69f51dd1..0827b7ef1 100644 --- a/docs/basics/_examples/DL-101-105-109 +++ b/docs/basics/_examples/DL-101-105-109 @@ -3,7 +3,5 @@ Long_Now__Seminars_About_Long_term_Thinking/2003_12_13__Peter_Schwartz__The_Art_ Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 get(ok): Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 (file) [from web...] get(ok): Long_Now__Seminars_About_Long_term_Thinking/2003_12_13__Peter_Schwartz__The_Art_Of_The_Really_Long_View.mp3 (file) [from web...] -Tried to get 3 files that had no content yet. Successfully obtained 2. 1 (failed). -/home/me/dl-101/DataLad-101/recordings/longnow/Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 [file] ... ok -/home/me/dl-101/DataLad-101/recordings/longnow/Long_Now__Seminars_About_Long_term_Thinking/2003_12_13__Peter_Schwartz__The_Art_Of_The_Really_Long_View.mp3 [file] ... ok -/home/me/dl-101/DataLad-101/recordings/longnow/Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 [file] ... notneeded +action summary: + get (notneeded: 1, ok: 2) diff --git a/docs/basics/_examples/DL-101-105-113 b/docs/basics/_examples/DL-101-105-113 index a35283c45..0f7d1cef5 100644 --- a/docs/basics/_examples/DL-101-105-113 +++ b/docs/basics/_examples/DL-101-105-113 @@ -1,4 +1,2 @@ $ datalad get Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 get(ok): Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 (file) [from web...] -Tried to get 1 file that had no content yet. Successfully obtained 1. -/home/me/dl-101/DataLad-101/recordings/longnow/Long_Now__Seminars_About_Long_term_Thinking/2004_01_10__George_Dyson__There_s_Plenty_of_Room_at_the_Top__Long_term_Thinking_About_Large_scale_Computing.mp3 [file] ... ok diff --git a/docs/basics/_examples/DL-101-106-101 b/docs/basics/_examples/DL-101-106-101 index 84b9d6ee0..63386a450 100644 --- a/docs/basics/_examples/DL-101-106-101 +++ b/docs/basics/_examples/DL-101-106-101 @@ -1,7 +1,7 @@ $ git log -p -n 2 -commit 72f6a7d29ff7a3c33109ece297c4da1d92a45e44 +commit 33f5bc7b046df6472994864c4eb9eb151b0e3ab9 Author: Elena Piscopia -Date: Mon Feb 17 08:50:02 2020 +0100 +Date: Tue Jun 23 21:03:46 2020 +0200 Add note on datalad clone @@ -20,22 +20,21 @@ index bfa64d7..18a0315 100644 +root of the superdataset with the '-d' option. + -commit 9bb3629f431bb1b34651a55e8c95e49c71035d1e +commit 029e10cbfbb00516653590e1df12b6f03ba54d66 Author: Elena Piscopia -Date: Mon Feb 17 08:49:32 2020 +0100 +Date: Tue Jun 23 21:03:04 2020 +0200 [DATALAD] Recorded changes diff --git a/.gitmodules b/.gitmodules new file mode 100644 -index 0000000..37b3468 +index 0000000..1b59b8c --- /dev/null +++ b/.gitmodules -@@ -0,0 +1,5 @@ +@@ -0,0 +1,4 @@ +[submodule "recordings/longnow"] + path = recordings/longnow + url = https://github.com/datalad-datasets/longnow-podcasts.git -+ branch = master + datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e diff --git a/recordings/longnow b/recordings/longnow new file mode 160000 @@ -45,9 +44,9 @@ index 0000000..dcc34fb @@ -0,0 +1 @@ +Subproject commit dcc34fbe669b06ced84ced381ba0db21cf5e665f -commit 12ced25277c47d5f52946937ef28df87e61b3d42 +commit 5a857d09e484cc86dfe7eae1ece09e686db3a956 Author: Elena Piscopia -Date: Mon Feb 17 08:49:29 2020 +0100 +Date: Tue Jun 23 21:03:01 2020 +0200 add note on datalad save @@ -64,9 +63,9 @@ index 3a7a1fe..bfa64d7 100644 +Always use informative, concise commit messages. + -commit 63d50c8818d6982bd158b14e34e1601db03c6a6e +commit 46bcde7044e54cb3129c07d5e07cf66819c5971a Author: Elena Piscopia -Date: Mon Feb 17 08:49:28 2020 +0100 +Date: Tue Jun 23 21:03:01 2020 +0200 Add notes on datalad create @@ -80,9 +79,9 @@ index 0000000..3a7a1fe +The dataset is created empty + -commit 8d3b831c9850ec783870c26d516db78ac4a5d1d1 +commit 2821a5aa03bb68633db1382fe73251f1ab0b9c83 Author: Elena Piscopia -Date: Mon Feb 17 08:49:26 2020 +0100 +Date: Tue Jun 23 21:02:59 2020 +0200 add beginners guide on bash @@ -95,9 +94,9 @@ index 0000000..00ca6bd +../.git/annex/objects/WF/Gq/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf \ No newline at end of file -commit 393f24fbefdddfa4df6f7c0691a73268eb881023 +commit 769bbe9a976265b2648ee771033b7e55d331d08f Author: Elena Piscopia -Date: Mon Feb 17 08:49:17 2020 +0100 +Date: Tue Jun 23 21:02:53 2020 +0200 add reference book about git @@ -110,9 +109,9 @@ index 0000000..c5d2ab2 +../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf \ No newline at end of file -commit 44aa3e27dfd88183567f22a6a835e042171391f0 +commit da1610a8597da3cbcb16c0b4afefcb9df12de97a Author: Elena Piscopia -Date: Mon Feb 17 08:49:12 2020 +0100 +Date: Tue Jun 23 21:02:49 2020 +0200 add books on Python and Unix to read later @@ -126,16 +125,16 @@ 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..58c0629 +index 0000000..adaec61 --- /dev/null +++ b/books/byte-of-python.pdf @@ -0,0 +1 @@ -+../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf ++../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf \ No newline at end of file -commit c74e2b7951db566d5ccce7faeb2f86584d4d6321 +commit a50e5c92a7fbe805284a4d85c8986155bf5fe60d Author: Elena Piscopia -Date: Mon Feb 17 08:48:47 2020 +0100 +Date: Tue Jun 23 21:02:42 2020 +0200 Instruct annex to add text files to Git @@ -152,9 +151,9 @@ index c3aaefe..519a1f9 100644 +* annex.largefiles=((mimeencoding=binary)and(largerthan=0)) \ No newline at end of file -commit dbaf9fae9f69b9bfea1a6b7e2f374335f41702c1 +commit c76005349f18dd0fe3eacad01deb433bee4e9f27 Author: Elena Piscopia -Date: Mon Feb 17 08:48:46 2020 +0100 +Date: Tue Jun 23 21:02:41 2020 +0200 [DATALAD] new dataset @@ -171,12 +170,12 @@ index 0000000..b540820 \ No newline at end of file diff --git a/.datalad/config b/.datalad/config new file mode 100644 -index 0000000..eadd52e +index 0000000..febb477 --- /dev/null +++ b/.datalad/config @@ -0,0 +1,2 @@ +[datalad "dataset"] -+ id = ed80af32-5159-11ea-a727-6533dd7bb2c6 ++ id = 1cdc8632-b584-11ea-90a2-3119e6b9cf19 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..c3aaefe diff --git a/docs/basics/_examples/DL-101-108-106 b/docs/basics/_examples/DL-101-108-106 index c3a857060..7617b9805 100644 --- a/docs/basics/_examples/DL-101-108-106 +++ b/docs/basics/_examples/DL-101-108-106 @@ -1,7 +1,7 @@ $ git log -p -n 1 -commit 4bf7418ceacc3deb3c533c75b4c030b272cb644a +commit eee1356bb7e8f921174e404c6df6aadcc1f158f0 Author: Elena Piscopia -Date: Mon Feb 17 08:50:04 2020 +0100 +Date: Tue Jun 23 21:03:48 2020 +0200 [DATALAD RUNCMD] create a list of podcast titles @@ -9,7 +9,7 @@ Date: Mon Feb 17 08:50:04 2020 +0100 { "chain": [], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [], diff --git a/docs/basics/_examples/DL-101-108-108 b/docs/basics/_examples/DL-101-108-108 index ff04df923..e9f34e0cf 100644 --- a/docs/basics/_examples/DL-101-108-108 +++ b/docs/basics/_examples/DL-101-108-108 @@ -1,12 +1,12 @@ $ git log --oneline -4bf7418 [DATALAD RUNCMD] create a list of podcast titles -42387da Add short script to write a list of podcast speakers and titles -72f6a7d Add note on datalad clone -9bb3629 [DATALAD] Recorded changes -12ced25 add note on datalad save -63d50c8 Add notes on datalad create -8d3b831 add beginners guide on bash -393f24f add reference book about git -44aa3e2 add books on Python and Unix to read later -c74e2b7 Instruct annex to add text files to Git -dbaf9fa [DATALAD] new dataset +eee1356 [DATALAD RUNCMD] create a list of podcast titles +0e5af8c Add short script to write a list of podcast speakers and titles +33f5bc7 Add note on datalad clone +029e10c [DATALAD] Recorded changes +5a857d0 add note on datalad save +46bcde7 Add notes on datalad create +2821a5a add beginners guide on bash +769bbe9 add reference book about git +da1610a add books on Python and Unix to read later +a50e5c9 Instruct annex to add text files to Git +c760053 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-109-105 b/docs/basics/_examples/DL-101-109-105 index 1859cd72e..76c7f1703 100644 --- a/docs/basics/_examples/DL-101-109-105 +++ b/docs/basics/_examples/DL-101-109-105 @@ -1,13 +1,13 @@ $ git log -n 2 -commit 2dd044ac4013a64dd3f872ac9b203b5b868160ac +commit 1e8802fbb7f3021045376369436ccb10d585e36d Author: Elena Piscopia -Date: Mon Feb 17 08:50:06 2020 +0100 +Date: Tue Jun 23 21:03:49 2020 +0200 BF: list both directories content -commit 4bf7418ceacc3deb3c533c75b4c030b272cb644a +commit eee1356bb7e8f921174e404c6df6aadcc1f158f0 Author: Elena Piscopia -Date: Mon Feb 17 08:50:04 2020 +0100 +Date: Tue Jun 23 21:03:48 2020 +0200 [DATALAD RUNCMD] create a list of podcast titles @@ -15,7 +15,7 @@ Date: Mon Feb 17 08:50:04 2020 +0100 { "chain": [], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [], diff --git a/docs/basics/_examples/DL-101-109-106 b/docs/basics/_examples/DL-101-109-106 index edea96960..2a1be84a3 100644 --- a/docs/basics/_examples/DL-101-109-106 +++ b/docs/basics/_examples/DL-101-109-106 @@ -1,5 +1,5 @@ -$ datalad rerun 4bf7418ceacc3deb3c533c75b4c030b272cb644a +$ datalad rerun eee1356bb7e8f921174e404c6df6aadcc1f158f0 [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== add(ok): recordings/podcasts.tsv (file) diff --git a/docs/basics/_examples/DL-101-109-107 b/docs/basics/_examples/DL-101-109-107 index 02629958f..90fbfbcad 100644 --- a/docs/basics/_examples/DL-101-109-107 +++ b/docs/basics/_examples/DL-101-109-107 @@ -1,17 +1,17 @@ $ git log -n 1 -commit c317c6fb28633a1ca1940eee2c0c541bd62c6c7b +commit 745e010fb984d0b172a79988decd904db346ade7 Author: Elena Piscopia -Date: Mon Feb 17 08:50:07 2020 +0100 +Date: Tue Jun 23 21:03:51 2020 +0200 [DATALAD RUNCMD] create a list of podcast titles === Do not change lines below === { "chain": [ - "4bf7418ceacc3deb3c533c75b4c030b272cb644a" + "eee1356bb7e8f921174e404c6df6aadcc1f158f0" ], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [], diff --git a/docs/basics/_examples/DL-101-109-112 b/docs/basics/_examples/DL-101-109-112 index f8a0cf467..d59c9817a 100644 --- a/docs/basics/_examples/DL-101-109-112 +++ b/docs/basics/_examples/DL-101-109-112 @@ -1,17 +1,17 @@ $ git log -- recordings/podcasts.tsv -commit c317c6fb28633a1ca1940eee2c0c541bd62c6c7b +commit 745e010fb984d0b172a79988decd904db346ade7 Author: Elena Piscopia -Date: Mon Feb 17 08:50:07 2020 +0100 +Date: Tue Jun 23 21:03:51 2020 +0200 [DATALAD RUNCMD] create a list of podcast titles === Do not change lines below === { "chain": [ - "4bf7418ceacc3deb3c533c75b4c030b272cb644a" + "eee1356bb7e8f921174e404c6df6aadcc1f158f0" ], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [], @@ -20,9 +20,9 @@ Date: Mon Feb 17 08:50:07 2020 +0100 } ^^^ Do not change lines above ^^^ -commit 4bf7418ceacc3deb3c533c75b4c030b272cb644a +commit eee1356bb7e8f921174e404c6df6aadcc1f158f0 Author: Elena Piscopia -Date: Mon Feb 17 08:50:04 2020 +0100 +Date: Tue Jun 23 21:03:48 2020 +0200 [DATALAD RUNCMD] create a list of podcast titles @@ -30,7 +30,7 @@ Date: Mon Feb 17 08:50:04 2020 +0100 { "chain": [], "cmd": "bash code/list_titles.sh > recordings/podcasts.tsv", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [], diff --git a/docs/basics/_examples/DL-101-110-102 b/docs/basics/_examples/DL-101-110-102 index 8a718daff..725de4b9e 100644 --- a/docs/basics/_examples/DL-101-110-102 +++ b/docs/basics/_examples/DL-101-110-102 @@ -5,7 +5,4 @@ convert-im6.q16: unable to open image `recordings/longnow/.datalad/feed_metadata convert-im6.q16: no images defined `recordings/salt_logo_small.jpg' @ error/convert.c/ConvertImageCommand/3258. [INFO] == Command exit (modification check follows) ===== [INFO] The command had a non-zero exit code. If this is expected, you can save the changes with 'datalad save -d . -r -F .git/COMMIT_EDITMSG' -CommandError: command 'convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg' failed with exitcode 1 -Failed to run 'convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg' under '/home/me/dl-101/DataLad-101'. Exit code=1. -stdout= -stderr= +CommandError: ''convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg'' failed with exitcode 1 under /home/me/dl-101/DataLad-101 diff --git a/docs/basics/_examples/DL-101-110-104 b/docs/basics/_examples/DL-101-110-104 index 16d0fe082..19abbba2b 100644 --- a/docs/basics/_examples/DL-101-110-104 +++ b/docs/basics/_examples/DL-101-110-104 @@ -10,7 +10,4 @@ $ datalad run -m "Resize logo for slides" \ convert-im6.q16: unable to open image `recordings/salt_logo_small.jpg': Permission denied @ error/blob.c/OpenBlob/2874. [INFO] == Command exit (modification check follows) ===== [INFO] The command had a non-zero exit code. If this is expected, you can save the changes with 'datalad save -d . -r -F .git/COMMIT_EDITMSG' -CommandError: command 'convert -resize 450x450 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg' failed with exitcode 1 -Failed to run 'convert -resize 450x450 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg' under '/home/me/dl-101/DataLad-101'. Exit code=1. -stdout= -stderr= +CommandError: ''convert -resize 450x450 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg'' failed with exitcode 1 under /home/me/dl-101/DataLad-101 diff --git a/docs/basics/_examples/DL-101-112-109 b/docs/basics/_examples/DL-101-112-109 index 9703a8fb5..ceb4effc2 100644 --- a/docs/basics/_examples/DL-101-112-109 +++ b/docs/basics/_examples/DL-101-112-109 @@ -1,7 +1,7 @@ $ git log -p -n 2 -commit a1f2c3f97f0d7236a741ce074d8136eca23dd53f +commit ae1402e7236dfe942e117b8ffda60d1ce2de900f Author: Elena Piscopia -Date: Mon Feb 17 08:50:21 2020 +0100 +Date: Tue Jun 23 21:04:04 2020 +0200 add note on clean datasets @@ -21,9 +21,9 @@ index b94942f..dea6ce7 100644 +to the files listed with --output flags. + -commit baf4fc53bc1e2f68ab8d36ca56aa9b86f9b37482 +commit 3dfc1b5e90d35241b6399cd9d9100a0bba185817 Author: Elena Piscopia -Date: Mon Feb 17 08:50:21 2020 +0100 +Date: Tue Jun 23 21:04:04 2020 +0200 [DATALAD RUNCMD] Resize logo for slides @@ -31,7 +31,7 @@ Date: Mon Feb 17 08:50:21 2020 +0100 { "chain": [], "cmd": "convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg", - "dsid": "ed80af32-5159-11ea-a727-6533dd7bb2c6", + "dsid": "1cdc8632-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [ diff --git a/docs/basics/_examples/DL-101-114-101 b/docs/basics/_examples/DL-101-114-101 index 79e08aca2..55a0e3354 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 -dbaf9fa [DATALAD] new dataset -c74e2b7 Instruct annex to add text files to Git -44aa3e2 add books on Python and Unix to read later -393f24f add reference book about git -8d3b831 add beginners guide on bash -63d50c8 Add notes on datalad create -12ced25 add note on datalad save -9bb3629 [DATALAD] Recorded changes -72f6a7d Add note on datalad clone -42387da Add short script to write a list of podcast speakers and titles -4bf7418 [DATALAD RUNCMD] create a list of podcast titles -2dd044a BF: list both directories content -c317c6f [DATALAD RUNCMD] create a list of podcast titles -c3623d0 add note datalad and git diff -523a6b1 add note on basic datalad run and datalad rerun -e8e2e95 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -8ffbc4a resized picture by hand -3219d48 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -66b01ae add additional notes on run options -a84115d [DATALAD RUNCMD] Resize logo for slides -baf4fc5 [DATALAD RUNCMD] Resize logo for slides -a1f2c3f add note on clean datasets +c760053 [DATALAD] new dataset +a50e5c9 Instruct annex to add text files to Git +da1610a add books on Python and Unix to read later +769bbe9 add reference book about git +2821a5a add beginners guide on bash +46bcde7 Add notes on datalad create +5a857d0 add note on datalad save +029e10c [DATALAD] Recorded changes +33f5bc7 Add note on datalad clone +0e5af8c Add short script to write a list of podcast speakers and titles +eee1356 [DATALAD RUNCMD] create a list of podcast titles +1e8802f BF: list both directories content +745e010 [DATALAD RUNCMD] create a list of podcast titles +7051e33 add note datalad and git diff +4229a3a add note on basic datalad run and datalad rerun +02e2a56 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +a9451fa resized picture by hand +88e4c27 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +2af9325 add additional notes on run options +a730b96 [DATALAD RUNCMD] Resize logo for slides +3dfc1b5 [DATALAD RUNCMD] Resize logo for slides +ae1402e add note on clean datasets diff --git a/docs/basics/_examples/DL-101-115-101 b/docs/basics/_examples/DL-101-115-101 index d501eceef..6a5953b22 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--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf -├── byte-of-python.pdf -> ../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf +├── byte-of-python.pdf -> ../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf ├── progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf └── TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-115-103 b/docs/basics/_examples/DL-101-115-103 index afdcc099d..9ee18d952 100644 --- a/docs/basics/_examples/DL-101-115-103 +++ b/docs/basics/_examples/DL-101-115-103 @@ -1,8 +1,8 @@ $ ls -lah total 24K -drwxr-xr-x 2 adina adina 4.0K Feb 17 08:49 . -drwxr-xr-x 7 adina adina 4.0K Feb 17 08:50 .. +drwxr-xr-x 2 adina adina 4.0K Jun 23 21:02 . +drwxr-xr-x 7 adina adina 4.0K Jun 23 21:03 .. lrwxrwxrwx 1 adina adina 131 Jan 19 2009 bash_guide.pdf -> ../.git/annex/objects/WF/Gq/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf -lrwxrwxrwx 1 adina adina 131 Apr 19 2017 byte-of-python.pdf -> ../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf +lrwxrwxrwx 1 adina adina 131 Jun 16 01:38 byte-of-python.pdf -> ../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf lrwxrwxrwx 1 adina adina 133 Jun 29 2019 progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf lrwxrwxrwx 1 adina adina 131 Jan 28 2019 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-116-102 b/docs/basics/_examples/DL-101-116-102 index a83b84385..a876e5f5d 100644 --- a/docs/basics/_examples/DL-101-116-102 +++ b/docs/basics/_examples/DL-101-116-102 @@ -1,6 +1,6 @@ $ cd mock_user $ datalad clone ../DataLad-101 --description "DataLad-101 in mock_user" -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/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 +[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 6b5a1d09d..aedf4a024 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--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf -│   ├── byte-of-python.pdf -> ../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf +│   ├── byte-of-python.pdf -> ../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf │   ├── progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf │   └── TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf ├── code diff --git a/docs/basics/_examples/DL-101-116-105 b/docs/basics/_examples/DL-101-116-105 index 046209a2f..56d2f347b 100644 --- a/docs/basics/_examples/DL-101-116-105 +++ b/docs/basics/_examples/DL-101-116-105 @@ -1,4 +1,4 @@ $ git annex whereis books/TLCL.pdf whereis books/TLCL.pdf (1 copy) - 283818cf-2b07-4a0e-ab28-2d5fcdb947ae -- me@muninn:~/dl-101/DataLad-101 [origin] + b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 -- me@muninn:~/dl-101/DataLad-101 [origin] ok diff --git a/docs/basics/_examples/DL-101-116-106 b/docs/basics/_examples/DL-101-116-106 index 3ceb76275..3a108194e 100644 --- a/docs/basics/_examples/DL-101-116-106 +++ b/docs/basics/_examples/DL-101-116-106 @@ -1,7 +1,7 @@ $ git annex whereis books/bash_guide.pdf whereis books/bash_guide.pdf (2 copies) 00000000-0000-0000-0000-000000000001 -- web - 283818cf-2b07-4a0e-ab28-2d5fcdb947ae -- me@muninn:~/dl-101/DataLad-101 [origin] + b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 -- me@muninn:~/dl-101/DataLad-101 [origin] web: http://www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf ok diff --git a/docs/basics/_examples/DL-101-116-107 b/docs/basics/_examples/DL-101-116-107 index b39fabdd4..9dd29682d 100644 --- a/docs/basics/_examples/DL-101-116-107 +++ b/docs/basics/_examples/DL-101-116-107 @@ -1,8 +1,5 @@ $ datalad get -n recordings/longnow -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/home/me/dl-101/mock_user/DataLad-101/recordings/longnow) [INFO] Attempting to clone from /home/me/dl-101/DataLad-101/recordings/longnow to /home/me/dl-101/mock_user/DataLad-101/recordings/longnow -[INFO] Completed clone attempts for -[INFO] Fetching updates for -[INFO] Failed to enable annex remote origin-2, could be a pure git or not accessible -[WARNING] Failed to determine if origin-2 carries annex. Remote was marked by annex as annex-ignore. Edit .git/config to reset if you think that was done by mistake due to absent connection etc +[INFO] Completed clone attempts for Dataset(/home/me/dl-101/mock_user/DataLad-101/recordings/longnow) 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 098382257..bf07c1b2a 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--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf -│   ├── byte-of-python.pdf -> ../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf +│   ├── byte-of-python.pdf -> ../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf │   ├── progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf │   └── TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf ├── code diff --git a/docs/basics/_examples/DL-101-117-101 b/docs/basics/_examples/DL-101-117-101 index 5e17b1789..d40c7432e 100644 --- a/docs/basics/_examples/DL-101-117-101 +++ b/docs/basics/_examples/DL-101-117-101 @@ -6,7 +6,7 @@ $ cd recordings/longnow $ git annex whereis Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 whereis Long_Now__Seminars_About_Long_term_Thinking/2003_11_15__Brian_Eno__The_Long_Now.mp3 (3 copies) 00000000-0000-0000-0000-000000000001 -- web - 4804d934-ff46-4834-939b-fc60ef612113 -- me@muninn:~/dl-101/DataLad-101/recordings/longnow [origin] + ac337669-ec84-4afb-a75c-8c43245bea06 -- me@muninn:~/dl-101/DataLad-101/recordings/longnow [origin] da3bf937-5bd2-43ea-a07b-bcbe71f3b875 -- mih@medusa:/tmp/seminars-on-longterm-thinking web: http://podcast.longnow.org/salt/redirect/salt-020031114-eno-podcast.mp3 diff --git a/docs/basics/_examples/DL-101-118-102 b/docs/basics/_examples/DL-101-118-102 index 94dee3224..0663e0b73 100644 --- a/docs/basics/_examples/DL-101-118-102 +++ b/docs/basics/_examples/DL-101-118-102 @@ -1,24 +1,24 @@ # lets view the history $ git log --oneline -a1f2c3f add note on clean datasets -baf4fc5 [DATALAD RUNCMD] Resize logo for slides -a84115d [DATALAD RUNCMD] Resize logo for slides -66b01ae add additional notes on run options -3219d48 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -8ffbc4a resized picture by hand -e8e2e95 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -523a6b1 add note on basic datalad run and datalad rerun -c3623d0 add note datalad and git diff -c317c6f [DATALAD RUNCMD] create a list of podcast titles -2dd044a BF: list both directories content -4bf7418 [DATALAD RUNCMD] create a list of podcast titles -42387da Add short script to write a list of podcast speakers and titles -72f6a7d Add note on datalad clone -9bb3629 [DATALAD] Recorded changes -12ced25 add note on datalad save -63d50c8 Add notes on datalad create -8d3b831 add beginners guide on bash -393f24f add reference book about git -44aa3e2 add books on Python and Unix to read later -c74e2b7 Instruct annex to add text files to Git -dbaf9fa [DATALAD] new dataset +ae1402e add note on clean datasets +3dfc1b5 [DATALAD RUNCMD] Resize logo for slides +a730b96 [DATALAD RUNCMD] Resize logo for slides +2af9325 add additional notes on run options +88e4c27 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +a9451fa resized picture by hand +02e2a56 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +4229a3a add note on basic datalad run and datalad rerun +7051e33 add note datalad and git diff +745e010 [DATALAD RUNCMD] create a list of podcast titles +1e8802f BF: list both directories content +eee1356 [DATALAD RUNCMD] create a list of podcast titles +0e5af8c Add short script to write a list of podcast speakers and titles +33f5bc7 Add note on datalad clone +029e10c [DATALAD] Recorded changes +5a857d0 add note on datalad save +46bcde7 Add notes on datalad create +2821a5a add beginners guide on bash +769bbe9 add reference book about git +da1610a add books on Python and Unix to read later +a50e5c9 Instruct annex to add text files to Git +c760053 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-118-103 b/docs/basics/_examples/DL-101-118-103 index 99b82259a..6d2b139d5 100644 --- a/docs/basics/_examples/DL-101-118-103 +++ b/docs/basics/_examples/DL-101-118-103 @@ -1,5 +1,5 @@ -$ datalad rerun baf4fc53bc1e2f68ab8d36ca56aa9b86f9b37482 +$ datalad rerun 3dfc1b5e90d35241b6399cd9d9100a0bba185817 [INFO] Making sure inputs are available (this may take some time) [WARNING] no content present; cannot unlock [unlock(/home/me/dl-101/mock_user/DataLad-101/recordings/salt_logo_small.jpg)] [INFO] == Command start (output follows) ===== diff --git a/docs/basics/_examples/DL-101-119-102 b/docs/basics/_examples/DL-101-119-102 index 5822733e7..9e53c72bc 100644 --- a/docs/basics/_examples/DL-101-119-102 +++ b/docs/basics/_examples/DL-101-119-102 @@ -1,4 +1,10 @@ $ datalad update --merge -[INFO] Fetching updates for -[INFO] Applying updates to +[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/master] update(ok): . (dataset) +action summary: + merge (ok: 1) + update (ok: 1) diff --git a/docs/basics/_examples/DL-101-121-103 b/docs/basics/_examples/DL-101-121-103 index 191e44453..c7ba657fe 100644 --- a/docs/basics/_examples/DL-101-121-103 +++ b/docs/basics/_examples/DL-101-121-103 @@ -1,7 +1,7 @@ $ git log -n 1 -p -commit 1639278d92c19c44350c63d5b1d2524299fee123 +commit 0292f7c5b3c5a56ff4224d2670c2d1d4ace4af78 Author: Elena Piscopia -Date: Mon Feb 17 08:50:41 2020 +0100 +Date: Tue Jun 23 21:04:21 2020 +0200 Include nesting demo from datalad website diff --git a/docs/basics/_examples/DL-101-121-106 b/docs/basics/_examples/DL-101-121-106 index 58549696d..b507cd971 100644 --- a/docs/basics/_examples/DL-101-121-106 +++ b/docs/basics/_examples/DL-101-121-106 @@ -1,3 +1,6 @@ $ datalad update -s roommate -[INFO] Fetching updates for +[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 e4fa6dcc4..efb0710c7 100644 --- a/docs/basics/_examples/DL-101-121-110 +++ b/docs/basics/_examples/DL-101-121-110 @@ -1,4 +1,7 @@ $ datalad update --merge -s roommate -[INFO] Fetching updates for -[INFO] Applying updates to +[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) +merge(ok): . (dataset) [Merged roommate/master] update(ok): . (dataset) +action summary: + merge (ok: 1) + update (ok: 1) diff --git a/docs/basics/_examples/DL-101-121-112 b/docs/basics/_examples/DL-101-121-112 index ef0126f40..80f69dd5a 100644 --- a/docs/basics/_examples/DL-101-121-112 +++ b/docs/basics/_examples/DL-101-121-112 @@ -1,28 +1,28 @@ $ git log --oneline -7462696 Merge remote-tracking branch 'refs/remotes/roommate/master' -1639278 Include nesting demo from datalad website -0ef8c62 add note about datalad update -e5df2d8 add note on git annex whereis -80c31dc add note about cloning from paths and recursive datalad get -a1f2c3f add note on clean datasets -baf4fc5 [DATALAD RUNCMD] Resize logo for slides -a84115d [DATALAD RUNCMD] Resize logo for slides -66b01ae add additional notes on run options -3219d48 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... -8ffbc4a resized picture by hand -e8e2e95 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... -523a6b1 add note on basic datalad run and datalad rerun -c3623d0 add note datalad and git diff -c317c6f [DATALAD RUNCMD] create a list of podcast titles -2dd044a BF: list both directories content -4bf7418 [DATALAD RUNCMD] create a list of podcast titles -42387da Add short script to write a list of podcast speakers and titles -72f6a7d Add note on datalad clone -9bb3629 [DATALAD] Recorded changes -12ced25 add note on datalad save -63d50c8 Add notes on datalad create -8d3b831 add beginners guide on bash -393f24f add reference book about git -44aa3e2 add books on Python and Unix to read later -c74e2b7 Instruct annex to add text files to Git -dbaf9fa [DATALAD] new dataset +388b5fd Merge remote-tracking branch 'roommate/master' +0292f7c Include nesting demo from datalad website +4fe212d add note about datalad update +78d2f4f add note on git annex whereis +e242f12 add note about cloning from paths and recursive datalad get +ae1402e add note on clean datasets +3dfc1b5 [DATALAD RUNCMD] Resize logo for slides +a730b96 [DATALAD RUNCMD] Resize logo for slides +2af9325 add additional notes on run options +88e4c27 [DATALAD RUNCMD] convert -resize 450x450 recordings/longn... +a9451fa resized picture by hand +02e2a56 [DATALAD RUNCMD] convert -resize 400x400 recordings/longn... +4229a3a add note on basic datalad run and datalad rerun +7051e33 add note datalad and git diff +745e010 [DATALAD RUNCMD] create a list of podcast titles +1e8802f BF: list both directories content +eee1356 [DATALAD RUNCMD] create a list of podcast titles +0e5af8c Add short script to write a list of podcast speakers and titles +33f5bc7 Add note on datalad clone +029e10c [DATALAD] Recorded changes +5a857d0 add note on datalad save +46bcde7 Add notes on datalad create +2821a5a add beginners guide on bash +769bbe9 add reference book about git +da1610a add books on Python and Unix to read later +a50e5c9 Instruct annex to add text files to Git +c760053 [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-122-101 b/docs/basics/_examples/DL-101-122-101 index 6f7616996..59b2a5838 100644 --- a/docs/basics/_examples/DL-101-122-101 +++ b/docs/basics/_examples/DL-101-122-101 @@ -5,7 +5,7 @@ $ cat .git/config bare = false logallrefupdates = true [annex] - uuid = 283818cf-2b07-4a0e-ab28-2d5fcdb947ae + uuid = b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 version = 5 backends = MD5E [submodule "recordings/longnow"] @@ -14,5 +14,5 @@ $ cat .git/config [remote "roommate"] url = ../mock_user/DataLad-101 fetch = +refs/heads/*:refs/remotes/roommate/* - annex-uuid = fa947123-aeb1-4096-9399-a47a5bb50446 + annex-uuid = e86f131b-c6f3-4bf9-91d1-f47f0117fee7 annex-ignore = false diff --git a/docs/basics/_examples/DL-101-122-103 b/docs/basics/_examples/DL-101-122-103 index 73cda78eb..b842fbf2e 100644 --- a/docs/basics/_examples/DL-101-122-103 +++ b/docs/basics/_examples/DL-101-122-103 @@ -6,7 +6,7 @@ $ cat .git/config logallrefupdates = true editor = nano [annex] - uuid = 283818cf-2b07-4a0e-ab28-2d5fcdb947ae + uuid = b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 version = 5 backends = MD5E [submodule "recordings/longnow"] @@ -15,5 +15,5 @@ $ cat .git/config [remote "roommate"] url = ../mock_user/DataLad-101 fetch = +refs/heads/*:refs/remotes/roommate/* - annex-uuid = fa947123-aeb1-4096-9399-a47a5bb50446 + annex-uuid = e86f131b-c6f3-4bf9-91d1-f47f0117fee7 annex-ignore = false diff --git a/docs/basics/_examples/DL-101-123-101 b/docs/basics/_examples/DL-101-123-101 index f5b7af5bf..383241bcc 100644 --- a/docs/basics/_examples/DL-101-123-101 +++ b/docs/basics/_examples/DL-101-123-101 @@ -2,4 +2,4 @@ $ cat .gitattributes * annex.backend=MD5E **/.git* annex.largefiles=nothing -* annex.largefiles=(not(mimetype=text/*)and(largerthan=0)) \ No newline at end of file +* annex.largefiles=((mimeencoding=binary)and(largerthan=0)) \ No newline at end of file diff --git a/docs/basics/_examples/DL-101-123-104 b/docs/basics/_examples/DL-101-123-104 index 5be143bc2..11d261755 100644 --- a/docs/basics/_examples/DL-101-123-104 +++ b/docs/basics/_examples/DL-101-123-104 @@ -2,5 +2,4 @@ $ cat .gitmodules [submodule "recordings/longnow"] path = recordings/longnow url = https://github.com/datalad-datasets/longnow-podcasts.git - branch = master datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e diff --git a/docs/basics/_examples/DL-101-123-105 b/docs/basics/_examples/DL-101-123-105 index 52e04ce2f..2b2d216d8 100644 --- a/docs/basics/_examples/DL-101-123-105 +++ b/docs/basics/_examples/DL-101-123-105 @@ -1,3 +1,3 @@ $ cat .datalad/config [datalad "dataset"] - id = ed80af32-5159-11ea-a727-6533dd7bb2c6 + id = 1cdc8632-b584-11ea-90a2-3119e6b9cf19 diff --git a/docs/basics/_examples/DL-101-123-108 b/docs/basics/_examples/DL-101-123-108 index 60d3edcef..d49f15083 100644 --- a/docs/basics/_examples/DL-101-123-108 +++ b/docs/basics/_examples/DL-101-123-108 @@ -1,12 +1,11 @@ $ git diff diff --git a/.gitmodules b/.gitmodules -index 37b3468..c6b1b68 100644 +index 1b59b8c..599864e 100644 --- a/.gitmodules +++ b/.gitmodules -@@ -1,5 +1,5 @@ +@@ -1,4 +1,4 @@ [submodule "recordings/longnow"] path = recordings/longnow - url = https://github.com/datalad-datasets/longnow-podcasts.git + url = git@github.com:datalad-datasets/longnow-podcasts.git - branch = master datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e diff --git a/docs/basics/_examples/DL-101-124-101 b/docs/basics/_examples/DL-101-124-101 index 5ce02e81b..c34fe8adf 100644 --- a/docs/basics/_examples/DL-101-124-101 +++ b/docs/basics/_examples/DL-101-124-101 @@ -1,7 +1,7 @@ $ datalad run-procedure --discover cfg_hirni (/home/adina/env/handbook/lib/python3.7/site-packages/datalad_hirni/resources/procedures/cfg_hirni.py) [python_script] -cfg_bids (/home/adina/repos/datalad-neuroimaging/datalad_neuroimaging/resources/procedures/cfg_bids.py) [python_script] ria_post_install (/home/adina/repos/git-annex-ria-remote/ria_remote/resources/procedures/ria_post_install.py) [python_script] +cfg_bids (/home/adina/repos/datalad-neuroimaging/datalad_neuroimaging/resources/procedures/cfg_bids.py) [python_script] cfg_metadatatypes (/home/adina/repos/datalad/datalad/resources/procedures/cfg_metadatatypes.py) [python_script] cfg_text2git (/home/adina/repos/datalad/datalad/resources/procedures/cfg_text2git.py) [python_script] cfg_yoda (/home/adina/repos/datalad/datalad/resources/procedures/cfg_yoda.py) [python_script] diff --git a/docs/basics/_examples/DL-101-130-105 b/docs/basics/_examples/DL-101-130-105 index 4d411ac70..f0f6f69bf 100644 --- a/docs/basics/_examples/DL-101-130-105 +++ b/docs/basics/_examples/DL-101-130-105 @@ -1,13 +1,13 @@ $ cd midterm_project # we are in midterm_project, thus -d . points to the root of it. $ datalad clone -d . https://github.com/datalad-handbook/iris_data.git input/ -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/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] Completed clone attempts for -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[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 install(ok): input (dataset) add(ok): input (file) add(ok): .gitmodules (file) diff --git a/docs/basics/_examples/DL-101-130-110 b/docs/basics/_examples/DL-101-130-110 index 8ff288bfb..64ec8e12b 100644 --- a/docs/basics/_examples/DL-101-130-110 +++ b/docs/basics/_examples/DL-101-130-110 @@ -1,7 +1,7 @@ $ git show ready4analysis -commit 8147ae7c0a1b67b8dccbe61afdb39e41c3034e8a +commit 95685fcc1bb0a356a3fe3e39d243df0a739f0e00 Author: Elena Piscopia -Date: Mon Feb 17 08:51:01 2020 +0100 +Date: Tue Jun 23 21:04:38 2020 +0200 add script for kNN classification and plotting diff --git a/docs/basics/_examples/DL-101-130-112 b/docs/basics/_examples/DL-101-130-112 index 9575f1dd3..3969c466e 100644 --- a/docs/basics/_examples/DL-101-130-112 +++ b/docs/basics/_examples/DL-101-130-112 @@ -1,6 +1,6 @@ $ git log --oneline -2ce757f [DATALAD RUNCMD] analyze iris data with classification analysis -8147ae7 add script for kNN classification and plotting -c70fe0a [DATALAD] Recorded changes -539b789 Apply YODA dataset setup -4db5c90 [DATALAD] new dataset +6e5d6d8 [DATALAD RUNCMD] analyze iris data with classification analysis +95685fc add script for kNN classification and plotting +6ec63b9 [DATALAD] Recorded changes +6987cf0 Apply YODA dataset setup +524e15b [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-130-117 b/docs/basics/_examples/DL-101-130-117 deleted file mode 100644 index d6e536caf..000000000 --- a/docs/basics/_examples/DL-101-130-117 +++ /dev/null @@ -1,3 +0,0 @@ -$ datalad siblings -.: here(+) [git] -.: github(-) [https://github.com/adswa/midtermproject.git (git)] diff --git a/docs/basics/_examples/DL-101-130-118 b/docs/basics/_examples/DL-101-130-118 index 5016b01e4..1afa5c20e 100644 --- a/docs/basics/_examples/DL-101-130-118 +++ b/docs/basics/_examples/DL-101-130-118 @@ -1,13 +1,21 @@ $ datalad push --to github +[INFO] Determine push target +[INFO] Push refspecs [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects [INFO] Start writing objects +[INFO] Transfer data +[INFO] Start annex operation +[INFO] pairwise_relationships.png +[INFO] Finished annex copy +[INFO] Update availability information [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects [INFO] Start writing objects +[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) publish(ok): . (dataset) [refs/heads/master->github:refs/heads/master [new branch]] copy(ok): pairwise_relationships.png (file) [to github...] copy(ok): prediction_report.csv (file) [to github...] -publish(ok): . (dataset) [refs/heads/git-annex->github:refs/heads/git-annex c1907f0..e3df704] +publish(ok): . (dataset) [refs/heads/git-annex->github:refs/heads/git-annex bd34124..44c5ade] diff --git a/docs/basics/_examples/DL-101-130-119 b/docs/basics/_examples/DL-101-130-119 index b1b3d3201..c83ca188c 100644 --- a/docs/basics/_examples/DL-101-130-119 +++ b/docs/basics/_examples/DL-101-130-119 @@ -1,12 +1,12 @@ $ cd ../../ $ datalad clone "https://github.com/adswa/midtermproject.git" -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/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 -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Completed clone attempts for Dataset(/home/me/dl-101/midtermproject) +[INFO] Remote origin not usable by git-annex; setting annex-ignore 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 aa50e243b..af999544c 100644 --- a/docs/basics/_examples/DL-101-130-120 +++ b/docs/basics/_examples/DL-101-130-120 @@ -1,14 +1,14 @@ $ cd midtermproject $ datalad get input/iris.csv -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/home/me/dl-101/midtermproject/input) [INFO] Attempting to clone from https://github.com/adswa/midtermproject.git/input to /home/me/dl-101/midtermproject/input [INFO] Attempting to clone from https://github.com/adswa/midtermproject.git/input/.git to /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] Completed clone attempts for -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Completed clone attempts for Dataset(/home/me/dl-101/midtermproject/input) +[INFO] Remote origin not usable by git-annex; setting annex-ignore 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: diff --git a/docs/basics/_examples/DL-101-132-101 b/docs/basics/_examples/DL-101-132-101 index fe9291552..173817275 100644 --- a/docs/basics/_examples/DL-101-132-101 +++ b/docs/basics/_examples/DL-101-132-101 @@ -1,7 +1,7 @@ $ git log --oneline -c5edf51 Provide project description -2ce757f [DATALAD RUNCMD] analyze iris data with classification analysis -8147ae7 add script for kNN classification and plotting -c70fe0a [DATALAD] Recorded changes -539b789 Apply YODA dataset setup -4db5c90 [DATALAD] new dataset +b68e502 Provide project description +6e5d6d8 [DATALAD RUNCMD] analyze iris data with classification analysis +95685fc add script for kNN classification and plotting +6ec63b9 [DATALAD] Recorded changes +6987cf0 Apply YODA dataset setup +524e15b [DATALAD] new dataset diff --git a/docs/basics/_examples/DL-101-132-112 b/docs/basics/_examples/DL-101-132-112 index cc9e12b52..1400782db 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 c6845ba51a1ce2c3f964ac6cd0f8082dc29d97f8 +commit ba534fa74afb0b3721489cd71b9e00ef159376f7 Author: Elena Piscopia -Date: Mon Feb 17 08:51:28 2020 +0100 +Date: Tue Jun 23 21:05:05 2020 +0200 finished my midterm project diff --git a/midterm_project b/midterm_project -index 539b789..c5edf51 160000 +index 6987cf0..b68e502 160000 --- a/midterm_project +++ b/midterm_project @@ -1 +1 @@ --Subproject commit 539b789d64035b1b5e4dd02da6029f0608f48626 -+Subproject commit c5edf51013817a61f0da5ed39c0130fde2b850bc +-Subproject commit 6987cf0f32d30045fc3038b8b4e20a1ecd17dd52 ++Subproject commit b68e5029eadc5dd975393852b75aac4cc4337789 diff --git a/docs/basics/_examples/DL-101-133-102 b/docs/basics/_examples/DL-101-133-102 index be7fc41d0..1a89aa42c 100644 --- a/docs/basics/_examples/DL-101-133-102 +++ b/docs/basics/_examples/DL-101-133-102 @@ -1,6 +1,6 @@ $ cat .datalad/config [datalad "dataset"] - id = 3a233abc-515a-11ea-a727-6533dd7bb2c6 + id = 5f313adc-b584-11ea-90a2-3119e6b9cf19 [datalad "containers.midterm-software"] updateurl = shub://adswa/resources:1 image = .datalad/environments/midterm-software/image diff --git a/docs/basics/_examples/DL-101-133-103 b/docs/basics/_examples/DL-101-133-103 index 521a080b0..860ad23ec 100644 --- a/docs/basics/_examples/DL-101-133-103 +++ b/docs/basics/_examples/DL-101-133-103 @@ -1,17 +1,17 @@ $ git log -n 1 -p -commit 48c34a2f551b67edf4f65573ac6f85ca8776b2c2 +commit 60034f1f1abf74322fbd6b793aa9489645ec8c74 Author: Elena Piscopia -Date: Mon Feb 17 08:52:16 2020 +0100 +Date: Tue Jun 23 21:05:50 2020 +0200 [DATALAD] Configure containerized environment 'midterm-software' diff --git a/.datalad/config b/.datalad/config -index 18fe28f..dc29cf7 100644 +index f0e73eb..ba9de82 100644 --- a/.datalad/config +++ b/.datalad/config @@ -1,2 +1,6 @@ [datalad "dataset"] - id = 3a233abc-515a-11ea-a727-6533dd7bb2c6 + id = 5f313adc-b584-11ea-90a2-3119e6b9cf19 +[datalad "containers.midterm-software"] + updateurl = shub://adswa/resources:1 + image = .datalad/environments/midterm-software/image diff --git a/docs/basics/_examples/DL-101-133-111 b/docs/basics/_examples/DL-101-133-111 index f36f9eb5e..33275ef6e 100644 --- a/docs/basics/_examples/DL-101-133-111 +++ b/docs/basics/_examples/DL-101-133-111 @@ -1,7 +1,7 @@ $ git log -p -n 1 -commit c7a17ea4eab9d1f338c1031a6e160f6ce3e275e9 +commit 9aaf66ad6ab1e38241e70e7de64e6017084f770a Author: Elena Piscopia -Date: Mon Feb 17 08:52:22 2020 +0100 +Date: Tue Jun 23 21:05:56 2020 +0200 [DATALAD RUNCMD] rerun analysis in container @@ -9,7 +9,7 @@ Date: Mon Feb 17 08:52:22 2020 +0100 { "chain": [], "cmd": "singularity exec .datalad/environments/midterm-software/image python3 code/script.py", - "dsid": "3a233abc-515a-11ea-a727-6533dd7bb2c6", + "dsid": "5f313adc-b584-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [ ".datalad/environments/midterm-software/image" diff --git a/docs/basics/_examples/DL-101-135-101 b/docs/basics/_examples/DL-101-135-101 index a5c4168f9..e328bddbd 100644 --- a/docs/basics/_examples/DL-101-135-101 +++ b/docs/basics/_examples/DL-101-135-101 @@ -1,2 +1,2 @@ $ datalad --version -datalad 0.12.2.dev166 +datalad 0.13.0 diff --git a/docs/basics/_examples/DL-101-135-102 b/docs/basics/_examples/DL-101-135-102 index 1eabab052..2864a2a86 100644 --- a/docs/basics/_examples/DL-101-135-102 +++ b/docs/basics/_examples/DL-101-135-102 @@ -2,22 +2,23 @@ $ datalad wtf # WTF ## configuration ## datalad - - full_version: 0.12.2.dev166-g68f26 - - version: 0.12.2.dev166 + - full_version: 0.13.0 + - version: 0.13.0 ## dataset - - id: ed80af32-5159-11ea-a727-6533dd7bb2c6 + - id: 1cdc8632-b584-11ea-90a2-3119e6b9cf19 - metadata: - path: /home/me/dl-101/DataLad-101 - repo: AnnexRepo ## dependencies + - annexremote: 1.3.1 - appdirs: 1.4.3 - boto: 2.49.0 - cmd:7z: 16.02 - cmd:annex: 7.20190819+git2-g908476a9b-1~ndall+1 - cmd:bundled-git: 2.20.1 - cmd:git: 2.20.1 - - cmd:system-git: 2.25.0 - - cmd:system-ssh: 8.1p1 + - cmd:system-git: 2.26.2 + - cmd:system-ssh: 8.2p1 - exifread: 2.1.2 - git: 3.0.5 - gitdb: 2.0.5 @@ -27,7 +28,7 @@ $ datalad wtf - keyrings.alt: 3.1.1 - msgpack: 0.6.1 - mutagen: 1.43.0 - - requests: 2.22.0 + - requests: 2.23.0 - scrapy: 1.7.4 - tqdm: 4.32.2 - wrapt: 1.11.2 @@ -35,7 +36,6 @@ $ datalad wtf - GIT_AUTHOR_EMAIL: elena@example.net - GIT_AUTHOR_NAME: Elena Piscopia - GIT_EDITOR: vim - - GIT_PYTHON_GIT_EXECUTABLE: /usr/lib/git-annex.linux/git - LANG: en_US.UTF-8 - LANGUAGE: en_US:en - LC_CTYPE: en_US.UTF-8 @@ -74,26 +74,7 @@ $ datalad wtf - containers_run - load_error: None - module: datalad_container - - version: 0.5.0 - - crawler: - - description: Crawl web resources - - entrypoints: - - datalad_crawler.crawl.Crawl: - - class: Crawl - - load_error: None - - module: datalad_crawler.crawl - - names: - - crawl - - datalad_crawler.crawl_init.CrawlInit: - - class: CrawlInit - - load_error: None - - module: datalad_crawler.crawl_init - - names: - - crawl-init - - crawl_init - - load_error: None - - module: datalad_crawler - - version: 0.4.4 + - version: 1.0.0 - hirni: - description: HIRNI workflows - entrypoints: @@ -127,7 +108,7 @@ $ datalad wtf - hirni_spec4anything - load_error: None - module: datalad_hirni - - version: 0.0.4 + - version: 0.0.6 - metalad: - description: DataLad semantic metadata command suite - entrypoints: @@ -199,7 +180,7 @@ $ datalad wtf - webapp - load_error: None - module: datalad_webapp - - version: 0.2 + - version: 0.3 ## git-annex - build flags: - Assistant @@ -390,6 +371,6 @@ $ datalad wtf - locale.prefered: UTF-8 - max_path_length: 283 - name: Linux - - release: 5.4.0-3-amd64 + - release: 5.6.0-1-amd64 - type: posix - - version: #1 SMP Debian 5.4.13-1 (2020-01-19) + - version: #1 SMP Debian 5.6.7-1 (2020-04-29) diff --git a/docs/basics/_examples/DL-101-135-103 b/docs/basics/_examples/DL-101-135-103 index 08fe73fab..6543846da 100644 --- a/docs/basics/_examples/DL-101-135-103 +++ b/docs/basics/_examples/DL-101-135-103 @@ -1,6 +1,7 @@ $ datalad get --help Usage: datalad get [-h] [-s LABEL] [-d PATH] [-r] [-R LEVELS] [-n] - [-D DESCRIPTION] [--reckless [{auto|ephemeral}]] [-J NJOBS] + [-D DESCRIPTION] [--reckless [auto|ephemeral|shared-...]] + [-J NJOBS] [PATH [PATH ...]] Get any dataset content (files/directories/subdatasets). @@ -35,7 +36,7 @@ Get contents of a directory:: Get all contents of the current dataset and its subdatasets:: - % datalad get . --recursive + % datalad get . -r Get (clone) a registered subdataset, but don't retrieve data:: @@ -83,26 +84,34 @@ Get (clone) a registered subdataset, but don't retrieve data:: Note that when a dataset is published, this information becomes available on the remote side. Constraints: value must be a string - --reckless [{auto|ephemeral}] - Set up the dataset to be able to obtain content in the - cheapest/fastest possible way, even if this poses a - potential risk the data integrity ('auto': hardlink - files from a local clone of the dataset, 'ephemeral': - symlink annex to origin's annex and discard local - availability info via git-annex-dead 'here'. Please - note, that with a symlinked annex you share the annex - with origin w/o git-annex knowing this. In case of a + --reckless [auto|ephemeral|shared-...] + set up the dataset in a potentially unsafe way for + performance, or access reasons -- use with care, any + dataset is marked as 'untrusted'. The reckless mode is + stored in a dataset's local configuration under + 'datalad.clone.reckless', and will be inherited to any + of its subdatasets. Supported modes are: ['auto']: + hard-link files between local clones. In-place + modification in any clone will alter original annex + content. ['ephemeral']: symlink annex to origin's + annex and discard local availability info via git- + annex-dead 'here'. Shares an annex between origin and + clone w/o git-annex being aware of it. In case of a change in origin you need to update the clone before - you're able to save new content on your end.). Use - with care, and limit to "read-only" use cases. With - this flag the installed dataset will be marked as - untrusted. The reckless mode is stored in a dataset's - local configuration under 'datalad.clone.reckless', - and will be inherited to any of its subdatasets. - Constraints: value must be one of (None, True, False, - 'auto', 'ephemeral') + you're able to save new content on your end. + Alternative to 'auto' when hardlinks are not an + option, or number of consumed inodes needs to be + minimized. ['shared-']: set up repository and + annex permission to enable multi-user access. This + disables the standard write protection of annex'ed + files. can be any value support by 'git init + --shared=', such as 'group', or 'all'. Constraints: + value must be one of (None, True, False, 'auto', + 'ephemeral'), or value must start with 'shared-' -J NJOBS, --jobs NJOBS - how many parallel jobs (where possible) to use. + how many parallel jobs (where possible) to use. "auto" + corresponds to the number defined by + 'datalad.runtime.max-annex-jobs' configuration item. Constraints: value must be convertible to type 'int', or value must be one of ('auto',) [Default: 'auto'] diff --git a/docs/basics/_examples/DL-101-136-101 b/docs/basics/_examples/DL-101-136-101 index 6b643885e..559c277d9 100644 --- a/docs/basics/_examples/DL-101-136-101 +++ b/docs/basics/_examples/DL-101-136-101 @@ -2,9 +2,9 @@ $ cd books/ $ mv TLCL.pdf The_Linux_Command_Line.pdf $ ls -lah total 24K -drwxr-xr-x 2 adina adina 4.0K Feb 17 08:52 . -drwxr-xr-x 8 adina adina 4.0K Feb 17 08:52 .. +drwxr-xr-x 2 adina adina 4.0K Jun 23 21:06 . +drwxr-xr-x 8 adina adina 4.0K Jun 23 21:05 .. lrwxrwxrwx 1 adina adina 131 Jan 19 2009 bash_guide.pdf -> ../.git/annex/objects/WF/Gq/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf/MD5E-s1198170--0ab2c121bcf68d7278af266f6a399c5f.pdf -lrwxrwxrwx 1 adina adina 131 Apr 19 2017 byte-of-python.pdf -> ../.git/annex/objects/F1/Wz/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf/MD5E-s4242644--f4e1c8ebfb5c89a69ff6d268eb2e63e3.pdf +lrwxrwxrwx 1 adina adina 131 Jun 16 01:38 byte-of-python.pdf -> ../.git/annex/objects/z1/Q8/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf/MD5E-s4208954--ab3a8c2f6b76b18b43c5949e0661e266.pdf lrwxrwxrwx 1 adina adina 133 Jun 29 2019 progit.pdf -> ../.git/annex/objects/G6/Gj/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf/MD5E-s12465653--05cd7ed561d108c9bcf96022bc78a92c.pdf lrwxrwxrwx 1 adina adina 131 Jan 28 2019 The_Linux_Command_Line.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-136-104 b/docs/basics/_examples/DL-101-136-104 index ff8c5c377..f060af454 100644 --- a/docs/basics/_examples/DL-101-136-104 +++ b/docs/basics/_examples/DL-101-136-104 @@ -1,7 +1,7 @@ $ git log -n 1 -p -commit 77c38d762508f5ee0bd5eb0e101dac7294972d31 +commit 47053ae54e1c28f8056ac3c593a64b1f4ff529e9 Author: Elena Piscopia -Date: Mon Feb 17 08:52:27 2020 +0100 +Date: Tue Jun 23 21:06:00 2020 +0200 rename the book diff --git a/docs/basics/_examples/DL-101-136-105 b/docs/basics/_examples/DL-101-136-105 index 580f62773..481270ea8 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 95dac60 add container and execute analysis within container +HEAD is now at 54c8935 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 edd9dd53e..f19ac6f42 100644 --- a/docs/basics/_examples/DL-101-136-109 +++ b/docs/basics/_examples/DL-101-136-109 @@ -1,4 +1,4 @@ $ git commit -m "rename book" -[master a3ce4d7] rename book +[master 6899ff8] 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 580f62773..481270ea8 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 95dac60 add container and execute analysis within container +HEAD is now at 54c8935 add container and execute analysis within container nothing to save, working tree clean diff --git a/docs/basics/_examples/DL-101-136-121 b/docs/basics/_examples/DL-101-136-121 index d0538d518..10621a4e8 100644 --- a/docs/basics/_examples/DL-101-136-121 +++ b/docs/basics/_examples/DL-101-136-121 @@ -1,3 +1,3 @@ $ cd ../ $ ls -l TLCL.pdf -lrwxrwxrwx 1 adina adina 131 Feb 17 08:52 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf +lrwxrwxrwx 1 adina adina 131 Jun 23 21:06 TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-136-122 b/docs/basics/_examples/DL-101-136-122 index 8537cd8f2..a16e84686 100644 --- a/docs/basics/_examples/DL-101-136-122 +++ b/docs/basics/_examples/DL-101-136-122 @@ -7,4 +7,4 @@ action summary: add (ok: 1) delete (ok: 1) save (ok: 1) -lrwxrwxrwx 1 adina adina 128 Feb 17 08:52 TLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf +lrwxrwxrwx 1 adina adina 128 Jun 23 21:06 TLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-136-123 b/docs/basics/_examples/DL-101-136-123 index 825a75524..a3f9d59bd 100644 --- a/docs/basics/_examples/DL-101-136-123 +++ b/docs/basics/_examples/DL-101-136-123 @@ -1,7 +1,7 @@ $ git log -n 1 -p -commit b57b451e07941294635654dfa2da982d8f384f1a +commit 07f538ce22d1d4ce87633d721449890f0bc9e571 Author: Elena Piscopia -Date: Mon Feb 17 08:52:30 2020 +0100 +Date: Tue Jun 23 21:06:02 2020 +0200 moved book into root diff --git a/docs/basics/_examples/DL-101-136-124 b/docs/basics/_examples/DL-101-136-124 index 3487d1d8d..d3998e307 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 95dac60 add container and execute analysis within container +HEAD is now at 54c8935 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 bc1af04dc..097134621 100644 --- a/docs/basics/_examples/DL-101-136-128 +++ b/docs/basics/_examples/DL-101-136-128 @@ -1,7 +1,7 @@ $ cd midterm_project $ git log notes.txt -commit dbc42541d643bba7db97eadcabe806c61c8c5859 +commit 956fb0aa39ead075b746b6e9df3be1613722bbd7 Author: Elena Piscopia -Date: Mon Feb 17 08:52:31 2020 +0100 +Date: Tue Jun 23 21:06:03 2020 +0200 moved notes.txt from root of top-ds to midterm subds diff --git a/docs/basics/_examples/DL-101-136-129 b/docs/basics/_examples/DL-101-136-129 index b0e1ccaf7..78b1182a3 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 c7a17ea [DATALAD RUNCMD] rerun analysis in container -HEAD is now at 95dac60 add container and execute analysis within container +HEAD is now at 9aaf66a [DATALAD RUNCMD] rerun analysis in container +HEAD is now at 54c8935 add container and execute analysis within container diff --git a/docs/basics/_examples/DL-101-136-132 b/docs/basics/_examples/DL-101-136-132 index 3a55daec2..89ab92d79 100644 --- a/docs/basics/_examples/DL-101-136-132 +++ b/docs/basics/_examples/DL-101-136-132 @@ -1,7 +1,7 @@ $ git log -n 1 -p -commit 9e2951173bcfc2fb9d6f950c6e620ea02bb7fd9a +commit 93496d22ea5dd04091ef5fd8c6cb12fbb5b91282 Author: Elena Piscopia -Date: Mon Feb 17 08:52:38 2020 +0100 +Date: Tue Jun 23 21:06:08 2020 +0200 add copy of TLCL.pdf diff --git a/docs/basics/_examples/DL-101-136-133 b/docs/basics/_examples/DL-101-136-133 index 5aa0b6406..841e279b2 100644 --- a/docs/basics/_examples/DL-101-136-133 +++ b/docs/basics/_examples/DL-101-136-133 @@ -1,4 +1,4 @@ $ ls -l copyofTLCL.pdf $ ls -l books/TLCL.pdf -lrwxrwxrwx 1 adina adina 128 Feb 17 08:52 copyofTLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf +lrwxrwxrwx 1 adina adina 128 Jun 23 21:06 copyofTLCL.pdf -> .git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf lrwxrwxrwx 1 adina adina 131 Jan 28 2019 books/TLCL.pdf -> ../.git/annex/objects/jf/3M/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf/MD5E-s2120211--06d1efcb05bb2c55cd039dab3fb28455.pdf diff --git a/docs/basics/_examples/DL-101-136-134 b/docs/basics/_examples/DL-101-136-134 index 9941249d9..370203857 100644 --- a/docs/basics/_examples/DL-101-136-134 +++ b/docs/basics/_examples/DL-101-136-134 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at 31ee306 move book back from midterm_project +HEAD is now at a1c3597 move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-137 b/docs/basics/_examples/DL-101-136-137 index 80c2b99cb..99e2bc8fb 100644 --- a/docs/basics/_examples/DL-101-136-137 +++ b/docs/basics/_examples/DL-101-136-137 @@ -7,7 +7,7 @@ midterm_project │   └── script.py ├── input │   └── iris.csv -> .git/annex/objects/qz/Jg/MD5E-s3975--341a3b5244f213282b7b0920b729c592.csv/MD5E-s3975--341a3b5244f213282b7b0920b729c592.csv -├── notes.txt -> .git/annex/objects/Wz/J2/MD5E-s5457--a55b6d35a8c79406f8301f58dda6dfc3.txt/MD5E-s5457--a55b6d35a8c79406f8301f58dda6dfc3.txt +├── notes.txt -> .git/annex/objects/W4/w9/MD5E-s5075--c59ea2194d50f9d0ddebcc257343d31f.txt/MD5E-s5075--c59ea2194d50f9d0ddebcc257343d31f.txt ├── pairwise_relationships.png -> .git/annex/objects/xZ/pk/MD5E-s175447--1f7f416d7c317c1f6208a940aa50c700.png/MD5E-s175447--1f7f416d7c317c1f6208a940aa50c700.png ├── prediction_report.csv -> .git/annex/objects/VF/27/MD5E-s347--7d984f53676358222aa7aa55980f205b.csv/MD5E-s347--7d984f53676358222aa7aa55980f205b.csv └── README.md diff --git a/docs/basics/_examples/DL-101-136-139 b/docs/basics/_examples/DL-101-136-139 index 0d12040db..750c5c068 100644 --- a/docs/basics/_examples/DL-101-136-139 +++ b/docs/basics/_examples/DL-101-136-139 @@ -1,7 +1,7 @@ $ cd midterm_project $ git log notes.txt -commit 35e8039dc27a13241fc86cd13937a88370f733a5 +commit c2975eb734525c64fd97760b5a1f761e68b03cf4 Author: Elena Piscopia -Date: Wed May 6 14:34:16 2020 +0200 +Date: Tue Jun 23 21:06:09 2020 +0200 [DATALAD] Recorded changes diff --git a/docs/basics/_examples/DL-101-136-140 b/docs/basics/_examples/DL-101-136-140 index ac930df44..51be25941 100644 --- a/docs/basics/_examples/DL-101-136-140 +++ b/docs/basics/_examples/DL-101-136-140 @@ -6,7 +6,7 @@ $ cat .git/config logallrefupdates = true editor = nano [annex] - uuid = 283818cf-2b07-4a0e-ab28-2d5fcdb947ae + uuid = b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 version = 5 backends = MD5E [submodule "recordings/longnow"] @@ -15,7 +15,7 @@ $ cat .git/config [remote "roommate"] url = ../mock_user/DataLad-101 fetch = +refs/heads/*:refs/remotes/roommate/* - annex-uuid = fa947123-aeb1-4096-9399-a47a5bb50446 + annex-uuid = e86f131b-c6f3-4bf9-91d1-f47f0117fee7 annex-ignore = false [submodule "midterm_project"] url = /home/me/dl-101/DataLad-101/midterm_project diff --git a/docs/basics/_examples/DL-101-136-142 b/docs/basics/_examples/DL-101-136-142 index 2dffc484e..06bcbd8e8 100644 --- a/docs/basics/_examples/DL-101-136-142 +++ b/docs/basics/_examples/DL-101-136-142 @@ -2,11 +2,10 @@ $ cd ../DataLad-101 # attempt a datalad update $ datalad update -[INFO] Fetching updates for -[ERROR] Cmd('/usr/lib/git-annex.linux/git') failed due to: exit code(128) -| cmdline: /usr/lib/git-annex.linux/git fetch --progress --prune --recurse-submodules=no -v roommate -| stderr: 'fatal: '../mock_user/DataLad-101' does not appear to be a git repository -| fatal: Could not read from remote repository. -| -| Please make sure you have the correct access rights -| and the repository exists.' [cmd.py:wait:415] (GitCommandError) +[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) +CommandError: 'git fetch --verbose --progress --prune --recurse-submodules=no roommate' failed with exitcode 128 under /home/me/dl-101/DataLad-101 +fatal: '../mock_user/DataLad-101' does not appear to be a git repository +fatal: Could not read from remote repository. + +Please make sure you have the correct access rights +and the repository exists. diff --git a/docs/basics/_examples/DL-101-136-144 b/docs/basics/_examples/DL-101-136-144 index 1b1caa052..5082f405b 100644 --- a/docs/basics/_examples/DL-101-136-144 +++ b/docs/basics/_examples/DL-101-136-144 @@ -6,7 +6,7 @@ $ cat .git/config logallrefupdates = true editor = nano [annex] - uuid = 283818cf-2b07-4a0e-ab28-2d5fcdb947ae + uuid = b2ff89c4-11a8-49b2-8fe5-e28fcd9cf621 version = 5 backends = MD5E [submodule "recordings/longnow"] @@ -15,7 +15,7 @@ $ cat .git/config [remote "roommate"] url = ../mock_user/onemoredir/DataLad-101 fetch = +refs/heads/*:refs/remotes/roommate/* - annex-uuid = fa947123-aeb1-4096-9399-a47a5bb50446 + annex-uuid = e86f131b-c6f3-4bf9-91d1-f47f0117fee7 annex-ignore = false [submodule "midterm_project"] url = /home/me/dl-101/DataLad-101/midterm_project diff --git a/docs/basics/_examples/DL-101-136-145 b/docs/basics/_examples/DL-101-136-145 index 8f8cbc6c7..994f13f24 100644 --- a/docs/basics/_examples/DL-101-136-145 +++ b/docs/basics/_examples/DL-101-136-145 @@ -1,3 +1,3 @@ $ datalad update -[INFO] Fetching updates for +[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-136-146 b/docs/basics/_examples/DL-101-136-146 index ab025a92d..bb5727eb4 100644 --- a/docs/basics/_examples/DL-101-136-146 +++ b/docs/basics/_examples/DL-101-136-146 @@ -1,3 +1,3 @@ $ cd ../mock_user && mv onemoredir/DataLad-101 . $ rm -r onemoredir -$ cd ../DataLad-101 && sed -i 's/..\/mock_user\/onemoredir\/DataLad-101/..\/mock_user\/DataLad-101/' .git/config +$ cd ../DataLad-101 && sed -i 's/..\/mock_user\/onemoredir\/DataLad-101/..\/mock_user\/DataLad-101/' .git/config diff --git a/docs/basics/_examples/DL-101-136-148 b/docs/basics/_examples/DL-101-136-148 index b47b2bc6b..44e7b1a56 100644 --- a/docs/basics/_examples/DL-101-136-148 +++ b/docs/basics/_examples/DL-101-136-148 @@ -1,7 +1,7 @@ $ git log -p -n 1 -commit b52a71418c9b561ca8571fdfce0b89e634d9b199 +commit 676981cee9b352581ac724a07bbb2a61f6eadd45 Author: Elena Piscopia -Date: Mon Feb 17 08:52:42 2020 +0100 +Date: Tue Jun 23 21:06:13 2020 +0200 content removed from git annex diff --git a/docs/basics/_examples/DL-101-136-152 b/docs/basics/_examples/DL-101-136-152 index 9941249d9..370203857 100644 --- a/docs/basics/_examples/DL-101-136-152 +++ b/docs/basics/_examples/DL-101-136-152 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at 31ee306 move book back from midterm_project +HEAD is now at a1c3597 move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-156 b/docs/basics/_examples/DL-101-136-156 index 4f24c1288..f5b3c86b3 100644 --- a/docs/basics/_examples/DL-101-136-156 +++ b/docs/basics/_examples/DL-101-136-156 @@ -1,3 +1,3 @@ $ git reset --hard HEAD~1 warning: unable to rmdir 'longnow': Directory not empty -HEAD is now at 31ee306 move book back from midterm_project +HEAD is now at a1c3597 move book back from midterm_project diff --git a/docs/basics/_examples/DL-101-136-160 b/docs/basics/_examples/DL-101-136-160 index a470c0ee9..adcd6de3c 100644 --- a/docs/basics/_examples/DL-101-136-160 +++ b/docs/basics/_examples/DL-101-136-160 @@ -2,12 +2,17 @@ $ datalad clone -d . \ https://github.com/datalad-datasets/disneyanimation-cloud.git \ cloud -[INFO] Cloning https://github.com/datalad-datasets/disneyanimation-cloud.git [1 other candidates] into '/home/me/dl-101/DataLad-101/cloud' -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Cloning dataset to Dataset(/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 +install(ok): cloud (dataset) add(ok): cloud (file) add(ok): .gitmodules (file) save(ok): . (dataset) -install(ok): cloud (dataset) action summary: add (ok: 2) install (ok: 1) diff --git a/docs/basics/_examples/DL-101-136-163 b/docs/basics/_examples/DL-101-136-163 index bf4760419..6caaedc9b 100644 --- a/docs/basics/_examples/DL-101-136-163 +++ b/docs/basics/_examples/DL-101-136-163 @@ -1,8 +1,13 @@ $ datalad get -n cloud # delete the subdataset $ datalad remove -m "remove obsolete subds" -d . cloud -[INFO] Cloning https://github.com/datalad-datasets/disneyanimation-cloud.git [1 other candidates] into '/home/me/dl-101/DataLad-101/cloud' -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Cloning dataset to Dataset(/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 install(ok): /home/me/dl-101/DataLad-101/cloud (dataset) [Installed subdataset in order to get /home/me/dl-101/DataLad-101/cloud] uninstall(ok): cloud (dataset) remove(ok): cloud (dataset) diff --git a/docs/basics/_examples/DL-101-136-164 b/docs/basics/_examples/DL-101-136-164 index 60653f59a..1f9dd3c53 100644 --- a/docs/basics/_examples/DL-101-136-164 +++ b/docs/basics/_examples/DL-101-136-164 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~2 -HEAD is now at b96ba14 save cropped logos to Git +HEAD is now at b0d5d02 Added flower mosaic from wikimedia diff --git a/docs/basics/_examples/DL-101-136-174 b/docs/basics/_examples/DL-101-136-174 index e23a20f4e..3c96d7c3c 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 92c6f73 Added flower mosaic from wikimedia +HEAD is now at b0d5d02 Added flower mosaic from wikimedia books code flowers.jpg diff --git a/docs/basics/_examples/DL-101-136-180 b/docs/basics/_examples/DL-101-136-180 index 60653f59a..1f9dd3c53 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 b96ba14 save cropped logos to Git +HEAD is now at b0d5d02 Added flower mosaic from wikimedia diff --git a/docs/basics/_examples/DL-101-136-184 b/docs/basics/_examples/DL-101-136-184 index a0b6068a9..5cdbd750d 100644 --- a/docs/basics/_examples/DL-101-136-184 +++ b/docs/basics/_examples/DL-101-136-184 @@ -1,5 +1,5 @@ $ git reset --hard HEAD~ $ cd ../ $ git reset --hard HEAD~ -HEAD is now at c7a17ea [DATALAD RUNCMD] rerun analysis in container -HEAD is now at 95dac60 add container and execute analysis within container +HEAD is now at 9aaf66a [DATALAD RUNCMD] rerun analysis in container +HEAD is now at 54c8935 add container and execute analysis within container diff --git a/docs/basics/_examples/DL-101-136-187 b/docs/basics/_examples/DL-101-136-187 index 6e05e253e..2552bd744 100644 --- a/docs/basics/_examples/DL-101-136-187 +++ b/docs/basics/_examples/DL-101-136-187 @@ -1,5 +1,5 @@ $ cd midterm_project $ git annex whereis TLCL.pdf whereis TLCL.pdf (1 copy) - e60f97df-aaec-46bb-acdc-bf95451126f5 -- me@muninn:~/dl-101/DataLad-101/midterm_project [here] + 772a622f-57c4-4e42-aa39-b580b1bfc717 -- me@muninn:~/dl-101/DataLad-101/midterm_project [here] ok diff --git a/docs/basics/_examples/DL-101-137-101 b/docs/basics/_examples/DL-101-137-101 index 3e3639315..d04525792 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 -b96ba14 save cropped logos to Git -b52a714 content removed from git annex -31ee306 move book back from midterm_project -3168683 move book into midterm_project -95dac60 add container and execute analysis within container -c6845ba finished my midterm project -b4d076f [DATALAD] Recorded changes -a19873b add note on DataLad's procedures -64f886c add note on configurations and git config -ad4fc86 Add note on adding siblings -7462696 Merge remote-tracking branch 'refs/remotes/roommate/master' -1639278 Include nesting demo from datalad website -0ef8c62 add note about datalad update -e5df2d8 add note on git annex whereis -80c31dc add note about cloning from paths and recursive datalad get +b0d5d02 Added flower mosaic from wikimedia +ee8624e save cropped logos to Git +676981c content removed from git annex +a1c3597 move book back from midterm_project +eff4144 move book into midterm_project +54c8935 add container and execute analysis within container +ba534fa finished my midterm project +a999fbb [DATALAD] Recorded changes +2ce328a add note on DataLad's procedures +3e7c596 add note on configurations and git config +ce2af86 Add note on adding siblings +388b5fd Merge remote-tracking branch 'roommate/master' +0292f7c Include nesting demo from datalad website +4fe212d add note about datalad update +78d2f4f add note on git annex whereis diff --git a/docs/basics/_examples/DL-101-137-105 b/docs/basics/_examples/DL-101-137-105 index 2b1e768c5..8a3ed3df2 100644 --- a/docs/basics/_examples/DL-101-137-105 +++ b/docs/basics/_examples/DL-101-137-105 @@ -1,7 +1,7 @@ $ git log -p -1 -commit b07afbce9dc01f43a27b9b16562ebfb4cb11a1bd +commit 792252cf99f8e0a22b221a5214b003dc5ee5f33b Author: Elena Piscopia -Date: Mon Feb 17 08:53:01 2020 +0100 +Date: Tue Jun 23 21:06:29 2020 +0200 [DATALAD] Recorded changes diff --git a/docs/basics/_examples/DL-101-137-106 b/docs/basics/_examples/DL-101-137-106 index f9af28dfb..742d3313d 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 -b07afbc [DATALAD] Recorded changes -b96ba14 save cropped logos to Git -b52a714 content removed from git annex +792252c [DATALAD] Recorded changes +b0d5d02 Added flower mosaic from wikimedia +ee8624e save cropped logos to Git diff --git a/docs/basics/_examples/DL-101-137-112 b/docs/basics/_examples/DL-101-137-112 index 643809b20..1e4156c8a 100644 --- a/docs/basics/_examples/DL-101-137-112 +++ b/docs/basics/_examples/DL-101-137-112 @@ -1,12 +1,12 @@ $ git log -2 -commit 2996ac291b15780dd9a255dc7f162d07e21d9294 +commit bb02715c2326bf6fece5f11b3e1925794eccb9ba Author: Elena Piscopia -Date: Mon Feb 17 08:53:02 2020 +0100 +Date: Tue Jun 23 21:06:29 2020 +0200 save my favorite Git joke -commit b96ba145e614e6fa12f2dae9bf9260ee8678ca5d +commit b0d5d0236c3e99dde55c170e6201323c7835298d Author: Elena Piscopia -Date: Mon Feb 17 08:52:42 2020 +0100 +Date: Tue Jun 23 21:06:15 2020 +0200 - save cropped logos to Git + Added flower mosaic from wikimedia diff --git a/docs/basics/_examples/DL-101-137-114 b/docs/basics/_examples/DL-101-137-114 index 0401bd217..670e3bdd4 100644 --- a/docs/basics/_examples/DL-101-137-114 +++ b/docs/basics/_examples/DL-101-137-114 @@ -1,2 +1,2 @@ $ ls -l apdffile.pdf -lrwxrwxrwx 1 adina adina 122 Feb 17 08:53 apdffile.pdf -> .git/annex/objects/xg/GF/MD5E-s1842--c4613feb0218f5589ccf5de9fd5a7d7c.pdf/MD5E-s1842--c4613feb0218f5589ccf5de9fd5a7d7c.pdf +lrwxrwxrwx 1 adina adina 122 Jun 23 21:06 apdffile.pdf -> .git/annex/objects/x7/gj/MD5E-s1842--e6ce7e00e2c21e8fd5d455dcfb46a2e2.pdf/MD5E-s1842--e6ce7e00e2c21e8fd5d455dcfb46a2e2.pdf diff --git a/docs/basics/_examples/DL-101-137-116 b/docs/basics/_examples/DL-101-137-116 index 1d27bcf41..c20f9bcb8 100644 --- a/docs/basics/_examples/DL-101-137-116 +++ b/docs/basics/_examples/DL-101-137-116 @@ -1,2 +1,2 @@ $ ls -l apdffile.pdf --rw-r--r-- 1 adina adina 1842 Feb 17 08:53 apdffile.pdf +-rw-r--r-- 1 adina adina 1842 Jun 23 21:06 apdffile.pdf diff --git a/docs/basics/_examples/DL-101-137-117 b/docs/basics/_examples/DL-101-137-117 index a8b9b4261..4823bebba 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 -e1bb29d [DATALAD] Recorded changes -2996ac2 save my favorite Git joke -b96ba14 save cropped logos to Git +ed8d3cb [DATALAD] Recorded changes +bb02715 save my favorite Git joke +b0d5d02 Added flower mosaic from wikimedia diff --git a/docs/basics/_examples/DL-101-137-119 b/docs/basics/_examples/DL-101-137-119 index e5192b7b8..4bdca9292 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 -2996ac2 save my favorite Git joke -b96ba14 save cropped logos to Git +bb02715 save my favorite Git joke +b0d5d02 Added flower mosaic from wikimedia diff --git a/docs/basics/_examples/DL-101-137-121 b/docs/basics/_examples/DL-101-137-121 index 618c88536..e3e145722 100644 --- a/docs/basics/_examples/DL-101-137-121 +++ b/docs/basics/_examples/DL-101-137-121 @@ -1,21 +1,21 @@ $ git log -n 20 --oneline -2996ac2 save my favorite Git joke -b96ba14 save cropped logos to Git -b52a714 content removed from git annex -31ee306 move book back from midterm_project -3168683 move book into midterm_project -95dac60 add container and execute analysis within container -c6845ba finished my midterm project -b4d076f [DATALAD] Recorded changes -a19873b add note on DataLad's procedures -64f886c add note on configurations and git config -ad4fc86 Add note on adding siblings -7462696 Merge remote-tracking branch 'refs/remotes/roommate/master' -1639278 Include nesting demo from datalad website -0ef8c62 add note about datalad update -e5df2d8 add note on git annex whereis -80c31dc add note about cloning from paths and recursive datalad get -a1f2c3f add note on clean datasets -baf4fc5 [DATALAD RUNCMD] Resize logo for slides -a84115d [DATALAD RUNCMD] Resize logo for slides -66b01ae add additional notes on run options +bb02715 save my favorite Git joke +b0d5d02 Added flower mosaic from wikimedia +ee8624e save cropped logos to Git +676981c content removed from git annex +a1c3597 move book back from midterm_project +eff4144 move book into midterm_project +54c8935 add container and execute analysis within container +ba534fa finished my midterm project +a999fbb [DATALAD] Recorded changes +2ce328a add note on DataLad's procedures +3e7c596 add note on configurations and git config +ce2af86 Add note on adding siblings +388b5fd Merge remote-tracking branch 'roommate/master' +0292f7c Include nesting demo from datalad website +4fe212d add note about datalad update +78d2f4f add note on git annex whereis +e242f12 add note about cloning from paths and recursive datalad get +ae1402e add note on clean datasets +3dfc1b5 [DATALAD RUNCMD] Resize logo for slides +a730b96 [DATALAD RUNCMD] Resize logo for slides diff --git a/docs/basics/_examples/DL-101-137-122 b/docs/basics/_examples/DL-101-137-122 index e2bfd6d63..41a6c8a3a 100644 --- a/docs/basics/_examples/DL-101-137-122 +++ b/docs/basics/_examples/DL-101-137-122 @@ -1,7 +1,7 @@ -$ git checkout a1f2c3f97f0d7236a741ce074d8136eca23dd53f +$ git checkout e242f12ab75215d8cea61fd4c775cf0f6c79848b warning: unable to rmdir 'midterm_project': Directory not empty -Note: switching to 'a1f2c3f97f0d7236a741ce074d8136eca23dd53f'. +Note: switching to 'e242f12ab75215d8cea61fd4c775cf0f6c79848b'. 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 a1f2c3f add note on clean datasets +HEAD is now at e242f12 add note about cloning from paths and recursive datalad get diff --git a/docs/basics/_examples/DL-101-137-123 b/docs/basics/_examples/DL-101-137-123 index 6c1f0367a..876605f33 100644 --- a/docs/basics/_examples/DL-101-137-123 +++ b/docs/basics/_examples/DL-101-137-123 @@ -37,3 +37,22 @@ dataset. A suboptimal alternative is the --explicit flag, used to record only those changes done to the files listed with --output flags. + +A source to install a dataset from can also be a path, +for example as in "datalad clone ../DataLad-101". + +Just as in creating datasets, you can add a +description on the location of the new dataset clone +with the -D/--description option. + +Note that subdatasets will not be installed by default, +but are only registered in the superdataset -- you will +have to do a "datalad get -n PATH/TO/SUBDATASET" +to install the subdataset for file availability meta data. +The -n/--no-data options prevents that file contents are +also downloaded. + +Note that a recursive "datalad get" would install all further +registered subdatasets underneath a subdataset, so a safer +way to proceed is to set a decent --recursion-limit: +"datalad get -n -r --recursion-limit 2 " diff --git a/docs/basics/_examples/DL-101-137-127 b/docs/basics/_examples/DL-101-137-127 index b717c1eee..458e52fbc 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 a1f2c3f97f0d7236a741ce074d8136eca23dd53f:notes.txt +$ git cat-file --textconv e242f12ab75215d8cea61fd4c775cf0f6c79848b:notes.txt One can create a new dataset with 'datalad create [--description] PATH'. The dataset is created empty @@ -38,3 +38,22 @@ dataset. A suboptimal alternative is the --explicit flag, used to record only those changes done to the files listed with --output flags. + +A source to install a dataset from can also be a path, +for example as in "datalad clone ../DataLad-101". + +Just as in creating datasets, you can add a +description on the location of the new dataset clone +with the -D/--description option. + +Note that subdatasets will not be installed by default, +but are only registered in the superdataset -- you will +have to do a "datalad get -n PATH/TO/SUBDATASET" +to install the subdataset for file availability meta data. +The -n/--no-data options prevents that file contents are +also downloaded. + +Note that a recursive "datalad get" would install all further +registered subdatasets underneath a subdataset, so a safer +way to proceed is to set a decent --recursion-limit: +"datalad get -n -r --recursion-limit 2 " diff --git a/docs/basics/_examples/DL-101-137-132 b/docs/basics/_examples/DL-101-137-132 index b1d58ca5c..03476903d 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 -f2e8973 add joke evaluation to joke -2996ac2 save my favorite Git joke +17f097c add joke evaluation to joke +bb02715 save my favorite Git joke diff --git a/docs/basics/_examples/DL-101-137-133 b/docs/basics/_examples/DL-101-137-133 index c612be7f7..6fe8cc0db 100644 --- a/docs/basics/_examples/DL-101-137-133 +++ b/docs/basics/_examples/DL-101-137-133 @@ -1,3 +1,3 @@ -$ git reset --hard 2996ac291b15780dd9a255dc7f162d07e21d9294 -HEAD is now at 2996ac2 save my favorite Git joke +$ git reset --hard bb02715c2326bf6fece5f11b3e1925794eccb9ba +HEAD is now at bb02715 save my favorite Git joke diff --git a/docs/basics/_examples/DL-101-137-144 b/docs/basics/_examples/DL-101-137-144 index 80e02dd7f..34ee4651e 100644 --- a/docs/basics/_examples/DL-101-137-144 +++ b/docs/basics/_examples/DL-101-137-144 @@ -1,5 +1,5 @@ -$ git revert da91ec2afa1f84eca68487d2e4c7e327b9383b11 -[master e0453db] Revert "did a bad modification" - Date: Mon Feb 17 08:53:06 2020 +0100 +$ git revert afce2cf307abadc6c4958fc98ea596942a2b6466 +[master aab27f8] Revert "did a bad modification" + Date: Tue Jun 23 21:06:33 2020 +0200 1 file changed, 1 deletion(-) diff --git a/docs/basics/_examples/DL-101-137-146 b/docs/basics/_examples/DL-101-137-146 index e830e98a2..f6fb5a610 100644 --- a/docs/basics/_examples/DL-101-137-146 +++ b/docs/basics/_examples/DL-101-137-146 @@ -1,20 +1,20 @@ $ git log -n 3 -commit e0453dbccdc0d7f136fc3bc868972e9451fe3932 +commit aab27f83f23f8a88861efff529da649148d9603c Author: Elena Piscopia -Date: Mon Feb 17 08:53:06 2020 +0100 +Date: Tue Jun 23 21:06:33 2020 +0200 Revert "did a bad modification" - This reverts commit da91ec2afa1f84eca68487d2e4c7e327b9383b11. + This reverts commit afce2cf307abadc6c4958fc98ea596942a2b6466. -commit 1be4a73f6d14fbcaa758572563eb5563d8e69685 +commit d9e8d6902395cb68e95b27e2567e120499818261 Author: Elena Piscopia -Date: Mon Feb 17 08:53:06 2020 +0100 +Date: Tue Jun 23 21:06:33 2020 +0200 add note on helpful git resource -commit da91ec2afa1f84eca68487d2e4c7e327b9383b11 +commit afce2cf307abadc6c4958fc98ea596942a2b6466 Author: Elena Piscopia -Date: Mon Feb 17 08:53:05 2020 +0100 +Date: Tue Jun 23 21:06:32 2020 +0200 did a bad modification diff --git a/docs/basics/_examples/DL-101-139-102 b/docs/basics/_examples/DL-101-139-102 index 658a958c7..8c4551e10 100644 --- a/docs/basics/_examples/DL-101-139-102 +++ b/docs/basics/_examples/DL-101-139-102 @@ -1,17 +1,29 @@ $ datalad push --to gin +[INFO] Determine push target +[INFO] Push refspecs [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects [INFO] Start writing objects [INFO] Start resolving deltas +[INFO] Transfer data +[INFO] Start annex operation +[INFO] books/TLCL.pdf +[INFO] books/bash_guide.pdf +[INFO] books/byte-of-python.pdf +[INFO] books/progit.pdf +[INFO] Finished annex copy +[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/dl-101/DataLad-101) publish(ok): . (dataset) [refs/heads/master->gin:refs/heads/master [new branch]] 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...] -publish(ok): . (dataset) [refs/heads/git-annex->gin:refs/heads/git-annex 9df4d51..2285f9d] +copy(ok): flowers.jpg (file) [to gin...] +publish(ok): . (dataset) [refs/heads/git-annex->gin:refs/heads/git-annex fa73e9b..adc3814] diff --git a/docs/basics/_examples/DL-101-139-104 b/docs/basics/_examples/DL-101-139-104 index 72726e87f..03fac956c 100644 --- a/docs/basics/_examples/DL-101-139-104 +++ b/docs/basics/_examples/DL-101-139-104 @@ -2,10 +2,8 @@ $ cat .gitmodules [submodule "recordings/longnow"] path = recordings/longnow url = https://github.com/datalad-datasets/longnow-podcasts.git - branch = master datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e [submodule "midterm_project"] path = midterm_project url = https://github.com/adswa/midtermproject - branch = master - datalad-id = 933e9fb6-647d-11ea-8652-27eb4f93a5dc + datalad-id = 5f313adc-b584-11ea-90a2-3119e6b9cf19 diff --git a/docs/basics/_examples/DL-101-139-106 b/docs/basics/_examples/DL-101-139-106 index ed6e7058f..d6b301540 100644 --- a/docs/basics/_examples/DL-101-139-106 +++ b/docs/basics/_examples/DL-101-139-106 @@ -1,6 +1,13 @@ $ datalad push --to gin +[INFO] Determine push target +[INFO] Push refspecs [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects [INFO] Start writing objects -publish(ok): . (dataset) [refs/heads/master->gin:refs/heads/master ab85415..a1aff52] +[INFO] Transfer data +[INFO] Start annex operation +[INFO] Finished +[INFO] Update availability information +[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) +publish(ok): . (dataset) [refs/heads/master->gin:refs/heads/master aab27f8..93af47b] diff --git a/docs/basics/_examples/DL-101-139-107 b/docs/basics/_examples/DL-101-139-107 index 3171002d5..59ee287f4 100644 --- a/docs/basics/_examples/DL-101-139-107 +++ b/docs/basics/_examples/DL-101-139-107 @@ -1,10 +1,10 @@ $ datalad clone https://gin.g-node.org/adswa/DataLad-101 -[INFO] Cloning dataset to +[INFO] Cloning dataset to Dataset(/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 +[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 344597bf7..ea00e08a1 100644 --- a/docs/basics/_examples/DL-101-141-101 +++ b/docs/basics/_examples/DL-101-141-101 @@ -1,7 +1,10 @@ $ datalad push --to roommate +[INFO] Determine push target +[INFO] Push refspecs [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects [INFO] Start writing objects [ERROR] refs/heads/master->roommate:refs/heads/master [remote rejected] (branch is currently checked out) [publish(/home/me/dl-101/DataLad-101)] +[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) publish(error): . (dataset) [refs/heads/master->roommate:refs/heads/master [remote rejected] (branch is currently checked out)] diff --git a/docs/beyond_basics/_examples/DL-101-179-107 b/docs/beyond_basics/_examples/DL-101-179-107 index 495a04380..50f4c4cc5 100644 --- a/docs/beyond_basics/_examples/DL-101-179-107 +++ b/docs/beyond_basics/_examples/DL-101-179-107 @@ -1,4 +1,4 @@ $ datalad siblings add -d . --name public --url git@github.com:datalad-handbook/DataLad-101.git -[INFO] Failed to enable annex remote public, could be a pure git or not accessible -[WARNING] Failed to determine if public carries annex. Remote was marked by annex as annex-ignore. Edit .git/config to reset if you think that was done by mistake due to absent connection etc +[INFO] Could not enable annex remote public. This is expected if public is a pure Git remote, or happens if it is not accessible. +[WARNING] Could not detect whether public carries an annex. If public is a pure Git remote, this is expected. Remote was marked by annex as annex-ignore. Edit .git/config to reset if you think that was done by mistake due to absent connection etc .: public(-) [git@github.com:datalad-handbook/DataLad-101.git (git)] diff --git a/docs/beyond_basics/_examples/DL-101-179-108 b/docs/beyond_basics/_examples/DL-101-179-108 index 3efd13887..b4261a732 100644 --- a/docs/beyond_basics/_examples/DL-101-179-108 +++ b/docs/beyond_basics/_examples/DL-101-179-108 @@ -1,4 +1,4 @@ $ datalad siblings add -d . --name public --url git@github.com:datalad-handbook/midterm_project.git -[INFO] Failed to enable annex remote public, could be a pure git or not accessible -[WARNING] Failed to determine if public carries annex. Remote was marked by annex as annex-ignore. Edit .git/config to reset if you think that was done by mistake due to absent connection etc +[INFO] Could not enable annex remote public. This is expected if public is a pure Git remote, or happens if it is not accessible. +[WARNING] Could not detect whether public carries an annex. If public is a pure Git remote, this is expected. Remote was marked by annex as annex-ignore. Edit .git/config to reset if you think that was done by mistake due to absent connection etc .: public(-) [git@github.com:datalad-handbook/midterm_project.git (git)] diff --git a/docs/intro/_examples/how-to-1 b/docs/intro/_examples/how-to-1 index 0f0e6b6fd..6b07f8d16 100644 --- a/docs/intro/_examples/how-to-1 +++ b/docs/intro/_examples/how-to-1 @@ -1,5 +1,5 @@ $ ls -l output.txt 24+0 records in 24+0 records out -25165824 bytes (25 MB, 24 MiB) copied, 0.0128546 s, 2.0 GB/s --rw-r--r-- 1 adina adina 25165824 Feb 17 08:54 output.txt +25165824 bytes (25 MB, 24 MiB) copied, 0.0133762 s, 1.9 GB/s +-rw-r--r-- 1 adina adina 25165824 Jun 23 21:06 output.txt diff --git a/docs/intro/_examples/how-to-2 b/docs/intro/_examples/how-to-2 index 081db07df..813893b49 100644 --- a/docs/intro/_examples/how-to-2 +++ b/docs/intro/_examples/how-to-2 @@ -1,4 +1,4 @@ $ ls -lh output.txt # note that short options can be combined! # or alternatively $ ls -l --human-readable output.txt --rw-r--r-- 1 adina adina 24M Feb 17 08:54 output.txt +-rw-r--r-- 1 adina adina 24M Jun 23 21:06 output.txt diff --git a/docs/usecases/_examples/HCP-12 b/docs/usecases/_examples/HCP-12 index 388435390..7e4f233fb 100644 --- a/docs/usecases/_examples/HCP-12 +++ b/docs/usecases/_examples/HCP-12 @@ -1,7 +1,7 @@ $ cd dataset-to-copy-to $ datalad get bvals anothercopyofbvecs 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters +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...] -get(ok): bvals (file) [from datalad...] action summary: get (ok: 3) diff --git a/docs/usecases/_examples/HCP-2 b/docs/usecases/_examples/HCP-2 index 291bcdc28..7c09723c4 100644 --- a/docs/usecases/_examples/HCP-2 +++ b/docs/usecases/_examples/HCP-2 @@ -9,24 +9,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130013 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130013/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130013/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/876/c9c98-2aa7-11ea-85a1-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130013/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/T1w) -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/T1w to /home/me/usecases/HCP/hcp/HCP1200/130013/T1w -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130013/T1w [INFO] Attempting to clone from http://store.datalad.org/8b5/6089e-2aa7-11ea-85a1-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130013/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130013/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/78a/4404e-2aa7-11ea-8c3f-002590496000/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130013/unprocessed [INFO] Attempting to clone from http://store.datalad.org/8e0/91aae-2aa7-11ea-85a1-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130013/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130013/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -41,24 +35,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130114 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130114/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130114/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/a71/ab0e4-2aa6-11ea-a248-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130114/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/T1w) -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/T1w to /home/me/usecases/HCP/hcp/HCP1200/130114/T1w -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130114/T1w [INFO] Attempting to clone from http://store.datalad.org/aa1/d4284-2aa6-11ea-a248-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130114/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130114/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/9a5/0b340-2aa6-11ea-81a2-002590496000/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130114/unprocessed [INFO] Attempting to clone from http://store.datalad.org/ac8/7ba5e-2aa6-11ea-a248-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130114/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130114/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -73,24 +61,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130316 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130316/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130316/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/439/61042-38ff-11ea-be90-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130316/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" -| This is unexpected; please check the network transport! +[INFO] This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/T1w) -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/T1w to /home/me/usecases/HCP/hcp/HCP1200/130316/T1w -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130316/T1w [INFO] Attempting to clone from http://store.datalad.org/452/2bbea-38ff-11ea-be90-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130316/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130316/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/411/a7f1a-38ff-11ea-8d6e-002590496000/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130316/unprocessed [INFO] Attempting to clone from http://store.datalad.org/46a/1cd80-38ff-11ea-be90-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130316/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130316/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -105,24 +87,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130417 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130417/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130417/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/e8f/5ce4e-2aa2-11ea-a418-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130417/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/T1w) -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/T1w to /home/me/usecases/HCP/hcp/HCP1200/130417/T1w -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130417/T1w [INFO] Attempting to clone from http://store.datalad.org/eb1/55924-2aa2-11ea-a418-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130417/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130417/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/da5/a3938-2aa2-11ea-b13f-0025904abcb0/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130417/unprocessed [INFO] Attempting to clone from http://store.datalad.org/ed2/969bc-2aa2-11ea-a418-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130417/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130417/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -137,24 +113,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130518 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130518/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130518/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/63f/8a1aa-2aa0-11ea-bf71-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130518/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/T1w) -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/T1w to /home/me/usecases/HCP/hcp/HCP1200/130518/T1w -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130518/T1w [INFO] Attempting to clone from http://store.datalad.org/658/7d860-2aa0-11ea-bf71-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130518/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130518/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/57a/9ec38-2aa0-11ea-b570-0025904abcb0/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130518/unprocessed [INFO] Attempting to clone from http://store.datalad.org/674/822f4-2aa0-11ea-bf71-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130518/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130518/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -169,24 +139,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130619 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130619/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130619/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/032/2a332-2a9e-11ea-a1e6-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130619/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/T1w) -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/T1w to /home/me/usecases/HCP/hcp/HCP1200/130619/T1w -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130619/T1w [INFO] Attempting to clone from http://store.datalad.org/04a/bbcde-2a9e-11ea-a1e6-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130619/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130619/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/f6a/43756-2a9d-11ea-8166-0025904abcb0/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130619/unprocessed [INFO] Attempting to clone from http://store.datalad.org/064/8fd7c-2a9e-11ea-a1e6-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130619/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130619/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -201,24 +165,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130720 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130720/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130720/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/700/ffce2-2a99-11ea-b8dd-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130720/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/T1w) -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/T1w to /home/me/usecases/HCP/hcp/HCP1200/130720/T1w -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130720/T1w [INFO] Attempting to clone from http://store.datalad.org/722/fef3c-2a99-11ea-b8dd-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130720/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130720/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/5a2/318b0-2a99-11ea-9cc0-0025904abcb0/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130720/unprocessed [INFO] Attempting to clone from http://store.datalad.org/76a/4579c-2a99-11ea-b8dd-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130720/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130720/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -233,24 +191,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130821 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130821/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130821/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/c4c/0f862-2a95-11ea-b221-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130821/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/T1w) -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/T1w to /home/me/usecases/HCP/hcp/HCP1200/130821/T1w -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130821/T1w [INFO] Attempting to clone from http://store.datalad.org/c7c/23094-2a95-11ea-b221-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130821/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130821/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/b85/e461a-2a95-11ea-bd37-002590496000/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130821/unprocessed [INFO] Attempting to clone from http://store.datalad.org/cb9/ea382-2a95-11ea-b221-002590496000 to /home/me/usecases/HCP/hcp/HCP1200/130821/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130821/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin @@ -265,24 +217,18 @@ $ datalad get -n -r HCP1200/130* | This is unexpected; please check the network transport! [INFO] Installing Dataset(/home/me/usecases/HCP/hcp) to get /home/me/usecases/HCP/hcp/HCP1200/130922 recursively [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/MNINonLinear) -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/MNINonLinear to /home/me/usecases/HCP/hcp/HCP1200/130922/MNINonLinear -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/MNINonLinear/.git to /home/me/usecases/HCP/hcp/HCP1200/130922/MNINonLinear [INFO] Attempting to clone from http://store.datalad.org/1d8/e51cc-2a93-11ea-bc67-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130922/MNINonLinear [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/MNINonLinear) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/T1w) -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/T1w to /home/me/usecases/HCP/hcp/HCP1200/130922/T1w -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/T1w/.git to /home/me/usecases/HCP/hcp/HCP1200/130922/T1w [INFO] Attempting to clone from http://store.datalad.org/239/fe7a6-2a93-11ea-bc67-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130922/T1w [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/T1w) [INFO] Failed to get annex.uuid configuration of repository origin | Instead, got: "core.repositoryformatversion\n0\NULcore.filemode\ntrue\NULcore.bare\ntrue\NUL" | This is unexpected; please check the network transport! [INFO] Cloning dataset to Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/unprocessed) -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/unprocessed to /home/me/usecases/HCP/hcp/HCP1200/130922/unprocessed -[INFO] Attempting to clone from http://store.datalad.org/100/a5212-2a93-11ea-b54a-0025904abcb0/unprocessed/.git to /home/me/usecases/HCP/hcp/HCP1200/130922/unprocessed [INFO] Attempting to clone from http://store.datalad.org/25e/ee1ba-2a93-11ea-bc67-0025904abcb0 to /home/me/usecases/HCP/hcp/HCP1200/130922/unprocessed [INFO] Completed clone attempts for Dataset(/home/me/usecases/HCP/hcp/HCP1200/130922/unprocessed) [INFO] Failed to get annex.uuid configuration of repository origin diff --git a/docs/usecases/_examples/collab-103 b/docs/usecases/_examples/collab-103 index d7516e519..1a6ca4cf8 100644 --- a/docs/usecases/_examples/collab-103 +++ b/docs/usecases/_examples/collab-103 @@ -1,9 +1,16 @@ $ datalad clone -d . https://github.com/psychoinformatics-de/studyforrest-data-structural.git src/forrest_structural -[INFO] Cloning https://github.com/psychoinformatics-de/studyforrest-data-structural.git [1 other candidates] into '/home/me/usecases/collab/myanalysis/src/forrest_structural' -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Cloning dataset to Dataset(/home/me/usecases/collab/myanalysis/src/forrest_structural) +[INFO] Attempting to clone from https://github.com/psychoinformatics-de/studyforrest-data-structural.git to /home/me/usecases/collab/myanalysis/src/forrest_structural +[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/usecases/collab/myanalysis/src/forrest_structural) +[INFO] Remote origin not usable by git-annex; setting annex-ignore +install(ok): src/forrest_structural (dataset) add(ok): src/forrest_structural (file) save(ok): . (dataset) -install(ok): src/forrest_structural (dataset) action summary: add (ok: 1) install (ok: 1) diff --git a/docs/usecases/_examples/collab-107 b/docs/usecases/_examples/collab-107 index 03048a00c..4e086f8b0 100644 --- a/docs/usecases/_examples/collab-107 +++ b/docs/usecases/_examples/collab-107 @@ -1,4 +1,6 @@ $ datalad clone /myanalysis bobs_analysis -[INFO] Cloning myanalysis into '/home/me/usecases/collab/bobs_analysis' +[INFO] Cloning dataset to Dataset(/home/me/usecases/collab/bobs_analysis) +[INFO] Attempting to clone from myanalysis to /home/me/usecases/collab/bobs_analysis +[INFO] Completed clone attempts for Dataset(/home/me/usecases/collab/bobs_analysis) install(ok): /home/me/usecases/collab/bobs_analysis (dataset) diff --git a/docs/usecases/_examples/collab-110 b/docs/usecases/_examples/collab-110 index af96c078b..ecea6a196 100644 --- a/docs/usecases/_examples/collab-110 +++ b/docs/usecases/_examples/collab-110 @@ -1,4 +1,10 @@ $ datalad update -s alice --merge -[INFO] Fetching updates for -[INFO] Applying updates to +[INFO] Fetching updates for Dataset(/home/me/usecases/collab/myanalysis) +[INFO] Start enumerating objects +[INFO] Start counting objects +[INFO] Start compressing objects +merge(ok): . (dataset) [Merged alice/master] update(ok): . (dataset) +action summary: + merge (ok: 1) + update (ok: 1) diff --git a/docs/usecases/_examples/dataset b/docs/usecases/_examples/dataset index 7761bfb65..28dc2eafc 100644 --- a/docs/usecases/_examples/dataset +++ b/docs/usecases/_examples/dataset @@ -1,4 +1,10 @@ $ datalad install https://github.com/psychoinformatics-de/studyforrest-data-phase2.git -[INFO] Cloning https://github.com/psychoinformatics-de/studyforrest-data-phase2.git [1 other candidates] into '/home/me/usecases/studyforrest/studyforrest-data-phase2' -[INFO] Remote origin not usable by git-annex; setting annex-ignore +[INFO] Cloning dataset to Dataset(/home/me/usecases/studyforrest/studyforrest-data-phase2) +[INFO] Attempting to clone from https://github.com/psychoinformatics-de/studyforrest-data-phase2.git to /home/me/usecases/studyforrest/studyforrest-data-phase2 +[INFO] Start enumerating objects +[INFO] Start counting objects +[INFO] Start receiving objects +[INFO] Start resolving deltas +[INFO] Completed clone attempts for Dataset(/home/me/usecases/studyforrest/studyforrest-data-phase2) +[INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): /home/me/usecases/studyforrest/studyforrest-data-phase2 (dataset) diff --git a/docs/usecases/_examples/dataset4 b/docs/usecases/_examples/dataset4 index db9affcc6..58a7841cb 100644 --- a/docs/usecases/_examples/dataset4 +++ b/docs/usecases/_examples/dataset4 @@ -1,5 +1,9 @@ $ git log --oneline --graph --decorate -* a6623bff (HEAD -> master, origin/master, origin/HEAD) [DATALAD] dataset aggregate metadata update +* b5306e2e (HEAD -> master, origin/master, origin/HEAD) Merge pull request #15 from adswa/ENH/README +|\ +| * 45a110f7 use standard textblock to explain DataLad datasets in README +|/ +* a6623bff [DATALAD] dataset aggregate metadata update * 72d535d5 Enable DataLad metadata extractors * 9c15094e [DATALAD] new dataset * d97455f5 [DATALAD] Set default backend for all files to be MD5E diff --git a/docs/usecases/_examples/prov-103 b/docs/usecases/_examples/prov-103 index ef9488d1a..9fe364569 100644 --- a/docs/usecases/_examples/prov-103 +++ b/docs/usecases/_examples/prov-103 @@ -1,7 +1,7 @@ $ git annex whereis sources/flowers.jpg whereis sources/flowers.jpg (2 copies) 00000000-0000-0000-0000-000000000001 -- web - f630c8c8-8d1d-4da2-8432-b0a7c5c964dd -- me@muninn:~/usecases/provenance/artproject [here] + bedd4a73-1508-4db9-9ccc-a85962c7a482 -- me@muninn:~/usecases/provenance/artproject [here] web: https://upload.wikimedia.org/wikipedia/commons/a/a5/Flower_poster_2.jpg ok diff --git a/docs/usecases/_examples/prov-106 b/docs/usecases/_examples/prov-106 index f4be9e062..5d4487f29 100644 --- a/docs/usecases/_examples/prov-106 +++ b/docs/usecases/_examples/prov-106 @@ -1,4 +1,4 @@ $ git log --oneline HEAD~3..HEAD -14d8e8f [DATALAD RUNCMD] extract pimpernel -999b4f5 [DATALAD RUNCMD] extract st-bernard lily -bc38bb3 Added flower mosaic from wikimedia +ed908ca [DATALAD RUNCMD] extract pimpernel +b20f959 [DATALAD RUNCMD] extract st-bernard lily +cbf8e0e Added flower mosaic from wikimedia diff --git a/docs/usecases/_examples/prov-109 b/docs/usecases/_examples/prov-109 index 4654a0008..1b87a8977 100644 --- a/docs/usecases/_examples/prov-109 +++ b/docs/usecases/_examples/prov-109 @@ -1,2 +1,2 @@ $ git log -1 --oneline HEAD -a6e322c [DATALAD RUNCMD] blur image +14a43c2 [DATALAD RUNCMD] blur image diff --git a/docs/usecases/_examples/prov-110 b/docs/usecases/_examples/prov-110 index 40a60366d..d2483ebde 100644 --- a/docs/usecases/_examples/prov-110 +++ b/docs/usecases/_examples/prov-110 @@ -1,5 +1,5 @@ -$ datalad rerun a6e322c794ef39bea0fb2a077f8eac293d943550 +$ datalad rerun 14a43c23e30c9a57e09655e9b7c714ba2aa33e73 [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/usecases/_examples/prov-111 b/docs/usecases/_examples/prov-111 index b626be076..0e1277f69 100644 --- a/docs/usecases/_examples/prov-111 +++ b/docs/usecases/_examples/prov-111 @@ -1,2 +1,2 @@ $ git reset --hard HEAD~1 -HEAD is now at a6e322c [DATALAD RUNCMD] blur image +HEAD is now at 14a43c2 [DATALAD RUNCMD] blur image diff --git a/docs/usecases/_examples/prov-113 b/docs/usecases/_examples/prov-113 index acf539548..93246031a 100644 --- a/docs/usecases/_examples/prov-113 +++ b/docs/usecases/_examples/prov-113 @@ -1,10 +1,10 @@ $ git log --oneline --graph master replay -* 2079cff [DATALAD RUNCMD] blur image -* 9b9ee7b [DATALAD RUNCMD] extract pimpernel -* 92a125b [DATALAD RUNCMD] extract st-bernard lily -| * a6e322c [DATALAD RUNCMD] blur image -| * 14d8e8f [DATALAD RUNCMD] extract pimpernel -| * 999b4f5 [DATALAD RUNCMD] extract st-bernard lily +* 0b0428a [DATALAD RUNCMD] blur image +* 3c25f9a [DATALAD RUNCMD] extract pimpernel +* 1c60430 [DATALAD RUNCMD] extract st-bernard lily +| * 14a43c2 [DATALAD RUNCMD] blur image +| * ed908ca [DATALAD RUNCMD] extract pimpernel +| * b20f959 [DATALAD RUNCMD] extract st-bernard lily |/ -* bc38bb3 Added flower mosaic from wikimedia -* e79b3ff [DATALAD] new dataset +* cbf8e0e Added flower mosaic from wikimedia +* 452093d [DATALAD] new dataset diff --git a/docs/usecases/_examples/prov-115 b/docs/usecases/_examples/prov-115 index 0e41120a2..8f3b5c246 100644 --- a/docs/usecases/_examples/prov-115 +++ b/docs/usecases/_examples/prov-115 @@ -1,7 +1,7 @@ $ git log --oneline --left-right --cherry-mark master...replay -> 2079cff [DATALAD RUNCMD] blur image -= 9b9ee7b [DATALAD RUNCMD] extract pimpernel -= 92a125b [DATALAD RUNCMD] extract st-bernard lily -< a6e322c [DATALAD RUNCMD] blur image -= 14d8e8f [DATALAD RUNCMD] extract pimpernel -= 999b4f5 [DATALAD RUNCMD] extract st-bernard lily +> 0b0428a [DATALAD RUNCMD] blur image += 3c25f9a [DATALAD RUNCMD] extract pimpernel += 1c60430 [DATALAD RUNCMD] extract st-bernard lily +< 14a43c2 [DATALAD RUNCMD] blur image += ed908ca [DATALAD RUNCMD] extract pimpernel += b20f959 [DATALAD RUNCMD] extract st-bernard lily diff --git a/docs/usecases/_examples/repro-102 b/docs/usecases/_examples/repro-102 index 50c2ca68d..cf4ffa374 100644 --- a/docs/usecases/_examples/repro-102 +++ b/docs/usecases/_examples/repro-102 @@ -1,10 +1,17 @@ $ cd demo $ datalad clone -d . ///openfmri/ds000001 inputs/ds000001 -[INFO] Cloning http://datasets.datalad.org/openfmri/ds000001 [1 other candidates] into '/home/me/usecases/repro/demo/inputs/ds000001' +[INFO] Cloning dataset to Dataset(/home/me/usecases/repro/demo/inputs/ds000001) +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000001 to /home/me/usecases/repro/demo/inputs/ds000001 +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000001/.git to /home/me/usecases/repro/demo/inputs/ds000001 +[INFO] Start counting objects +[INFO] Start compressing objects +[INFO] Start receiving objects +[INFO] Start resolving deltas +[INFO] Completed clone attempts for Dataset(/home/me/usecases/repro/demo/inputs/ds000001) +install(ok): inputs/ds000001 (dataset) add(ok): inputs/ds000001 (file) add(ok): .gitmodules (file) save(ok): . (dataset) -install(ok): inputs/ds000001 (dataset) action summary: add (ok: 2) install (ok: 1) diff --git a/docs/usecases/_examples/repro-103 b/docs/usecases/_examples/repro-103 index 39b8f4ca0..50946382c 100644 --- a/docs/usecases/_examples/repro-103 +++ b/docs/usecases/_examples/repro-103 @@ -1,10 +1,17 @@ $ cd demo $ datalad clone -d . ///openfmri/ds000002 inputs/ds000002 -[INFO] Cloning http://datasets.datalad.org/openfmri/ds000002 [1 other candidates] into '/home/me/usecases/repro/demo/inputs/ds000002' +[INFO] Cloning dataset to Dataset(/home/me/usecases/repro/demo/inputs/ds000002) +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000002 to /home/me/usecases/repro/demo/inputs/ds000002 +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000002/.git to /home/me/usecases/repro/demo/inputs/ds000002 +[INFO] Start counting objects +[INFO] Start compressing objects +[INFO] Start receiving objects +[INFO] Start resolving deltas +[INFO] Completed clone attempts for Dataset(/home/me/usecases/repro/demo/inputs/ds000002) +install(ok): inputs/ds000002 (dataset) add(ok): inputs/ds000002 (file) add(ok): .gitmodules (file) save(ok): . (dataset) -install(ok): inputs/ds000002 (dataset) action summary: add (ok: 2) install (ok: 1) diff --git a/docs/usecases/_examples/repro-106 b/docs/usecases/_examples/repro-106 index 0b69bd397..2e85c1d94 100644 --- a/docs/usecases/_examples/repro-106 +++ b/docs/usecases/_examples/repro-106 @@ -1,4 +1,6 @@ $ datalad -C inputs/ds000001 status --annex $ datalad -C inputs/ds000002 status --annex 130 annex'd files (2.3 GB recorded total size) +nothing to save, working tree clean 274 annex'd files (2.7 GB recorded total size) +nothing to save, working tree clean diff --git a/docs/usecases/_examples/repro-110 b/docs/usecases/_examples/repro-110 index 120b47626..98ebac77a 100644 --- a/docs/usecases/_examples/repro-110 +++ b/docs/usecases/_examples/repro-110 @@ -1,7 +1,7 @@ $ git show --stat -commit 5de61bab79e7bb1acd4f1ce988cb83e5266ac99d +commit 27ca92d1ec7a0ba8185bfe444a4a31a73b82f555 Author: Elena Piscopia -Date: Thu Dec 19 09:57:00 2019 +0100 +Date: Tue Jun 23 20:45:32 2020 +0200 [DATALAD RUNCMD] run brain extract workflow @@ -9,7 +9,7 @@ Date: Thu Dec 19 09:57:00 2019 +0100 { "chain": [], "cmd": "bash -e code/brain_extraction.sh inputs/ds000001/sub-01/anat/sub-01_T1w.nii.gz inputs/ds000002/sub-01/anat/sub-01_T1w.nii.gz", - "dsid": "78292bba-223d-11ea-af8b-e86a64c8054c", + "dsid": "a89af03a-b581-11ea-90a2-3119e6b9cf19", "exit": 0, "extra_inputs": [], "inputs": [ diff --git a/docs/usecases/_examples/repro-117 b/docs/usecases/_examples/repro-117 index b0b6eaa59..b6e187595 100644 --- a/docs/usecases/_examples/repro-117 +++ b/docs/usecases/_examples/repro-117 @@ -1,7 +1,19 @@ $ datalad rerun [INFO] Making sure inputs are available (this may take some time) -[INFO] Cloning http://datasets.datalad.org/openfmri/ds000001/.git into '/home/me/usecases/repro/demo/inputs/ds000001' -[INFO] Cloning http://datasets.datalad.org/openfmri/ds000002/.git into '/home/me/usecases/repro/demo/inputs/ds000002' +[INFO] Cloning dataset to Dataset(/home/me/usecases/repro/demo/inputs/ds000001) +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000001/.git to /home/me/usecases/repro/demo/inputs/ds000001 +[INFO] Start counting objects +[INFO] Start compressing objects +[INFO] Start receiving objects +[INFO] Start resolving deltas +[INFO] Completed clone attempts for Dataset(/home/me/usecases/repro/demo/inputs/ds000001) +[INFO] Cloning dataset to Dataset(/home/me/usecases/repro/demo/inputs/ds000002) +[INFO] Attempting to clone from http://datasets.datalad.org/openfmri/ds000002/.git to /home/me/usecases/repro/demo/inputs/ds000002 +[INFO] Start counting objects +[INFO] Start compressing objects +[INFO] Start receiving objects +[INFO] Start resolving deltas +[INFO] Completed clone attempts for Dataset(/home/me/usecases/repro/demo/inputs/ds000002) [INFO] == Command start (output follows) ===== action summary: get (notneeded: 4) From 13d7157fed80019b130ddd60313ef8a62acf1e59 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Tue, 23 Jun 2020 21:21:19 +0200 Subject: [PATCH 6/7] update submodule --- docs/artwork | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/artwork b/docs/artwork index bff3572d1..5a3538d7e 160000 --- a/docs/artwork +++ b/docs/artwork @@ -1 +1 @@ -Subproject commit bff3572d18e2e7563a0a8f0893710c3f8a40eba5 +Subproject commit 5a3538d7ead8d6c81005ab6b6485d5ca5268adea From 24bd7b20b046f64d78cccd58d5519f6873d05d8b Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Tue, 23 Jun 2020 21:23:08 +0200 Subject: [PATCH 7/7] add @DorienHuijser to zenodo.json --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index d6d6eb761..e5badf993 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -121,6 +121,11 @@ "name": "Mönch, Christian", "affiliation": "Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7)" }, + { + "affiliation": "Erasmus School of Social and Behavioral Sciences, Erasmus University Rotterdam", + "name": "Huijser, Dorien", + "orcid": "0000-0003-3282-8083" + }, { "name": "Hanke, Michael", "affiliation": "Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany and Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany",