From d3b31eff814e67c562dcd0f2f8ea99d47ededadc Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Thu, 2 Nov 2023 09:41:10 +0100 Subject: [PATCH 1/3] Add more log filters --- docs/conf.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index f4f9698ae..48c991d1c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -75,6 +75,11 @@ (r'\n\[INFO\] Downloading \S+ into .*', ''), (r'\n\[INFO\] Completed clone attempts for Dataset.*', ''), (r'\n\[INFO\] Fetching updates for Dataset.*', ''), + (r'\n\[INFO\] Unlocking files', ''), + (r'\n\[INFO\] Recording unlocked state in git', ''), + (r'\n\[INFO\] Completed unlocking files', ''), + (r'\n\[INFO\] Making sure inputs are available (this may take some time)', ''), + (r'\n\[INFO\] Creating a new annex repo at .*', ''), # annoying always-true test for a non-annex git remote (r'\n\[INFO\] \S+/config download failed: Not Found', ''), # datalad push step-progress @@ -82,6 +87,7 @@ (r'\n\[INFO\] Push refspecs', ''), (r'\n\[INFO\] Transfer data', ''), (r'\n\[INFO\] Update availability information', ''), + (r'\n\[INFO\] Finished push of Dataset.*', ''), ] # pre-crafted artificial environment to run the code examples in # start with all datalad settings From 4ef928f88821778b3b69c004d27d24e33fc0662d Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Thu, 2 Nov 2023 09:57:30 +0100 Subject: [PATCH 2/3] Fix log filters The command *output* is filtered. So the respective first line will not start with a newline. The change removes the newline *after* the message, rather than that in front of it. --- docs/conf.py | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 48c991d1c..9007b7ffa 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -68,26 +68,26 @@ (r'(action summary:(\n^ \S+ \(\S+(? Date: Thu, 2 Nov 2023 10:33:13 +0100 Subject: [PATCH 3/3] apply diff --- docs/basics/_examples/DL-101-102-112 | 1 - docs/basics/_examples/DL-101-105-102 | 1 - docs/basics/_examples/DL-101-111-101 | 3 --- docs/basics/_examples/DL-101-112-104 | 3 --- docs/basics/_examples/DL-101-112-106 | 3 --- docs/basics/_examples/DL-101-116-102 | 1 - docs/basics/_examples/DL-101-116-107 | 1 - docs/basics/_examples/DL-101-119-102 | 1 - docs/basics/_examples/DL-101-121-101 | 1 - docs/basics/_examples/DL-101-121-106 | 1 - docs/basics/_examples/DL-101-121-110 | 1 - docs/basics/_examples/DL-101-130-102 | 1 - docs/basics/_examples/DL-101-130-105 | 1 - docs/basics/_examples/DL-101-130-118 | 2 -- docs/basics/_examples/DL-101-130-119 | 1 - docs/basics/_examples/DL-101-130-120 | 1 - docs/basics/_examples/DL-101-130-121 | 2 +- docs/basics/_examples/DL-101-133-105 | 3 --- docs/basics/_examples/DL-101-136-162 | 1 - docs/basics/_examples/DL-101-136-165 | 1 - docs/basics/_examples/DL-101-136-170 | 1 - docs/basics/_examples/DL-101-136-181 | 1 - docs/basics/_examples/DL-101-136-183 | 1 - docs/basics/_examples/DL-101-137-114 | 2 +- docs/basics/_examples/DL-101-137-115 | 3 --- docs/basics/_examples/DL-101-137-117 | 2 +- docs/basics/_examples/DL-101-139-102 | 2 -- docs/basics/_examples/DL-101-139-106 | 2 -- docs/basics/_examples/DL-101-139-107 | 1 - docs/basics/_examples/DL-101-141-101 | 2 -- docs/beyond_basics/_examples/DL-101-147-104 | 4 ++-- docs/beyond_basics/_examples/DL-101-147-107 | 3 --- docs/beyond_basics/_examples/DL-101-147-108 | 4 ++-- docs/beyond_basics/_examples/DL-101-147-110 | 3 --- docs/beyond_basics/_examples/DL-101-147-112 | 10 +++++----- docs/beyond_basics/_examples/DL-101-147-124 | 1 - docs/beyond_basics/_examples/DL-101-147-127 | 1 - docs/beyond_basics/_examples/DL-101-149-01 | 1 - docs/beyond_basics/_examples/DL-101-149-02 | 1 - docs/beyond_basics/_examples/DL-101-149-12 | 4 ++-- docs/beyond_basics/_examples/DL-101-168-104 | 1 - docs/beyond_basics/_examples/DL-101-168-110 | 2 +- docs/beyond_basics/_examples/DL-101-168-114 | 1 - docs/beyond_basics/_examples/DL-101-168-131 | 1 - docs/beyond_basics/_examples/DL-101-168-141 | 4 +--- docs/beyond_basics/_examples/DL-101-168-151 | 2 +- docs/beyond_basics/_examples/DL-101-168-155 | 2 +- docs/beyond_basics/_examples/DL-101-168-159 | 2 +- docs/beyond_basics/_examples/DL-101-168-160 | 2 +- docs/beyond_basics/_examples/DL-101-168-165 | 4 ++-- docs/beyond_basics/_examples/DL-101-168-166 | 6 +++--- docs/beyond_basics/_examples/DL-101-168-178 | 9 +++------ docs/beyond_basics/_examples/DL-101-168-179 | 6 +++--- docs/beyond_basics/_examples/DL-101-181-101 | 1 - docs/beyond_basics/_examples/DL-101-181-108 | 2 +- 55 files changed, 32 insertions(+), 92 deletions(-) diff --git a/docs/basics/_examples/DL-101-102-112 b/docs/basics/_examples/DL-101-102-112 index 5cc9407bc..2014e5e9a 100644 --- a/docs/basics/_examples/DL-101-102-112 +++ b/docs/basics/_examples/DL-101-102-112 @@ -3,7 +3,6 @@ $ datalad download-url \ --dataset . \ -m "add beginners guide on bash" \ -O books/bash_guide.pdf -[INFO] Downloading 'https://www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf' into '/home/me/dl-101/DataLad-101/books/bash_guide.pdf' download_url(ok): /home/me/dl-101/DataLad-101/books/bash_guide.pdf (file) add(ok): books/bash_guide.pdf (file) save(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-105-102 b/docs/basics/_examples/DL-101-105-102 index 055fa8518..c20936891 100644 --- a/docs/basics/_examples/DL-101-105-102 +++ b/docs/basics/_examples/DL-101-105-102 @@ -1,6 +1,5 @@ $ datalad clone --dataset . \ https://github.com/datalad-datasets/longnow-podcasts.git recordings/longnow -[INFO] Attempting a clone into /home/me/dl-101/DataLad-101/recordings/longnow [INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): recordings/longnow (dataset) add(ok): recordings/longnow (dataset) diff --git a/docs/basics/_examples/DL-101-111-101 b/docs/basics/_examples/DL-101-111-101 index 4c9976a66..6aa3c81d0 100644 --- a/docs/basics/_examples/DL-101-111-101 +++ b/docs/basics/_examples/DL-101-111-101 @@ -1,5 +1,2 @@ $ datalad unlock recordings/salt_logo_small.jpg -[INFO] Unlocking files unlock(ok): recordings/salt_logo_small.jpg (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files diff --git a/docs/basics/_examples/DL-101-112-104 b/docs/basics/_examples/DL-101-112-104 index 7f1ba6057..e8272d739 100644 --- a/docs/basics/_examples/DL-101-112-104 +++ b/docs/basics/_examples/DL-101-112-104 @@ -3,10 +3,7 @@ $ datalad run -m "Resize logo for slides" \ --output "recordings/interval_logo_small.jpg" \ "convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_interval.jpg recordings/interval_logo_small.jpg" [INFO] Making sure inputs are available (this may take some time) -[INFO] Unlocking files unlock(ok): recordings/interval_logo_small.jpg (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101 (dataset) [convert -resize 400x400 recordings/longn...] diff --git a/docs/basics/_examples/DL-101-112-106 b/docs/basics/_examples/DL-101-112-106 index dd0c1d124..52b90863c 100644 --- a/docs/basics/_examples/DL-101-112-106 +++ b/docs/basics/_examples/DL-101-112-106 @@ -4,10 +4,7 @@ $ datalad run -m "Resize logo for slides" \ --explicit \ "convert -resize 400x400 recordings/longnow/.datalad/feed_metadata/logo_salt.jpg recordings/salt_logo_small.jpg" [INFO] Making sure inputs are available (this may take some time) -[INFO] Unlocking files unlock(ok): recordings/salt_logo_small.jpg (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101 (dataset) [convert -resize 400x400 recordings/longn...] diff --git a/docs/basics/_examples/DL-101-116-102 b/docs/basics/_examples/DL-101-116-102 index 3ea1bd6bc..97a061a03 100644 --- a/docs/basics/_examples/DL-101-116-102 +++ b/docs/basics/_examples/DL-101-116-102 @@ -1,4 +1,3 @@ $ cd mock_user $ datalad clone --description "DataLad-101 in mock_user" ../DataLad-101 -[INFO] Attempting a clone into /home/me/dl-101/mock_user/DataLad-101 install(ok): /home/me/dl-101/mock_user/DataLad-101 (dataset) diff --git a/docs/basics/_examples/DL-101-116-107 b/docs/basics/_examples/DL-101-116-107 index 482e55c94..0cd2e9f78 100644 --- a/docs/basics/_examples/DL-101-116-107 +++ b/docs/basics/_examples/DL-101-116-107 @@ -1,4 +1,3 @@ $ datalad get -n recordings/longnow -[INFO] Attempting a clone into /home/me/dl-101/mock_user/DataLad-101/recordings/longnow [INFO] Remote origin not usable by git-annex; setting annex-ignore 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-101-119-102 b/docs/basics/_examples/DL-101-119-102 index c227b704b..888f04260 100644 --- a/docs/basics/_examples/DL-101-119-102 +++ b/docs/basics/_examples/DL-101-119-102 @@ -1,5 +1,4 @@ $ datalad update --how merge -[INFO] Fetching updates for Dataset(/home/me/dl-101/mock_user/DataLad-101) merge(ok): . (dataset) [Merged origin/main] update.annex_merge(ok): . (dataset) [Merged annex branch] update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-121-101 b/docs/basics/_examples/DL-101-121-101 index 1b68e4328..e06e8f2fa 100644 --- a/docs/basics/_examples/DL-101-121-101 +++ b/docs/basics/_examples/DL-101-121-101 @@ -7,7 +7,6 @@ $ datalad download-url \ -m "Include nesting demo from datalad website" \ -O code/nested_repos.sh \ https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1/content/asciicast/seamless_nested_repos.sh -[INFO] Downloading 'https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1/content/asciicast/seamless_nested_repos.sh' into '/home/me/dl-101/mock_user/DataLad-101/code/nested_repos.sh' download_url(ok): /home/me/dl-101/mock_user/DataLad-101/code/nested_repos.sh (file) add(ok): code/nested_repos.sh (file) save(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-121-106 b/docs/basics/_examples/DL-101-121-106 index 5db41d76b..22543bfe4 100644 --- a/docs/basics/_examples/DL-101-121-106 +++ b/docs/basics/_examples/DL-101-121-106 @@ -1,3 +1,2 @@ $ datalad update -s roommate -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-121-110 b/docs/basics/_examples/DL-101-121-110 index 14b1e5102..9bc135662 100644 --- a/docs/basics/_examples/DL-101-121-110 +++ b/docs/basics/_examples/DL-101-121-110 @@ -1,5 +1,4 @@ $ datalad update --how merge -s roommate -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) merge(ok): . (dataset) [Merged roommate/main] update.annex_merge(ok): . (dataset) [Merged annex branch] update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-130-102 b/docs/basics/_examples/DL-101-130-102 index 08d14c34c..1a982639d 100644 --- a/docs/basics/_examples/DL-101-130-102 +++ b/docs/basics/_examples/DL-101-130-102 @@ -1,6 +1,5 @@ $ cd iris_data $ datalad download-url https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv -[INFO] Downloading 'https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad✂SHA1/iris.csv' into '/home/me/dl-101/iris_data/' download_url(ok): /home/me/dl-101/iris_data/iris.csv (file) add(ok): iris.csv (file) save(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-130-105 b/docs/basics/_examples/DL-101-130-105 index f995014b1..9b15e6169 100644 --- a/docs/basics/_examples/DL-101-130-105 +++ b/docs/basics/_examples/DL-101-130-105 @@ -3,7 +3,6 @@ $ cd midterm_project $ datalad clone -d . \ https://github.com/datalad-handbook/iris_data.git \ input/ -[INFO] Attempting a clone into /home/me/dl-101/DataLad-101/midterm_project/input [INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): input (dataset) add(ok): input (dataset) diff --git a/docs/basics/_examples/DL-101-130-118 b/docs/basics/_examples/DL-101-130-118 index ede9e474d..159d4ea9b 100644 --- a/docs/basics/_examples/DL-101-130-118 +++ b/docs/basics/_examples/DL-101-130-118 @@ -1,7 +1,5 @@ $ datalad push --to github -[INFO] Determine push target 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 ✂FROM✂..✂TO✂] publish(ok): . (dataset) [refs/heads/main->github:refs/heads/main [new branch]] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) diff --git a/docs/basics/_examples/DL-101-130-119 b/docs/basics/_examples/DL-101-130-119 index e1c3eb6bd..bc25f836f 100644 --- a/docs/basics/_examples/DL-101-130-119 +++ b/docs/basics/_examples/DL-101-130-119 @@ -1,5 +1,4 @@ $ cd ../../ $ datalad clone "https://github.com/adswa/midtermproject.git" -[INFO] Attempting a clone into /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 7cf37d2e8..2698c8c26 100644 --- a/docs/basics/_examples/DL-101-130-120 +++ b/docs/basics/_examples/DL-101-130-120 @@ -1,6 +1,5 @@ $ cd midtermproject $ datalad get input/iris.csv -[INFO] Attempting a clone into /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...] diff --git a/docs/basics/_examples/DL-101-130-121 b/docs/basics/_examples/DL-101-130-121 index df8709f57..03c2298c8 100644 --- a/docs/basics/_examples/DL-101-130-121 +++ b/docs/basics/_examples/DL-101-130-121 @@ -1,3 +1,3 @@ $ datalad get prediction_report.csv pairwise_relationships.png -get(error): pairwise_relationships.png (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): prediction_report.csv (file) [not available; (Note that these git remotes have annex-ignore set: origin)] +get(error): pairwise_relationships.png (file) [not available; (Note that these git remotes have annex-ignore set: origin)] diff --git a/docs/basics/_examples/DL-101-133-105 b/docs/basics/_examples/DL-101-133-105 index f5aaba0a9..3726c3140 100644 --- a/docs/basics/_examples/DL-101-133-105 +++ b/docs/basics/_examples/DL-101-133-105 @@ -5,11 +5,8 @@ $ datalad containers-run -m "rerun analysis in container" \ --output "prediction_report.csv" \ "python3 code/script.py {inputs} {outputs}" [INFO] Making sure inputs are available (this may take some time) -[INFO] Unlocking files unlock(ok): pairwise_relationships.png (file) unlock(ok): prediction_report.csv (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/dl-101/DataLad-101/midterm_project (dataset) [singularity exec -B /home/me/dl-101/Data...] diff --git a/docs/basics/_examples/DL-101-136-162 b/docs/basics/_examples/DL-101-136-162 index 136206626..fceca12e0 100644 --- a/docs/basics/_examples/DL-101-136-162 +++ b/docs/basics/_examples/DL-101-136-162 @@ -2,7 +2,6 @@ $ cd ../DataLad-101 # attempt a datalad update $ datalad update -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) update(error): . (dataset) [Fetch failed: CommandError(CommandError: 'git -c diff.ignoreSubmodules=none -c core.quotepath=false fetch --verbose --progress --no-recurse-submodules --prune roommate' failed with exitcode 128 under /home/me/dl-101/DataLad-101 [err: 'fatal: '../mock_user/DataLad-101' does not appear to be a git repository fatal: Could not read from remote repository. diff --git a/docs/basics/_examples/DL-101-136-165 b/docs/basics/_examples/DL-101-136-165 index 994f13f24..7933cae3f 100644 --- a/docs/basics/_examples/DL-101-136-165 +++ b/docs/basics/_examples/DL-101-136-165 @@ -1,3 +1,2 @@ $ datalad update -[INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) update(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-136-170 b/docs/basics/_examples/DL-101-136-170 index 65ddc776d..85e3d89e9 100644 --- a/docs/basics/_examples/DL-101-136-170 +++ b/docs/basics/_examples/DL-101-136-170 @@ -3,7 +3,6 @@ $ datalad download-url -m "Added flower mosaic from wikimedia" \ https://upload.wikimedia.org/wikipedia/commons/a/a5/Flower_poster_2.jpg \ --path flowers.jpg $ ls -l flowers.jpg -[INFO] Downloading 'https://upload.wikimedia.org/wikipedia/commons/a/a5/Flower_poster_2.jpg' into '/home/me/dl-101/DataLad-101/flowers.jpg' download_url(ok): /home/me/dl-101/DataLad-101/flowers.jpg (file) add(ok): flowers.jpg (file) save(ok): . (dataset) diff --git a/docs/basics/_examples/DL-101-136-181 b/docs/basics/_examples/DL-101-136-181 index 0f9104dbc..fdaab2963 100644 --- a/docs/basics/_examples/DL-101-136-181 +++ b/docs/basics/_examples/DL-101-136-181 @@ -2,7 +2,6 @@ $ datalad clone -d . \ https://github.com/datalad-datasets/disneyanimation-cloud.git \ cloud -[INFO] Attempting a clone into /home/me/dl-101/DataLad-101/cloud [INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): cloud (dataset) add(ok): cloud (dataset) diff --git a/docs/basics/_examples/DL-101-136-183 b/docs/basics/_examples/DL-101-136-183 index 446424376..be6a622c9 100644 --- a/docs/basics/_examples/DL-101-136-183 +++ b/docs/basics/_examples/DL-101-136-183 @@ -1,4 +1,3 @@ $ datalad get -n cloud -[INFO] Attempting a clone into /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] diff --git a/docs/basics/_examples/DL-101-137-114 b/docs/basics/_examples/DL-101-137-114 index c0cea3fa7..2dd4e4521 100644 --- a/docs/basics/_examples/DL-101-137-114 +++ b/docs/basics/_examples/DL-101-137-114 @@ -1,2 +1,2 @@ $ ls -l apdffile.pdf -lrwxrwxrwx 1 elena elena 122 2019-06-18 16:13 apdffile.pdf -> .git/annex/objects/W8/PK/✂/MD5E-s1216--8bddf647✂MD5.pdf +lrwxrwxrwx 1 elena elena 122 2019-06-18 16:13 apdffile.pdf -> .git/annex/objects/JQ/ZF/✂/MD5E-s1216--e18f278f✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-137-115 b/docs/basics/_examples/DL-101-137-115 index 72a1bae28..4e957ce01 100644 --- a/docs/basics/_examples/DL-101-137-115 +++ b/docs/basics/_examples/DL-101-137-115 @@ -1,5 +1,2 @@ $ datalad unlock apdffile.pdf -[INFO] Unlocking files unlock(ok): apdffile.pdf (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files diff --git a/docs/basics/_examples/DL-101-137-117 b/docs/basics/_examples/DL-101-137-117 index 27d3a0bab..aa720288a 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 -98eb974 [DATALAD] Recorded changes +ecab714 [DATALAD] Recorded changes 4bdb06c save my favorite Git joke 996f459 remove obsolete subds diff --git a/docs/basics/_examples/DL-101-139-102 b/docs/basics/_examples/DL-101-139-102 index 038caea78..9a862378d 100644 --- a/docs/basics/_examples/DL-101-139-102 +++ b/docs/basics/_examples/DL-101-139-102 @@ -1,9 +1,7 @@ $ datalad push --to gin -[INFO] Determine push target 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 ✂FROM✂..✂TO✂] publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main [new branch]] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) diff --git a/docs/basics/_examples/DL-101-139-106 b/docs/basics/_examples/DL-101-139-106 index d22a45da3..c39407a45 100644 --- a/docs/basics/_examples/DL-101-139-106 +++ b/docs/basics/_examples/DL-101-139-106 @@ -1,6 +1,4 @@ $ datalad push --to gin -[INFO] Determine push target publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main 6d3d93b..344b0ec] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) action summary: publish (notneeded: 1, ok: 1) diff --git a/docs/basics/_examples/DL-101-139-107 b/docs/basics/_examples/DL-101-139-107 index 4fb9280e1..6cedf0e6d 100644 --- a/docs/basics/_examples/DL-101-139-107 +++ b/docs/basics/_examples/DL-101-139-107 @@ -1,3 +1,2 @@ $ datalad clone https://gin.g-node.org/adswa/DataLad-101 -[INFO] Attempting a clone into /home/me/dl-101/clone_of_dl-101/DataLad-101 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 e0b0bb945..22dccc744 100644 --- a/docs/basics/_examples/DL-101-141-101 +++ b/docs/basics/_examples/DL-101-141-101 @@ -1,12 +1,10 @@ $ datalad push --to roommate -[INFO] Determine push target copy(ok): books/TLCL.pdf (file) [to roommate...] copy(ok): books/bash_guide.pdf (file) [to roommate...] copy(ok): books/byte-of-python.pdf (file) [to roommate...] [INFO] Finished publish(ok): . (dataset) [refs/heads/git-annex->roommate:refs/heads/git-annex ✂FROM✂..✂TO✂] publish(error): . (dataset) [refs/heads/main->roommate:refs/heads/main [remote rejected] (branch is currently checked out)] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) action summary: copy (ok: 3) publish (error: 1, ok: 1) diff --git a/docs/beyond_basics/_examples/DL-101-147-104 b/docs/beyond_basics/_examples/DL-101-147-104 index 96edc7f9e..7a6aeae05 100644 --- a/docs/beyond_basics/_examples/DL-101-147-104 +++ b/docs/beyond_basics/_examples/DL-101-147-104 @@ -1,6 +1,6 @@ $ datalad siblings .: here(+) [git] -.: ria-backup-storage(+) [ora] -.: gin(+) [/home/me/pushes/DataLad-101 (git)] .: roommate(+) [../mock_user/DataLad-101 (git)] .: ria-backup(-) [/home/me/myriastore/e3e/70682-c209-4cac-629f-6fbed82c07cd (git)] +.: gin(+) [/home/me/pushes/DataLad-101 (git)] +.: ria-backup-storage(+) [ora] diff --git a/docs/beyond_basics/_examples/DL-101-147-107 b/docs/beyond_basics/_examples/DL-101-147-107 index 501574ec4..22e584c3b 100644 --- a/docs/beyond_basics/_examples/DL-101-147-107 +++ b/docs/beyond_basics/_examples/DL-101-147-107 @@ -1,10 +1,7 @@ $ datalad push --to ria-backup -[INFO] Determine push target copy(ok): books/TLCL.pdf (file) [to ria-backup-storage...] copy(ok): books/bash_guide.pdf (file) [to ria-backup-storage...] copy(ok): books/byte-of-python.pdf (file) [to ria-backup-storage...] copy(ok): books/progit.pdf (file) [to ria-backup-storage...] publish(ok): . (dataset) [refs/heads/main->ria-backup:refs/heads/main [new branch]] publish(ok): . (dataset) [refs/heads/git-annex->ria-backup:refs/heads/git-annex [new branch]] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101) diff --git a/docs/beyond_basics/_examples/DL-101-147-108 b/docs/beyond_basics/_examples/DL-101-147-108 index 51eb74326..6e527eb4e 100644 --- a/docs/beyond_basics/_examples/DL-101-147-108 +++ b/docs/beyond_basics/_examples/DL-101-147-108 @@ -47,8 +47,8 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-94b1d055✂SHA1.idx -│   │   └── pack-94b1d055✂SHA1.pack +│   │   ├── pack-f1636323✂SHA1.idx +│   │   └── pack-f1636323✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-147-110 b/docs/beyond_basics/_examples/DL-101-147-110 index 0ef0e795d..31d9349aa 100644 --- a/docs/beyond_basics/_examples/DL-101-147-110 +++ b/docs/beyond_basics/_examples/DL-101-147-110 @@ -1,9 +1,6 @@ $ datalad push --to ria-backup -[INFO] Determine push target copy(ok): .datalad/environments/midterm-software/image (file) [to ria-backup-storage...] copy(ok): pairwise_relationships.png (file) [to ria-backup-storage...] copy(ok): prediction_report.csv (file) [to ria-backup-storage...] publish(ok): . (dataset) [refs/heads/main->ria-backup:refs/heads/main [new branch]] publish(ok): . (dataset) [refs/heads/git-annex->ria-backup:refs/heads/git-annex [new branch]] -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) -[INFO] Finished push of Dataset(/home/me/dl-101/DataLad-101/midterm_project) diff --git a/docs/beyond_basics/_examples/DL-101-147-112 b/docs/beyond_basics/_examples/DL-101-147-112 index 6e79a2cbf..4ba2035d9 100644 --- a/docs/beyond_basics/_examples/DL-101-147-112 +++ b/docs/beyond_basics/_examples/DL-101-147-112 @@ -43,9 +43,9 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-8a336fbd✂SHA1.idx -│   │   └── pack-8a336fbd✂SHA1.pack -│   ├── ora-remote-5762bcab-e464-4ccd-898f-77e45c8dab51 +│   │   ├── pack-5020f73a✂SHA1.idx +│   │   └── pack-5020f73a✂SHA1.pack +│   ├── ora-remote-644719fb-0077-49d2-b1c7-006cc9f7c7c5 │   │   └── transfer │   ├── refs │   │   ├── heads @@ -98,8 +98,8 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-94b1d055✂SHA1.idx -│   │   └── pack-94b1d055✂SHA1.pack +│   │   ├── pack-f1636323✂SHA1.idx +│   │   └── pack-f1636323✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-147-124 b/docs/beyond_basics/_examples/DL-101-147-124 index e48f08cd3..f0e5de10c 100644 --- a/docs/beyond_basics/_examples/DL-101-147-124 +++ b/docs/beyond_basics/_examples/DL-101-147-124 @@ -1,5 +1,4 @@ datalad clone ria+file:///home/me/myriastore#~midterm_project -[INFO] Attempting a clone into /home/me/beyond_basics/midterm_project [INFO] Configure additional publication dependency on "ria-backup-storage" configure-sibling(ok): . (sibling) install(ok): /home/me/beyond_basics/midterm_project (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-147-127 b/docs/beyond_basics/_examples/DL-101-147-127 index 19b895677..4707583af 100644 --- a/docs/beyond_basics/_examples/DL-101-147-127 +++ b/docs/beyond_basics/_examples/DL-101-147-127 @@ -1,4 +1,3 @@ $ datalad get -n midterm_project -[INFO] Attempting a clone into /home/me/beyond_basics/myclone/midterm_project [INFO] Configure additional publication dependency on "ria-backup-storage" install(ok): /home/me/beyond_basics/myclone/midterm_project (dataset) [Installed subdataset in order to get /home/me/beyond_basics/myclone/midterm_project] diff --git a/docs/beyond_basics/_examples/DL-101-149-01 b/docs/beyond_basics/_examples/DL-101-149-01 index 287c3f110..d093987ef 100644 --- a/docs/beyond_basics/_examples/DL-101-149-01 +++ b/docs/beyond_basics/_examples/DL-101-149-01 @@ -1,3 +1,2 @@ $ datalad clone https://github.com/datalad-datasets/human-connectome-project-openaccess.git hcp -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp install(ok): /home/me/beyond_basics/HPC/hcp (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-149-02 b/docs/beyond_basics/_examples/DL-101-149-02 index ef8ec44de..8ef52d2f3 100644 --- a/docs/beyond_basics/_examples/DL-101-149-02 +++ b/docs/beyond_basics/_examples/DL-101-149-02 @@ -1,6 +1,5 @@ $ cd hcp $ datalad get -n -r HCP1200/130* -[INFO] Attempting a clone into /home/me/beyond_basics/HPC/hcp/HCP1200/130013 install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013 (dataset) [Installed subdataset in order to get /home/me/beyond_basics/HPC/hcp/HCP1200/130013] [INFO] Ensuring presence of Dataset(/home/me/beyond_basics/HPC/hcp) to get /home/me/beyond_basics/HPC/hcp/HCP1200/130013 install(ok): /home/me/beyond_basics/HPC/hcp/HCP1200/130013/MNINonLinear (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-149-12 b/docs/beyond_basics/_examples/DL-101-149-12 index df4159134..05977200b 100644 --- a/docs/beyond_basics/_examples/DL-101-149-12 +++ b/docs/beyond_basics/_examples/DL-101-149-12 @@ -1,5 +1,5 @@ $ cd dataset-to-copy-to $ datalad get bvals anothercopyofbvecs 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters -get(ok): 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters (file) [from datalad...] -get(ok): bvals (file) [from datalad...] get(ok): anothercopyofbvecs (file) [from datalad...] +get(ok): bvals (file) [from datalad...] +get(ok): 130114/T1w/Diffusion/eddylogs/eddy_unwarped_images.eddy_parameters (file) [from datalad...] diff --git a/docs/beyond_basics/_examples/DL-101-168-104 b/docs/beyond_basics/_examples/DL-101-168-104 index 8f801de4a..8d72a127e 100644 --- a/docs/beyond_basics/_examples/DL-101-168-104 +++ b/docs/beyond_basics/_examples/DL-101-168-104 @@ -3,7 +3,6 @@ $ datalad download-url -m "download scripts for ML analysis" \ https://raw.githubusercontent.com/datalad-handbook/data-version-control/master/src/{train,prepare,evaluate}.py \ -O 'code/' -[INFO] Downloading 'https://raw.githubusercontent.com/datalad-handbook/data-version-control/master/src/train.py' into '/home/me/DVCvsDL/DVC-DataLad/code/' download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/train.py (file) download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/prepare.py (file) download_url(ok): /home/me/DVCvsDL/DVC-DataLad/code/evaluate.py (file) diff --git a/docs/beyond_basics/_examples/DL-101-168-110 b/docs/beyond_basics/_examples/DL-101-168-110 index 7bdbc05d3..b8595f2a4 100644 --- a/docs/beyond_basics/_examples/DL-101-168-110 +++ b/docs/beyond_basics/_examples/DL-101-168-110 @@ -12,7 +12,7 @@ To enable auto staging, run: To track the changes with git, run: - git add data/raw/.gitignore data/raw/val.dvc + git add data/raw/val.dvc data/raw/.gitignore To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-114 b/docs/beyond_basics/_examples/DL-101-168-114 index 6f811ed5f..437edd24b 100644 --- a/docs/beyond_basics/_examples/DL-101-168-114 +++ b/docs/beyond_basics/_examples/DL-101-168-114 @@ -5,7 +5,6 @@ $ datalad download-url \ --message "Download Imagenette dataset" \ https://osf.io/d6qbz/download \ -O 'data/raw/' -[INFO] Downloading 'https://osf.io/d6qbz/download' into '/home/me/DVCvsDL/DVC-DataLad/data/raw/' download_url(ok): /home/me/DVCvsDL/DVC-DataLad/data/raw/imagenette2-160.tgz (file) add(ok): data/raw/imagenette2-160.tgz (file) save(ok): . (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-168-131 b/docs/beyond_basics/_examples/DL-101-168-131 index 4620c70ec..0cfe96113 100644 --- a/docs/beyond_basics/_examples/DL-101-168-131 +++ b/docs/beyond_basics/_examples/DL-101-168-131 @@ -2,6 +2,5 @@ # outside of a dataset $ datalad clone https://github.com/datalad-handbook/DVC-DataLad.git DVC-DataLad-2 $ cd DVC-DataLad-2 -[INFO] Attempting a clone into /home/me/DVCvsDL/DVC-DataLad-2 [INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): /home/me/DVCvsDL/DVC-DataLad-2 (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-168-141 b/docs/beyond_basics/_examples/DL-101-168-141 index bc20011b7..44896e47b 100644 --- a/docs/beyond_basics/_examples/DL-101-168-141 +++ b/docs/beyond_basics/_examples/DL-101-168-141 @@ -1,6 +1,4 @@ ### DVC-DataLad $ datalad push --to mysibling -[INFO] Determine push target -[INFO] Finished push of Dataset(/home/me/DVCvsDL/DVC-DataLad) -publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex eed90ebd..3e75bdaa] +publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex 4d0fc528..3c522222] publish(ok): . (dataset) [refs/heads/main->mysibling:refs/heads/main [new branch]] diff --git a/docs/beyond_basics/_examples/DL-101-168-151 b/docs/beyond_basics/_examples/DL-101-168-151 index 9a854cc10..5780e3f37 100644 --- a/docs/beyond_basics/_examples/DL-101-168-151 +++ b/docs/beyond_basics/_examples/DL-101-168-151 @@ -12,7 +12,7 @@ Updating lock file 'dvc.lock' To track the changes with git, run: - git add data/prepared/.gitignore dvc.yaml dvc.lock + git add data/prepared/.gitignore dvc.lock dvc.yaml To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-155 b/docs/beyond_basics/_examples/DL-101-168-155 index 1e5fc1fa0..93246ab4a 100644 --- a/docs/beyond_basics/_examples/DL-101-168-155 +++ b/docs/beyond_basics/_examples/DL-101-168-155 @@ -12,7 +12,7 @@ Updating lock file 'dvc.lock' To track the changes with git, run: - git add dvc.lock model/.gitignore dvc.yaml + git add dvc.yaml dvc.lock model/.gitignore To enable auto staging, run: diff --git a/docs/beyond_basics/_examples/DL-101-168-159 b/docs/beyond_basics/_examples/DL-101-168-159 index bcb834b0d..d0049baa7 100644 --- a/docs/beyond_basics/_examples/DL-101-168-159 +++ b/docs/beyond_basics/_examples/DL-101-168-159 @@ -1,4 +1,4 @@ ### DVC $ dvc metrics show Path accuracy -metrics/accuracy.json 0.75919 +metrics/accuracy.json 0.67934 diff --git a/docs/beyond_basics/_examples/DL-101-168-160 b/docs/beyond_basics/_examples/DL-101-168-160 index f25ace59c..d2d807cf4 100644 --- a/docs/beyond_basics/_examples/DL-101-168-160 +++ b/docs/beyond_basics/_examples/DL-101-168-160 @@ -6,7 +6,7 @@ $ git push --set-upstream origin sgd-pipeline $ git tag -a sgd -m "Trained SGD as DVC pipeline." $ git push origin --tags $ dvc push -[sgd-pipeline 9238080] Add SGD pipeline +[sgd-pipeline d6ce694] Add SGD pipeline 5 files changed, 83 insertions(+) create mode 100644 dvc.lock create mode 100644 dvc.yaml diff --git a/docs/beyond_basics/_examples/DL-101-168-165 b/docs/beyond_basics/_examples/DL-101-168-165 index fda480c70..fde8674ef 100644 --- a/docs/beyond_basics/_examples/DL-101-168-165 +++ b/docs/beyond_basics/_examples/DL-101-168-165 @@ -6,8 +6,8 @@ $ git push --set-upstream origin random-forest $ git tag -a randomforest -m "Random Forest classifier with 80.99% accuracy." $ git push origin --tags $ dvc push -[random-forest 64a8207] Train Random Forest classifier - 3 files changed, 11 insertions(+), 17 deletions(-) +[random-forest 715b446] Train Random Forest classifier + 3 files changed, 12 insertions(+), 18 deletions(-) To /home/me/pushes/data-version-control * [new branch] random-forest -> random-forest branch 'random-forest' set up to track 'origin/random-forest'. diff --git a/docs/beyond_basics/_examples/DL-101-168-166 b/docs/beyond_basics/_examples/DL-101-168-166 index 84c6c0eca..6d0877dfc 100644 --- a/docs/beyond_basics/_examples/DL-101-168-166 +++ b/docs/beyond_basics/_examples/DL-101-168-166 @@ -1,6 +1,6 @@ ### DVC $ dvc metrics show -T Revision Path accuracy -workspace metrics/accuracy.json 0.82129 -randomforest metrics/accuracy.json 0.82129 -sgd metrics/accuracy.json 0.75919 +workspace metrics/accuracy.json 0.79848 +randomforest metrics/accuracy.json 0.79848 +sgd metrics/accuracy.json 0.67934 diff --git a/docs/beyond_basics/_examples/DL-101-168-178 b/docs/beyond_basics/_examples/DL-101-168-178 index 4ebad9f17..e2d29bb6f 100644 --- a/docs/beyond_basics/_examples/DL-101-168-178 +++ b/docs/beyond_basics/_examples/DL-101-168-178 @@ -1,17 +1,14 @@ $ datalad rerun --branch="randomforest" -m "Recompute classification with random forest classifier" ready-for-analysis..SGD -[INFO] checkout commit 97457b0; -[INFO] run commit c8eb8dc; (Train an SGD clas...) +[INFO] checkout commit 0c478ea; +[INFO] run commit 8ac7f88; (Train an SGD clas...) [INFO] Making sure inputs are available (this may take some time) -[INFO] Unlocking files unlock(ok): model/model.joblib (file) -[INFO] Recording unlocked state in git -[INFO] Completed unlocking files [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [python code/train.py] add(ok): model/model.joblib (file) save(ok): . (dataset) -[INFO] run commit b0793d4; (Evaluate SGD clas...) +[INFO] run commit c1606cc; (Evaluate SGD clas...) [INFO] Making sure inputs are available (this may take some time) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/beyond_basics/_examples/DL-101-168-179 b/docs/beyond_basics/_examples/DL-101-168-179 index 468cd9faf..19d15d1f2 100644 --- a/docs/beyond_basics/_examples/DL-101-168-179 +++ b/docs/beyond_basics/_examples/DL-101-168-179 @@ -1,10 +1,10 @@ $ git diff SGD -- metrics/accuracy.json diff --git a/metrics/accuracy.json b/metrics/accuracy.json -index 1058d868..9279f676 100644 +index 74a1ee15..f6e7ded9 100644 --- a/metrics/accuracy.json +++ b/metrics/accuracy.json @@ -1 +1 @@ --{"accuracy": 0.7718631178707225} +-{"accuracy": 0.7629911280101395} \ No newline at end of file -+{"accuracy": 0.8149556400506971} ++{"accuracy": 0.8124207858048162} \ No newline at end of file diff --git a/docs/beyond_basics/_examples/DL-101-181-101 b/docs/beyond_basics/_examples/DL-101-181-101 index 9bbb6f10f..34c630f88 100644 --- a/docs/beyond_basics/_examples/DL-101-181-101 +++ b/docs/beyond_basics/_examples/DL-101-181-101 @@ -1,5 +1,4 @@ $ datalad clone https://github.com/datalad-handbook/cozy-screensavers.git $ cd cozy-screensavers -[INFO] Attempting a clone into /home/me/beyond_basics/meta/cozy-screensavers [INFO] Remote origin not usable by git-annex; setting annex-ignore install(ok): /home/me/beyond_basics/meta/cozy-screensavers (dataset) diff --git a/docs/beyond_basics/_examples/DL-101-181-108 b/docs/beyond_basics/_examples/DL-101-181-108 index fa135186e..cc743088b 100644 --- a/docs/beyond_basics/_examples/DL-101-181-108 +++ b/docs/beyond_basics/_examples/DL-101-181-108 @@ -9,7 +9,7 @@ $ datalad meta-extract -d . metalad_core | jq "extractor_name": "metalad_core", "extractor_version": "1", "extraction_parameter": {}, - "extraction_time": 1698845024.5401418, + "extraction_time": 1698916640.0831163, "agent_name": "Elena Piscopia", "agent_email": "elena@example.net", "extracted_metadata": {