From c7ec936fd389cbba032bf1480ec3783562cd6100 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Thu, 2 Nov 2023 11:38:31 +0100 Subject: [PATCH 1/2] Another pass of the log filter setup --- docs/conf.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 9007b7ffa..808b52740 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -78,8 +78,9 @@ (r'\[INFO\] Unlocking files$\n', ''), (r'\[INFO\] Recording unlocked state in git$\n', ''), (r'\[INFO\] Completed unlocking files$\n', ''), - (r'\[INFO\] Making sure inputs are available (this may take some time)$\n', ''), + (r'\[INFO\] Making sure inputs are available \(this may take some time\).*$\n', ''), (r'\[INFO\] Creating a new annex repo at .*$\n', ''), + (r'\[INFO\] Copying non-annexed file or copy into non-annex dataset:.*$\n', ''), # annoying always-true test for a non-annex git remote (r'\[INFO\] \S+/config download failed: Not Found$\n', ''), # datalad push step-progress @@ -88,6 +89,7 @@ (r'\[INFO\] Transfer data$\n', ''), (r'\[INFO\] Update availability information$\n', ''), (r'\[INFO\] Finished push of Dataset.*$\n', ''), + (r'\[INFO\] Finished$\n', ''), ] # pre-crafted artificial environment to run the code examples in # start with all datalad settings From cde17a18ee9b6889d4d73bdf4a8cae6a61eb8d79 Mon Sep 17 00:00:00 2001 From: Adina Wagner Date: Thu, 2 Nov 2023 14:51:42 +0100 Subject: [PATCH 2/2] add diff --- docs/basics/_examples/DL-101-110-103 | 1 - docs/basics/_examples/DL-101-110-104 | 1 - docs/basics/_examples/DL-101-111-105 | 1 - docs/basics/_examples/DL-101-112-104 | 1 - docs/basics/_examples/DL-101-112-106 | 1 - docs/basics/_examples/DL-101-118-103 | 1 - docs/basics/_examples/DL-101-130-111 | 1 - docs/basics/_examples/DL-101-130-121 | 2 +- docs/basics/_examples/DL-101-130-122 | 1 - docs/basics/_examples/DL-101-133-105 | 1 - docs/basics/_examples/DL-101-136-145 | 1 - docs/basics/_examples/DL-101-137-114 | 2 +- docs/basics/_examples/DL-101-137-117 | 2 +- docs/basics/_examples/DL-101-141-101 | 1 - docs/beyond_basics/_examples/DL-101-147-108 | 4 ++-- docs/beyond_basics/_examples/DL-101-147-112 | 10 +++++----- docs/beyond_basics/_examples/DL-101-168-141 | 2 +- docs/beyond_basics/_examples/DL-101-168-160 | 2 +- docs/beyond_basics/_examples/DL-101-168-165 | 4 ++-- docs/beyond_basics/_examples/DL-101-168-171 | 1 - docs/beyond_basics/_examples/DL-101-168-173 | 1 - docs/beyond_basics/_examples/DL-101-168-174 | 1 - docs/beyond_basics/_examples/DL-101-168-178 | 8 +++----- 23 files changed, 17 insertions(+), 33 deletions(-) diff --git a/docs/basics/_examples/DL-101-110-103 b/docs/basics/_examples/DL-101-110-103 index 8c8424235..e1e07a5ca 100644 --- a/docs/basics/_examples/DL-101-110-103 +++ b/docs/basics/_examples/DL-101-110-103 @@ -5,7 +5,6 @@ $ datalad run -m "Resize logo for slides" \ $ datalad run -m "Resize logo for slides" \ -i "recordings/longnow/.datalad/feed_metadata/logo_salt.jpg" \ "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) get(ok): recordings/longnow/.datalad/feed_metadata/logo_salt.jpg (file) [from web...] [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-110-104 b/docs/basics/_examples/DL-101-110-104 index c3b1d5fe1..0a8c3a637 100644 --- a/docs/basics/_examples/DL-101-110-104 +++ b/docs/basics/_examples/DL-101-110-104 @@ -5,7 +5,6 @@ $ datalad run -m "Resize logo for slides" \ $ datalad run -m "Resize logo for slides" \ -i "recordings/longnow/.datalad/feed_metadata/logo_salt.jpg" \ "convert -resize 450x450 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] == Command start (output follows) ===== convert convert: Unable to open file (recordings/salt_logo_small.jpg) [Permission denied]. [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-111-105 b/docs/basics/_examples/DL-101-111-105 index 7a6b23cb7..96bf616cd 100644 --- a/docs/basics/_examples/DL-101-111-105 +++ b/docs/basics/_examples/DL-101-111-105 @@ -8,7 +8,6 @@ $ datalad run -m "Resize logo for slides" \ -i "recordings/longnow/.datalad/feed_metadata/logo_interval.jpg" \ -o "recordings/interval_logo_small.jpg" \ "convert -resize 450x450 recordings/longnow/.datalad/feed_metadata/logo_interval.jpg recordings/interval_logo_small.jpg" -[INFO] Making sure inputs are available (this may take some time) get(ok): recordings/longnow/.datalad/feed_metadata/logo_interval.jpg (file) [from web...] [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-112-104 b/docs/basics/_examples/DL-101-112-104 index e8272d739..b9e200fc6 100644 --- a/docs/basics/_examples/DL-101-112-104 +++ b/docs/basics/_examples/DL-101-112-104 @@ -2,7 +2,6 @@ $ datalad run -m "Resize logo for slides" \ --input "recordings/longnow/.datalad/feed_metadata/logo_interval.jpg" \ --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) unlock(ok): recordings/interval_logo_small.jpg (file) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-112-106 b/docs/basics/_examples/DL-101-112-106 index 52b90863c..65d25b790 100644 --- a/docs/basics/_examples/DL-101-112-106 +++ b/docs/basics/_examples/DL-101-112-106 @@ -3,7 +3,6 @@ $ datalad run -m "Resize logo for slides" \ --output "recordings/salt_logo_small.jpg" \ --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) unlock(ok): recordings/salt_logo_small.jpg (file) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-118-103 b/docs/basics/_examples/DL-101-118-103 index 2eb5ac639..4a8f88eee 100644 --- a/docs/basics/_examples/DL-101-118-103 +++ b/docs/basics/_examples/DL-101-118-103 @@ -1,7 +1,6 @@ $ datalad rerun fd4a25e6✂SHA1 [INFO] run commit fd4a25e; (Resize logo for s...) -[INFO] Making sure inputs are available (this may take some time) get(ok): recordings/longnow/.datalad/feed_metadata/logo_salt.jpg (file) [from web...] run.remove(ok): recordings/salt_logo_small.jpg (file) [Removed file] [INFO] == Command start (output follows) ===== diff --git a/docs/basics/_examples/DL-101-130-111 b/docs/basics/_examples/DL-101-130-111 index 7101c9db7..0a5525972 100644 --- a/docs/basics/_examples/DL-101-130-111 +++ b/docs/basics/_examples/DL-101-130-111 @@ -3,7 +3,6 @@ $ datalad run -m "analyze iris data with classification analysis" \ --output "pairwise_relationships.png" \ --output "prediction_report.csv" \ "python3 code/script.py {inputs} {outputs}" -[INFO] Making sure inputs are available (this may take some time) get(ok): input/iris.csv (file) [from web...] [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== diff --git a/docs/basics/_examples/DL-101-130-121 b/docs/basics/_examples/DL-101-130-121 index 03c2298c8..df8709f57 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): 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)] +get(error): prediction_report.csv (file) [not available; (Note that these git remotes have annex-ignore set: origin)] diff --git a/docs/basics/_examples/DL-101-130-122 b/docs/basics/_examples/DL-101-130-122 index 6c17b5d01..afeabd465 100644 --- a/docs/basics/_examples/DL-101-130-122 +++ b/docs/basics/_examples/DL-101-130-122 @@ -1,7 +1,6 @@ $ datalad rerun d715890b✂SHA1 [INFO] run commit d715890; (analyze iris data...) -[INFO] Making sure inputs are available (this may take some time) run.remove(ok): pairwise_relationships.png (file) [Removed file] run.remove(ok): prediction_report.csv (file) [Removed file] [INFO] == Command start (output follows) ===== diff --git a/docs/basics/_examples/DL-101-133-105 b/docs/basics/_examples/DL-101-133-105 index 3726c3140..262fe4a18 100644 --- a/docs/basics/_examples/DL-101-133-105 +++ b/docs/basics/_examples/DL-101-133-105 @@ -4,7 +4,6 @@ $ datalad containers-run -m "rerun analysis in container" \ --output "pairwise_relationships.png" \ --output "prediction_report.csv" \ "python3 code/script.py {inputs} {outputs}" -[INFO] Making sure inputs are available (this may take some time) unlock(ok): pairwise_relationships.png (file) unlock(ok): prediction_report.csv (file) [INFO] == Command start (output follows) ===== diff --git a/docs/basics/_examples/DL-101-136-145 b/docs/basics/_examples/DL-101-136-145 index fecc35796..413e24a5b 100644 --- a/docs/basics/_examples/DL-101-136-145 +++ b/docs/basics/_examples/DL-101-136-145 @@ -1,5 +1,4 @@ $ datalad copy-file notes.txt midterm_project -d midterm_project -[INFO] Copying non-annexed file or copy into non-annex dataset: /home/me/dl-101/DataLad-101/notes.txt -> .git/annex/objects/JQ/ZF/✂/MD5E-s1216--e18f278f✂MD5.pdf +lrwxrwxrwx 1 elena elena 122 2019-06-18 16:13 apdffile.pdf -> .git/annex/objects/zZ/v7/✂/MD5E-s1216--b954106f✂MD5.pdf diff --git a/docs/basics/_examples/DL-101-137-117 b/docs/basics/_examples/DL-101-137-117 index aa720288a..0c3d18a6d 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 -ecab714 [DATALAD] Recorded changes +9b3495b [DATALAD] Recorded changes 4bdb06c save my favorite Git joke 996f459 remove obsolete subds diff --git a/docs/basics/_examples/DL-101-141-101 b/docs/basics/_examples/DL-101-141-101 index 22dccc744..8761eee7d 100644 --- a/docs/basics/_examples/DL-101-141-101 +++ b/docs/basics/_examples/DL-101-141-101 @@ -2,7 +2,6 @@ $ datalad push --to roommate 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)] action summary: diff --git a/docs/beyond_basics/_examples/DL-101-147-108 b/docs/beyond_basics/_examples/DL-101-147-108 index 6e527eb4e..d2a8eff36 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-f1636323✂SHA1.idx -│   │   └── pack-f1636323✂SHA1.pack +│   │   ├── pack-a02f2380✂SHA1.idx +│   │   └── pack-a02f2380✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-147-112 b/docs/beyond_basics/_examples/DL-101-147-112 index 4ba2035d9..c26dd67c9 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-5020f73a✂SHA1.idx -│   │   └── pack-5020f73a✂SHA1.pack -│   ├── ora-remote-644719fb-0077-49d2-b1c7-006cc9f7c7c5 +│   │   ├── pack-e79ad660✂SHA1.idx +│   │   └── pack-e79ad660✂SHA1.pack +│   ├── ora-remote-aa9031bf-0855-4611-aa21-da0698cce020 │   │   └── transfer │   ├── refs │   │   ├── heads @@ -98,8 +98,8 @@ $ tree /home/me/myriastore │   ├── objects │   │   ├── info │   │   └── pack -│   │   ├── pack-f1636323✂SHA1.idx -│   │   └── pack-f1636323✂SHA1.pack +│   │   ├── pack-a02f2380✂SHA1.idx +│   │   └── pack-a02f2380✂SHA1.pack │   ├── ora-remote-46b169aa-bb91-42d6-be06-355d957fb4f7 │   │   └── transfer │   ├── refs diff --git a/docs/beyond_basics/_examples/DL-101-168-141 b/docs/beyond_basics/_examples/DL-101-168-141 index 44896e47b..92e498c32 100644 --- a/docs/beyond_basics/_examples/DL-101-168-141 +++ b/docs/beyond_basics/_examples/DL-101-168-141 @@ -1,4 +1,4 @@ ### DVC-DataLad $ datalad push --to mysibling -publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex 4d0fc528..3c522222] +publish(ok): . (dataset) [refs/heads/git-annex->mysibling:refs/heads/git-annex a19cf78a..2592d518] publish(ok): . (dataset) [refs/heads/main->mysibling:refs/heads/main [new branch]] diff --git a/docs/beyond_basics/_examples/DL-101-168-160 b/docs/beyond_basics/_examples/DL-101-168-160 index d2d807cf4..8540a97b9 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 d6ce694] Add SGD pipeline +[sgd-pipeline c400246] 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 fde8674ef..fcf1382a3 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 715b446] Train Random Forest classifier - 3 files changed, 12 insertions(+), 18 deletions(-) +[random-forest c565b15] Train Random Forest classifier + 3 files changed, 11 insertions(+), 17 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-101-168-171 b/docs/beyond_basics/_examples/DL-101-168-171 index f982ab995..63c822ed3 100644 --- a/docs/beyond_basics/_examples/DL-101-168-171 +++ b/docs/beyond_basics/_examples/DL-101-168-171 @@ -3,7 +3,6 @@ $ datalad run --message "Prepare the train and testing data" \ --input "data/raw/*" \ --output "data/prepared/*" \ python code/prepare.py -[INFO] Making sure inputs are available (this may take some time) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [python code/prepare.py] diff --git a/docs/beyond_basics/_examples/DL-101-168-173 b/docs/beyond_basics/_examples/DL-101-168-173 index d6540cc40..06f896dcc 100644 --- a/docs/beyond_basics/_examples/DL-101-168-173 +++ b/docs/beyond_basics/_examples/DL-101-168-173 @@ -3,7 +3,6 @@ $ datalad run --message "Train an SGD classifier" \ --input "data/prepared/*" \ --output "model/model.joblib" \ python code/train.py -[INFO] Making sure inputs are available (this may take some time) [INFO] == Command start (output follows) ===== VIRTUALENV/lib/python3.8/site-packages/sklearn/linear_model/_stochastic_gradient.py:713: ConvergenceWarning: Maximum number of iteration reached before convergence. Consider increasing max_iter to improve the fit. warnings.warn( diff --git a/docs/beyond_basics/_examples/DL-101-168-174 b/docs/beyond_basics/_examples/DL-101-168-174 index 425effe14..e6e9ed3f4 100644 --- a/docs/beyond_basics/_examples/DL-101-168-174 +++ b/docs/beyond_basics/_examples/DL-101-168-174 @@ -3,7 +3,6 @@ $ datalad run --message "Evaluate SGD classifier model" \ --input "model/model.joblib" \ --output "metrics/accuracy.json" \ python code/evaluate.py -[INFO] Making sure inputs are available (this may take some time) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [python code/evaluate.py] diff --git a/docs/beyond_basics/_examples/DL-101-168-178 b/docs/beyond_basics/_examples/DL-101-168-178 index e2d29bb6f..5fbbcd0d8 100644 --- a/docs/beyond_basics/_examples/DL-101-168-178 +++ b/docs/beyond_basics/_examples/DL-101-168-178 @@ -1,15 +1,13 @@ $ datalad rerun --branch="randomforest" -m "Recompute classification with random forest classifier" ready-for-analysis..SGD -[INFO] checkout commit 0c478ea; -[INFO] run commit 8ac7f88; (Train an SGD clas...) -[INFO] Making sure inputs are available (this may take some time) +[INFO] checkout commit 1b3b757; +[INFO] run commit 88a6e86; (Train an SGD clas...) unlock(ok): model/model.joblib (file) [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 c1606cc; (Evaluate SGD clas...) -[INFO] Making sure inputs are available (this may take some time) +[INFO] run commit 2d07713; (Evaluate SGD clas...) [INFO] == Command start (output follows) ===== [INFO] == Command exit (modification check follows) ===== run(ok): /home/me/DVCvsDL/DVC-DataLad (dataset) [python code/evaluate.py]