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datalad-handbook · Nov 2, 2023 · cde17a1 · cde17a1
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 -> <datalad.local.copy_file._CachedRepo object at ✂MEMORYADDRESS✂
 copy_file(ok): /home/me/dl-101/DataLad-101/notes.txt
 add(ok): notes.txt (file)
 save(ok): . (dataset)
diff --git 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/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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]