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Frequently Asked Questions

How do I sync my notebook and all of its data and models to S3 as a package?

p = quilt3.Package()
p.set_dir(".", ".")
p.push("USR/PKG", message="MSG", registry="s3://BUCKET")
Use a .quiltignore file for more control over which files set_dir() includes.

How does Quilt versioning relate to S3 object versioning?

Quilt packages are one level of abstraction above S3 object versions. Object versions track mutations to a single file, whereas a quilt package references a collection files and assigns this collection a unique version.
It is strongly recommended that you enable object versioning on the S3 buckets that you push Quilt packages to. Object versioning ensures that mutations to every object are tracked, and provides some protection against deletion.

Where are the Quilt 2 packages?

Visit legacy.quiltdata.com and use quilt on PyPI.

Does quilt3 collect anonymous usage statistics?

Yes, to find bugs and prioritize features.
You can disable anonymous usage collection with an environment variable:
export QUILT_DISABLE_USAGE_METRICS=true
Or call quilt3.disable_telemetry() to persistently disable anonymous usage statistics.

Can I turn off TQDM progress bars for log files?

Yes:
export QUILT_MINIMIZE_STDOUT=true

Which version of Quilt are you on?

Python client

quilt3 --version

CloudFormation application

  1. 1.
    Go to CloudFormation > Stacks > YourQuiltStack > Outputs
  2. 2.
    Copy the row labeled TemplateBuildMetadata
  3. 3.
    "git_revision" is your template version

Hashing takes a long time. Can I speed it up?

Yes. Follow these steps:
  1. 1.
    Run your compute in the same region as your S3 bucket (as opposed to a local machine or foreign region)—I/O is much faster.
  2. 2.
    Use a larger instance with more vCPUs.
  3. 3.
    Increase QUILT_TRANSFER_MAX_CONCURRENCY above its default to match your available vCPUs.

Does Quilt work with R?

In the scientific computing community, the R Project is commonly used as an alternative, or companion, to Python. It is a language and environment for statistical computing and graphics, and is available as Free Software under the GNU General Public License.
Currently there are no plans to release a Quilt package for distribution through the CRAN package repository. However, you can still use Quilt with R, using either:
  1. 1.
    The Command Line Interface (CLI) API
  2. 2.

Using the Quilt CLI API with R

You can script the Quilt CLI directly from your shell environment and chain it with your R scripts to create a unified workflow:
quilt3 install my-package # download Quilt data package
[Run R commands or scripts] # modify the data in Quilt data package using R
quilt3 push --dir path/to/remote-registry my-package # upload Quilt data package to the remote registry

Using Quilt with Reticulate

The Reticulate package provides a set of tools for interoperability between Python and R by embedding a Python session within your R session.

How do I delete a data package and all of the objects in the data package?

You may have a test data package that you wish to delete at some point to ensure your data repository is clean and organized. Please do this very carefully! In favor of immutability, Quilt makes deletion a bit tricky. First, note that quilt3.Package.delete only deletes the package manifest, not the underlying objects. If you wish to delete the entire package and its objects, delete the objects first.
Warning: the objects you delete will be lost forever. Ditto for the package revision.
To delete, first browse the package then walk it, deleting its entry objects as follows:
import boto3
import quilt3 as q3
s3 = boto3.client("s3")
reg = "s3://quilt-bio-staging"
pname = "akarve/delete-object"
p = q3.Package.browse(pname, registry=reg)
for (k, e) in p.walk():
pk = e.physical_key
s3.delete_object(Bucket=pk.bucket, Key=pk.path, VersionId=pk.version_id)
You can then follow the above with q3.Package.delete(pname, registry=reg, top_hash=p.top_hash).
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On this page
How do I sync my notebook and all of its data and models to S3 as a package?
How does Quilt versioning relate to S3 object versioning?
Where are the Quilt 2 packages?
Does quilt3 collect anonymous usage statistics?
Can I turn off TQDM progress bars for log files?
Which version of Quilt are you on?
Hashing takes a long time. Can I speed it up?
Does Quilt work with R?
How do I delete a data package and all of the objects in the data package?