# Frequently Asked Questions

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

```python
p = quilt3.Package()
p.set_dir(".", ".")
p.push("USR/PKG", message="MSG", registry="s3://BUCKET")
```

> Use a [.quiltignore file](https://docs.quilt.bio/advanced-usage/.quiltignore) 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](https://legacy.quiltdata.com/) and use [`quilt`](https://pypi.org/project/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:

```bash
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:

```bash
export QUILT_MINIMIZE_STDOUT=true
```

### Which version of Quilt are you on?

#### Python client

```bash
quilt3 --version
```

#### CloudFormation application

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

This information is also available in the footer of the main page of the Catalog.

### Hashing during `push` takes a long time. Can I speed it up?

Yes. Follow these steps:

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. Use a larger instance with more vCPUs.
3. Increase [`QUILT_TRANSFER_MAX_CONCURRENCY`](/quilt-python-sdk/api-reference/cli.md#quilt_transfer_max_concurrency) above its default to match your available vCPUs.
4. If you are using Quilt Catalog 1.51 (released Feb 2024), you can enable the `ChunkedChecksums` CloudFormation parameter so it will calculate the checksums in parallel, or reuse them if already existing in S3. Parallel checksums are also available by default in `quilt3` v6 or later (pre-released Feb 2024).

### Does Quilt work with R?

In the scientific computing community, the [R Project](https://www.r-project.org/) 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](https://www.r-project.org/COPYING).

Currently there are no plans to release a Quilt package for distribution through the [CRAN package repository](https://cloud.r-project.org/). However, you can still use Quilt with R, using either:

1. The Command Line Interface (CLI) API
2. [Reticulate](https://rstudio.github.io/reticulate/)

#### 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:

```bash
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](https://rstudio.github.io/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:

```python
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.delete_package(pname, registry=reg, top_hash=p.top_hash)`.

### Do I have to login via quilt3 to use the Quilt APIs?

### How do I push to Quilt from a headless environment like a Docker container?

Configure [AWS CLI credentials](https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-configure.html) and `quilt3` will use the same for its API calls.

> Be sure to run `quilt3 logout` if you've previously logged in.

Select among multiple profiles in your shell as follows:

```bash
export AWS_PROFILE=your_profile
```

The S3 permissions needed by `quilt3` are similar to [this bucket policy](https://docs.quilt.bio/advanced/crossaccount#bucket-policies) but `quilt3` does not need either `s3:GetBucketNotification` or `s3:PutBucketNotification`.

### How complex can my Athena queries be?

Amazon Athena supports a subset of Data Definition Language (DDL) and Data Manipulation Language (DML) statements, functions, operators, and data types, based on [Presto](https://prestodb.io/) and [Trino](https://trino.io/).

This allows for extremely granular querying of your data package name, metadata, and contents and includes logical operators, comparison functions, conditional expressions, mathematical functions, bitwise functions, date and time functions and operators, regular expression functions, and aggregate functions. Please review the references linked below to learn more.

#### Helpful examples

`regexp_extract_all(string, pattern)`

Return the substring(s) matched by the regular expression `pattern` in `string`

```sql
SELECT regexp_extract_all('1a 2b 14m', '\d+');
```

#### Considerations and limitations

There are [many considerations and limitations](https://docs.aws.amazon.com/athena/latest/ug/other-notable-limitations.html) when writing Amazon Athena queries.

#### References

* [SQL reference for Amazon Athena](https://docs.aws.amazon.com/athena/latest/ug/ddl-sql-reference.html)
* [Functions in Amazon Athena](https://docs.aws.amazon.com/athena/latest/ug/presto-functions.html)

### Are there any limitations on characters in Quilt filenames?

Yes. Quilt is built on top of Amazon S3, and has the same character limitations. Although any UTF-8 character is supported in an object key name (filename), using certain characters can result in problems with some applications and protocols. The following guideline will help you maximize compliance. For a comprehensive list of safe characters, characters that might require special handling, and characters to avoid, please review the official Amazon S3 documentation linked below.

#### List of safe characters

* Alphanumeric characters:
  * 0-9
  * a-z
  * A-Z
* Special characters:
  * Exclamation point (`!`)
  * Hyphen (`-`)
  * Underscore (`_`)
  * Period (`.`)
  * Asterisk (`*`)
  * Single quote (`'`)
  * Open parenthesis (`(`)
  * Close parenthesis (`)`)

For more details, see [Creating object key names](https://docs.aws.amazon.com/AmazonS3/latest/userguide/object-keys.html) in the Amazon S3 documentation.

### How many IPs does a standard Quilt stack require?

Currently, a full size, multi-Availability Zone deployment (without [Voila](https://docs.quilt.bio/catalog/visualizationdashboards#voila)) requires at least 256 IPs. This means a minimum CIDR block of `/24`.

Optional additional features (such as automated data packaging) require additional IPs.

### The "Last Modified" column in the Quilt catalog is empty

Amazon S3 is a key-value store with prefixes but no true "folders". In the Quilt Catalog Bucket view, as in AWS Console, only objects have a "Last modified" value, whereas package entries and prefixes do not.


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