2.4. Version and sharing data with Quilt¶
Conducting modeling reproducibly and collaboratively requires versioning and sharing data. Although Git/GitHub is well suited to versioning and sharing code and models, Git/GitHub is not well-suited to data because Git is based on line-by-line differencing of text files, because Git is designed for small files under 100 MB, and because Git requires the entire package and its history to be cloned. Quilt is a new system for versioning and sharing data with similar functionality to Git/GitHub and Docker/DockerHub.
Quilt is based on versioning packages of data, which are hierarhical trees of directories and files.
Quilt provides the following features:
- Capability to version data packages
- Capability to share packages with collaborators and with the world
- Programmatic access to upload, download, and update packages
- Web pages with READMEs to view and browse packages, including their histories
2.4.2. Using Quilt¶
First, create a Quilt account at https://quiltdata.com/signup.
Second, run the following command to install Quilt:
pip install quilt
Third, you can use the install command to install and upgrade Quilt packages. For example, run the following command to install the iris package from uciml:
quilt install uciml/iris
Fourth, you can use the inspect command to view the contents of packages and you can use the log command to view the histories of packages. For example, run the following commands to inspect the iris package:
quilt inspect uciml/iris quilt log uciml/iris
Fifth, you can use the export command to unpack packages to directories and files. For example, run the following command to unpack the iris package:
quilt export uciml/iris /tmp/iris/
Sixth, you can use the build command to create packages from directories and the version add command to annotate the version of the created package. For example, run the following commands to build a new package containing the same iris data and annotate the version of the package:
quilt build <username>/iris /tmp/iris/ quilt version add <username>/iris 0.0.1 <hash>
Seventh, you can use the push command to upload packages to the Quilt server. For example, run the following commands to push the new package to the Quilt server. Optionally, you can use the –public flag to share the package with the world:
quilt login quilt push --public <username>/iris/
In addition, Quilt provides the following utility commands:
- quilt ls: lists the packages installed on your system
- quilt rm <owner>/<package>: removes a package from your system
- quilt delete <owner>/<package>: removes a package from the Quilt server
2.4.3. Limitations and troubleshooting¶
Because Quilt is new, Quilt still has several quirks:
- Quilt automatically converts Excel files to CSV, losing all formatting.
- Node names cannot contain “.”.
- Only the package owner can push packages and create versions. Packages can’t be authored collaboratively.
- Quilt doesn’t support comments on revisions like Git
- The Quilt Python API prints results to stdout and doesn’t return values.
- The Quilt user and package pages are rudimentary
- There is little documentation for Quilt