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Changelog

4.0.0 - 2022-01-31

Python API

  • [Added] Declared compatibility with jsonschema==4.*.

  • [Added] --host and --port parameters for quilt3 catalog.

  • [Added] --no-browser parameter for quilt3 catalog.

  • [Changed] quilt3 catalog now requires quilt3 to be installed with catalog extra dependency (pip install quilt3[catalog]).

  • [Changed] Dependencies on flask and dnspython are dropped.

  • [Removed] Deprecated passing subpackage as part of package name for Package.install(), use path parameter instead.

  • [Removed] Deprecated calling of Package.resolve_hash() without specifying name parameter.

  • [Removed] Deprecated PackageEntry.physical_keys, use PackageEntry.physical_key instead.

CLI

  • [Removed] Deprecated passing subpackage as part of package name for quilt3 install, use --path parameter instead.

Catalog, Lambdas

  • [Changed] pkgselect: make directly invocable, always use execution role (#2560)

  • [Changed] Move package listing / querying to GraphQL (#2552)

  • [Changed] Fix performance of countPages in thumbnail lambda (#2616).

  • [Changed] pkgpush lambda now uses dedicated lambda for hashing files to push larger packages faster from catalog.

  • [Changed] Local-mode-specific adjustments to landing page and catalog UI (#2611)

  • [Changed] PDF preview: count pages again (#2621)

  • [Changed] Make Vega download data files from S3 via proxy to avoid CORS issues (#2631)

  • [Changed] Don't support packages in out-of-stack-buckets (#2641)

  • [Fixed] Improve upload performance and stability, fix some hashing-related errors (#2532)

  • [Added] Echarts renderer (#2382)

  • [Added] Set height for quilt_summarize.json files (#2474)

  • [Added] Add a "transcode" lambda for previewing video files (#2366)

  • [Added] Add object-level metadata editor and move package metadata editor to popup (#2510)

  • [Added] Video previews (#2540)

  • [Added] Audio previews (#2547)

  • [Added] Powerpoint (.pptx) preview (#2598, #2626)

3.6.0 - 2021-10-15

Python API

  • [Added] Validation of package names with handle_pattern in workflows config.

  • [Added] Validation of package entries with entries_schema in workflows config.

3.5.0 - 2021-09-07

Python API

  • [Added] Size of each manifest record is now limited by 1 MB. This constraint is added to ensure that S3 select, Athena and downstream services work correctly. This limit can be overridden with QUILT_MANIFEST_MAX_RECORD_SIZE environment variable. (#2114)

  • [Changed] Decrease size of Package in-memory representation (#1943)

CLI

  • [Added] --workflow argument to push command (#2279)

Catalog, Lambdas

  • [Added] Prepopulate today date for metadata (#2121)

  • [Added] Limit and offset parameters in pkgselect lambda (#2124)

  • [Added] File listing: "load more" button to fetch more entries from S3 (#2150)

  • [Added] Voila Notebooks format support (#2163)

  • [Added] Ability to add files from S3 while revising a package (#2171)

  • [Added] Lambdas for pushing an existing package/creation of package (#2147, #2180)

  • [Added] Custom navbar link configurable via admin UI (#2192)

  • [Added] Adding S3 objects to packages from configurable source buckets while revising (#2193)

  • [Added] Add Athena SQL queries initial viewer and runner (#2197)

  • [Added] Managing per-bucket permissions via admin UI (#2228)

  • [Added] Deep search indexing for Excel (#2247)

  • [Added] Deep search indexing for PDF (#2256)

  • [Added] Add Vega/JSON view switcher for Vega files (#2236)

  • [Added] Subpackage download (#2258)

  • [Added] Per-bucket deep indexing settings (#2290)

  • [Added] Embed: IPC, more debug features, docs (#2314)

  • [Added] Download button on Summary page (#2367)

  • [Added] Validation of package names and entries, pattern for default package name (2364)

  • [Changed] New DataGrid-based file listing UI with arbitrary sorting and filtering (#2097)

  • [Changed] Item selection in folder-to-package dialog (#2122)

  • [Changed] Don't preview .tif (but keep .tiff), preview .results as plain text (#2128)

  • [Changed] Sort packages by modification time by default (#2126)

  • [Changed] Resolve logical keys in summaries and vega inside packages (#2140)

  • [Changed] Embed: load polyfills, bring back prefix filtering, load more (#2153)

  • [Changed] Scan more bytes (first 128 KiB) when trying to detect if a JSON file is a Vega visualization (#2229)

  • [Changed] Use GraphQL for fetching and editing buckets (#2240)

  • [Changed] Use registry for search requests (#2242)

  • [Changed] Enhance quilt_summarize.json format, support title, description and multi-column layout (#2245)

  • [Changed] PDF preview: don't count pages (#2276)

  • [Changed] Default bucket icon changed from Quilt logo to more neutral (#2287)

  • [Changed] Cachebust revision list request (#2298)

  • [Changed] Wrap wide Vega charts with horizontal scroll (#2304)

  • [Changed] Unify package creation and update dialogs (support adding S3 files in both) (#2302)

  • [Changed] Warmer chart colors (#2329, #2338)

  • [Fixed] UnicodeDecodeError in indexer and pkgselect lambdas (#2123)

  • [Fixed] Catch and display package-related errors properly ("no such package" and "bad revision") (#2160)

  • [Fixed] Crashing pkgselect lambda's folder view on an empty manifest (#2147)

  • [Fixed] Infinite spinner on logout (#2232)

  • [Fixed] Dismiss error page when navigating from it (#2291)

  • [Fixed] Avoid crash on non-existent logical keys in pkgselect detail view (#2307

  • [Fixed] Error while rendering a preview inside a package (#2328)

  • [FIxed] Bring back missing username at Admin/Users table (#2339)

3.4.0 - 2021-03-15

Python API

  • [Added] QUILT_TRANSFER_MAX_CONCURRENCY environment variable (#2092)

  • [Added] QUILT_DISABLE_CACHE environment variable (#2091)

  • [Added] Support for callable dest parameter in Package.push() (#2095)

  • [Changed] Removed unused dependency on packaging (#2090)

  • [Fixed] Possible downloading of truncated manifests (#1977)

  • [Fixed] TypeError on import when running with PYTHONOPTIMIZE=2 (#2102)

Catalog, Lambdas

  • [Added] Support for EventBridge S3 events to es/indexer (#1987)

  • [Added] Generate and resolve Quilt package URIs (#1935)

  • [Added] Buttons for copying canonical package URIs (#1990)

  • [Added] Additional validation for package name (#1998)

  • [Added] Populate package name with username prefix (#2016)

  • [Added] Link from bucket overview page to bucket settings (#2022)

  • [Added] Folder to package dialog (#2040)

  • [Added] Search lambda: freeform action API and UI (#2087, #2088)

  • [Added] Spreadsheets Drag'n'Drop to Metadata (#2094)

  • [Changed] Tree view for files in package update dialog (#1989)

  • [Changed] Lambda indexing retry logic to not fail content extraction (#2007)

  • [Changed] Number of retries per ES and S3 failure in indexing Lambda (#1987)

  • [Changed] Handle delete markers in ES (#1997, #2000, #2003, #2017, #2023)

  • [Changed] Two-column layout for package dialogs (#2001)

  • [Changed] Show Schema validation errors in text mode (#2010)

  • [Changed] Toolchain: use webpack@5 (#2036) and TypeScript (#2043), ditch babel

  • [Changed] Use polyfill.io instead of bundled polyfills (#2043)

  • [Changed] Render JSON with custom tree-like viewer (#2037)

  • [Changed] Set JSON Schema defaults (#2053)

  • [Changed] Don't upload unmodified files while revising a package (#2080)

  • [Fixed] Bug that caused search to miss delete object and delete package events (#1987)

  • [Fixed] lambda previews for time series AICSImage data (potential IndexError if odd number of time points) (#1945)

  • [Fixed] Handle folders in search results (#1992, #1994)

  • [Fixed] Use EncodingType=url for S3 list requests to handle special chars in keys / prefixes (#2026)

  • [Fixed] Empty response from pkgselect folder view for packages with all non-string logical_keys or physical_keys (#1947)

  • [Fixed] "Download Directory" bug that caused 502 or failed downloads when any files contained the "+" character (#2067)

  • [Added] Ability to log in with Microsoft Azure Active Directory via OIDC (#2089)

3.3.0 - 2020-12-08

Python API

  • [Added] Metadata quality API (#1855). For details see this section.

  • [Changed] Improved formatting of package load progress bar (#1897)

  • [Fixed] Crash during load of package manifest with unicode symbols with non-unicode locale set (#1931)

Catalog, Lambdas

  • [Added] Ad hoc package updates (#1856)

  • [Added] Copy packages from one bucket to another (#1932)

  • [Added] Enhanced JSON editor and schema validation for package metadata (#1867)

  • [Added] Preview .pdbqt files as plain text (#1855)

  • [Added] Retry logic for failed queries, minimize load on ES for sample, images overviews (#1864)

  • [Added] Buttons to download packages and directories as .zip archives (#1868)

  • [Added] Search help dropdown for the index landing page (#1838)

  • [Changed] Get package revisions from ElasticSearch, not S3 (#1851)

  • [Changed] Render vega specs smaller than 20 MiB right away, render larger ones after pressing a button (#1873)

  • [Changed] Prefix filtering for directory view similar to AWS Console (#1876, #1880)

  • [Changed] Preview *notes files as plain text (#1896)

  • [Changed] Default search operator to "AND" (was "OR") for more precise searches (#1924)

  • [Changed] top_hash-based package routes (timestamp routes are still supported in the same way) (#1938)

  • [Fixed] Incomplete package stats for empty packages in es/indexer Lambda (#1869)

  • [Fixed] Slow parquet preview rendering (and probably other occurrences of JsonDisplay) (#1878)

3.2.1 - 2020-10-14

Python API

  • [Performance] 2X to 5X faster multi-threaded hashing of S3 objects (#1816, #1788)

  • [Fixed] Bump minimum required version of tqdm. Fixes a crash (UnseekableStreamError) during upload retry. (#1853)

CLI

  • [Added] --meta argument to push (#1793)

  • [Fixed] Crash in list-packages (#1852)

Catalog, Lambdas

  • [Added] Ability to preview larger Jupyter notebooks; warning when cells are elided (#1823, #1822)

  • [Added] Object size to package browsing experience in catalog (#1744)

  • [Added] Total number of packages to catalog Overview tab (#1808)

  • [Added] PDF and other file formats, including .gz ones, to catalog Overview tab

  • [Added] Drag-n-drop package creation (#1786)

  • [Added] Glacier support (#1794, #1796)

  • [Added] Show package metadata (#1806)

  • [Added] Search facets help (#1828)

  • [Added] Admin/buckets: re-index and repair (#1824)

  • [Changed] Case-insensitive package filtering (#1807)

  • [Changed] Show PDFs in bucket overviews (#1811)

  • [Changed] Admin/buckets: adjust SNS ARN input, make it possible to not subscribe to a topic (#1824)

  • [Changed] Show "push package" button when there's no packages in a bucket (#1843)

  • [Fixed] Bugs involving bad or missing package stats during S3 Select calls (#1829)

  • [Fixed] Overly aggressive 40X retry logic in es/indexer (#1804)

  • [Fixed] Semantic bugs in ElasticSearch timeouts (queries now time out properly) (#1803)

  • [Fixed] Missing Helvetica issues for PDFs (#1792)

  • [Fixed] Bulletproof file downloads via HTTP header override (#1787)

  • [Fixed] Previews not rendering in global search (#1787)

3.2.0 - 2020-09-08 - Package Registry Refactor

Python

  • Refactors local and s3 storage-layer code around a new PackageRegistry base class (to support improved file layouts in future releases)

  • Multi-threaded download for large files, 2X to 5X performance gains when installing packages with large files, especially on larger EC2 instances

  • Package name added to Package.resolve_hash

  • Bugfix: remove package revision by shorthash

  • Performance improvements for build and push

Catalog & Lambdas

  • PDF previews

  • Browse full package contents (no longer limited to 1000 files)

  • Indexing and search package-level metadata

  • Fixed issue with download button for certain text files

  • FCS files: content indexing and preview

  • Catalog sign-in with email (or username)

  • Catalog support for sign-in with Okta

3.1.14 - 2020-06-13 - Python API features, fixes, catalog capabilities, backend optimizations

Catalog

  • .cef preview

  • allow hiding download button

  • only show stats for 2-level extensions for .gz files

Python

  • quilt3.logged_in()

  • fix retries during hashing

  • improve progress bars

  • fix quilt3 catalog

  • expanded documentation

  • reduce pyyaml requirements to prevent version conflicts

Backend

  • improve unit test coverage for indexing lambdas

  • fix real-time delete handling (incl. for unversioned objects)

  • handle all s3:ObjectCreated: and ObjectRemoved: events (fixes ES search state and bucket Overview)

3.1.13 - 2020-04-15 - Windows Support

Python API

  • Official support for Windows

  • Add support for Python 3.7, 3.8

  • Fix Package import in Python

  • Updated libraries for stability and security

  • Quiet TQDM for log files ($ export QUILT_MINIMIZE_STDOUT=true )

  • CLI setting of config parameters

Catalog

  • new feature to filter large S3 directories with regex

  • more reliable bucket region inference

  • Support preview of larger Jupyter notebooks in S3 (via transparent GZIP)

  • JS (catalog) dependencies for stability and security

  • extended Parquet file support (for files without a .parquet extension)

  • Improvements to catalog signing logic for external and in-stack buckets

Special thanks to @NathanDeMaria (CLI and Windows support) and @JacksonMaxfield for contributing code to this release.

3.1.12 - 2020-03-11 - Command line push

Python

  • Add push to CLI

3.1.11 - 2020-03-10 - New command line features, bug fixes

Catalog

  • Updated JS dependencies

  • Display package truncation warning in Packages

Python

  • quilt3 install foo/bar/subdirectory

  • Bug fixes for CopyObject and other exceptions

3.1.10 - 2020-01-29

Python Client

  • Fix bug introduced in 3.1.9 where uploads fail due to incorrect error checking after a HEAD request to see if an object already exists (#1512)

3.1.9 - 2020-01-29

Python Client

  • quilt3 install now displays the tophash of the installed package (#1461)

  • Added quilt3 --version (#1495)

  • Added quilt3 disable-telemetry CLI command (#1496)

  • CLI command to launch catalog directly to file viewer - quilt3 catalog $S3_URL (#1470, #1487)

  • No longer run local container for quilt3 catalog (#1504). See (#1468, #1483, #1482) for various bugs leading to this decision.

  • Add PhysicalKey class to abstract away local files vs unversioned s3 object vs versioned s3 object (#1456, #1473, #1478)

  • Changed cache directory location (#1466)

  • More informative progress bars (#1506)

  • Improve support for downloading from public buckets (#1503)

  • Always disable telemetry during tests (#1494)

  • Bug fix: prevent misleading CLI argument abbreviations (#1481) such as --to referring to --tophash

  • Bug fix: background upload/download threads are now killed if the main thread is interrupted (#1486)

  • Performance improvements: load JSONL manifest faster (#1480)

  • Performance improvement: If there is an error when copying files, fail quickly (#1488)

Catalog

  • Better package listing UX (#1462)

  • Improve bucket stats visualization when there are many categories (#1469)

3.1.8 - 2019-12-20 - Catalog Command Fixes and Performance Improvements

Python API

  • Bug-fixes for quilt3.config and quilt3.catalog

  • Performance improvements for Packages

Catalog

  • Updated landing page

3.1.7 - 2019-12-13 - Package Cache

Catalog

  • New LOCAL mode for running the catalog on localhost

Python API

  • quilt3 catalog command to run the Quilt catalog on your local machine

  • quilt3 verify compares the state of a directory to the contents of a package version

  • Added a local file cache for installed packages

  • Performance improvements for upload and download

  • Support for short hashes to identify package versions

  • Adding telemetry for API calls

3.1.6 - 2019-12-03 - Package rollback

API Improvements

  • Implement Package.rollback

  • Drop support for object metadata (outside of packages)

  • Change the number of threads used when installing and pushing from 4 to 10 (S3 default)

  • Misc bug fixes

3.1.5 - 2019-11-20 - Catalog and API improvements

Catalog

  • Fix package listing for packages with more 100 revisions

  • Add stacked area charts for downloads

  • 2-level file-extensions for bucket summary

Python

  • Fix uploads of very large files

  • Remove unnecessary copying during push

3.1.4 - 2019-10-17

3.1.3 - 2019-10-11

  • Bug fix: when adding python objects to a package a temporary file would be created and then deleted when the object was pushed, leading to a crash if you tried to push that package again (PR #1264)

3.1.2 - 2019-10-11

  • Added support for adding an in-memory object (such as a pandas.DataFrame) to a package via package.set()

  • Fix to work with pyarrow 0.15.0

  • Performance improvements for list_packages and delete_package

  • Added list_package_versions function

3.0.0 - 2019-05-24 - Quilt 3 (formerly Quilt T4) Initial Release

This is the initial release of the new and improved Quilt 3 (formerly Quilt T4). For more information refer to the documentation.

2.9.15 - 2019-01-09 - Teams Config

Compiler

Adds a feature to allow quilt config to set a registry URL for a private Teams registry.

2.9.14 - 2018-12-20 - Push Package by Hash

Compiler

  • Adding a hash argument to quilt.push to allow pushing any package version to a registry.

Registry

  • Make object sizes required.

  • Update urllib3 version for security patch

Docs

  • Improved instructions for running registries.

2.9.13 - 2018-11-12 - Fix ascii decoding bug

  • Fix an ascii decoding issue related to ellipses …

2.9.12 - 2018-10-11 - Pyarrow 0.11 compatibility

Make Quilt work with pyarrow 0.11

  • Update Parquet reading code to match the API change in pyarrow 0.11.

  • Fix downloading of zero-byte files

2.9.11 - 2018-09-11 - Save Objects to Existing Packages

Compiler

  • New helper function quilt.save adds an object (e.g., a Pandas DataFrame) to an existing package by performing a sub-package build and push in a single step

  • BugFix: quilt.load now correctly returns sub-packages (fixes issue #741)

Registry

  • Send a welcome email to new users after activation

2.9.10 - 2018-08-08 - Minor updates and improved documentation

Compiler

  • fixes an issue with packages created on older versions of pyarrow

  • improves readability for quilt inspect

  • allow adding a node with metadata using sub-package build/push

Registry

  • adds documentation for running a private registry in AWS

2.9.9 - 2018-07-31 - Bug fixes

  • Suppress numpy warnings under Python 2.7

  • Fix subpackage build and push

2.9.8 - 2018-07-30 - Flask-internal Authentication

Compiler

  • Added support for sub-package build and push to allow updates to allow adding nodes to large packages without materializing the whole package

  • First-class support for ndarray

Registry

  • Replaced dependence on external OAuth2 provider with a built-in authentication and session management

  • Registry support for sub-package push

Catalog

  • Updated to support new registry authentication

2.9.7 - 2018-07-11 - Asa extensions

Compiler

  • added Bracket accessor for GroupNodes

  • asa.plot to show images in packages

  • asa.torch to convert packages to PyTorch Datasets

  • Enforce fragment store as read-only

Catalog

  • Added source maps and CI for catalog testing

2.9.6 - 2018-06-13 - Documentation and Bugfixes

Documentation

Expands and improves documentation for working with Quilt packages.

Bug fixes and small improvements

  • Load packages by hash

  • Choose a custom loader for DataNodes with asa=

Registry

  • Specify Ubuntu version in Dockerfiles

2.9.5 - 2018-05-23 - Package Filtering

Catalog

  • display package traffic stats in catalog

Compiler

  • filter packages based on per-node metadata

  • get/set metadata for package nodes

  • support custom loaders in the _data method

Registry

  • package commenting

2.9.4 - 2018-04-20 - Metadata only package install

Compiler

  • Metadata-only package install

  • Build DataFrames from existing Parquet files

  • Remove HDF5 dependencies

  • Code cleanup and refactoring

Registry

  • Option for metadata-only package installs

  • New endpoint for fetching missing fragments (e.g., from partially installed packages)

  • Improved full-text search

2.9.3 - 2018-03-20 - Package Composition

Compiler

  • Allow building packages out of other packages and elements from other packages. A new build-file keyword, package inserts a package (or sub-package) as an element in the package being built.

Catalog

  • Upgrade router and other dependencies

  • Display packages by author

2.9.2 - 2018-03-01 - Quilt Teams

Catalog Changes to support private registries

  • Amin UI for controlling users and access

  • Auditing views

Globbing for package builds

  • Allow specifying sets of input files in build.yml

Command-line support for private registries

  • Specify teams packages

  • Admin commands to create and activate/deactivate users

2.9.1 - 2018-02-06 - Better Progress Bar

Version 2.9.1 introduces a better progress bar for installing (downloading) Quilt packages. Quilt push now sends objects' uncompressed size to the registry. The progress bar is now based on the total bytes downloaded instead of the number of files.

2.9.0 - 2018-02-02 - Shared Local Package Storage

Shared Local Package Storage

Import packages from shared local directories to save storage overhead and network traffic when sharing packages on the same local network.

Registry Install Stats

Log package installs in the registry to display stats on package use.

New Python API commands

  • generate

  • rm

  • search

Drop support for Python 3.4

(BETA) Team Registries

Updates to commands and local storage to allow users to connect to different registries to support teams running private registries for internal sharing.

2.8.4 - 2018-01-24 - Fix download retry

Fixes a bug in download that prevented retrying failed downloads.

2.8.3 - 2018-01-19 - Remove Unneeded Pandas dependency

#186 introduced an undeclared dependency on Pandas >= 0.21.0 (by catching ParserError during CSV parsing). This release removes that dependency and resolves #291.

2.8.2 - 2018-01-17 - Hotfix for several quilt commands

PR https://github.com/quiltdata/quilt/pull/290

2.8.1 - 2018-01-10 - Add Quilt Catalog

Quilt Catalog

Source for the Quilt data catalog is now included in this repository.

MySQL->Postgres

Ported the Quilt registry from MySQL to Postgres

Docker Compose

Improvements to the docker configuration that allows running the registry, catalog, database and authentication service from Docker compose.

Parallel Download

Data fragments can now be downloaded in parallel leading to much faster package installs for large packages.

2.8.0 - 2017-12-07 - Centralized Local Package Store

Release Highlights

Quilt packages live in a centralized location on your machine

Quilt data packages are now available wherever you run Python. We recommend that users quilt push all local packages to the registry before upgrading. Further details on migration are here.

Faster builds with build cache

Quilt now caches build intermediates. So if you wish to update the README of a multi-gigabyte package, you can rebuild the entire package in one second.

Group-level build parameters

You can now specify build parameters (like transform) for all children of a group in one shot. The updated syntax and docs are here.

quilt.yml is like requirments.txt but for data

You can now express dependencies on multiple packages in a single file. Docs here.

Experimental: build a package from a GitHub repo

Quilt build now accepts GitHub URLs. If you use data stored on GitHub you can turn it into a Quilt package with quilt build.

2.7.1 - 2017-11-09 - Checks: unit tests for data packages

Version 2.7.1 includes several minor bug fixes and one new feature, checks. Checks allow a user to specify data integrity checks that are enforced during quilt build.

2.7.0 - 2017-08-18 - Subpackages and more efficient uploads/downloads

  • Support installing subpackages as quilt install usr/pkg/path

  • Upload fragments in parallel

  • Use http sessions when accessing S3

2.6.3 - 2017-07-22 - Clear session to prevent quilt.login() bugs in Jupyter

2.6.1 - 2017-07-20 - Package Delete

This release adds a new command to delete a package including all versions and history from the registry.

2.6.0 - 2017-07-14 - Fast Builds for Large Packages

Building a package from a directory of input files now skips generating a build file. That speeds up the build process and makes it easier to change the package contents and rebuild.

2.5.1 - 2017-07-06 - Push Public Packages

This release includes support for paid plans on quiltdata.com and is recommended for all individual and business-plan users. It adds a shortcut to push packages and make them public in a single command and improves documentation.

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