v0.13rc1

Vendoring cloudpickle 2.2

Vendoring cloudpickle 2.2 for internal use allows cloudpickle version 3 to be used with, for example, Dask in delayed functions.

What's Changed

• Fill in missing API docs by @nickvigilante in #687
• Rename vcf.ingestionq to vcf.ingestion by @nickvigilante in #688
• Vendor cloudpickle by @sgillies in #686
• Fix credentials discrepancy between Bioimaging/VCF and SOMA registration UDFs by @sgillies in #685

Full Changelog: v0.12.31...v0.13rc1

v0.12.31

Run VCF queries as TileDB batch task graphs

This option enables the tiledb.cloud.vcf.read distributed query to use batch task graphs (as opposed to realtime), which is slower but more robust.

What's Changed

• Add a batch_mode flag to VCF scalable queries by @gspowley in #683

Full Changelog: v0.12.30...v0.12.31

v0.12.30

New read/write/delete organization role, SOMA ingestion improvements, and better user experience for the tiledb namespace

Version 0.12.30 allows use of the TileDB platform's new "read_write_delete" (permission to read, write, and delete assets) organization role. It's one step less privileged than the existing "admin" role.

The tiledb.cloud.soma.ingest module has been refactored and a defect in registering multiple SOMA groups has been fixed. The cloud storage location of output groups has changed slightly. All groups are now output to OUTPUT_URI/NAME, where OUTPUT_URI is the given parameter, like s3://bucket/prefix/, and NAME is the base/stem of an H5ad file.

Lastly, tiledb is a namespace package, and in your environment may include modules from tiledb, tiledb.vector_search and tiledb.cloud distributions. Previously, importing tiledb or tiledb.vector_search in an environment where tiledb.cloud is also installed would trigger a warning about your need to login, even if you don't have any intent to use tiledb.cloud methods. This warning no longer happens needlessly and only shows up when appropriate.

What's Changed

• Re-generate generated API to add new r/w/d organization role. by @NullHypothesis in #644
• fix obs and var defaults to return all values if none spec'd by @spencerseale in #676
• Move test requirements, adjust and streamline CI YAML by @sgillies in #674
• Register ingested groups using the correct URI by @sgillies in #679
• Defer loading of cloud.json file by @sgillies in #681
• typ{o,e} fixes by @ryan-williams in #680
• Patch config._config, not config.config by @sgillies in #682
• Expose deadline argument for DAG by @ktsitsi in #678

Full Changelog: v0.12.29...v0.12.30

v0.12.29

Bio-imaging and SOMA ingestion improvements

Finer control over the resources used to run UDFs during Bio-imaging and SOMA data ingestion, and full support for ingesting folders of multiple H5ad files are highlights of this release.

The Bio-imaging, SOMA, and VCF ingestion entry points now all take an ingest_resources argument. Its value is the same as the existing resources argument. The new ingest_resources argument isn't consumed by task graph construction and is propagated to the most resource-intensive tasks of ingestion graphs.

The previous version of this package allowed ingestion of single H5ad files. Now, folders of multiple files can be ingested by passing the URI of the folder and a pattern argument, such as *.h5ad, that matches only H5ad files in the folder.

What's Changed

• Adding PNG support and enabling experimental reader in kwargs by @ktsitsi in #654
• Add Panel dashboard wrapper for Voila by @gspowley in #667
• Add a tag name check for releases and some words about releases by @sgillies in #668
• Propagate resources to ingest_h5ad node by @sgillies in #669
• Skip sub-folders and make pattern matching more useful by @sgillies in #670
• Add ingest_resources for use with UI by @sgillies in #671
• Remove value registration wrappers by @sgillies in #672
• Tests have been xpass-ing, no longer need xfail marks by @sgillies in #673

Full Changelog: v0.12.28...v0.12.29

v0.12.28

What's Changed

• Add tests of with_metadata option by @sgillies in #657
• Add http(s) scheme if missing when logging in by @sgillies in #658
• Remove xfail on 3 graph connection tests by @sgillies in #659
• Remove run_on from docstrings by @ktsitsi in #662
• Recategorize API reference by @sgillies in #663
• Revert "Workaround for object_type in py>=0.32.0" by @ktsitsi in #665

Full Changelog: v0.12.27...v0.12.28

v0.12.27

What's Changed

• xfail 5 tests because of 2 upstream issues by @sgillies in #648
• Un-xfail two tests that are no longer x'd to fail. by @thetorpedodog in #652
• Only follow a limited number of redirects. by @thetorpedodog in #651
• Add datetime parsing for executing UDFs at timestamps. by @thetorpedodog in #653
• Move our custom logger from _common.py to logging.py by @sgillies in #650
• Improve missing object detection in upload_wheel by @gspowley in #655
• Workaround for object_type in py>=0.32.0 by @ktsitsi in #656

Full Changelog: v0.12.26...v0.12.27

v0.12.26

What's Changed

• Fix urllib3.BaseHTTPResponse type hint. by @JohnMoutafis in #647
• Default to venv autodetect in install_wheel by @spencerseale in #649

Full Changelog: v0.12.25...v0.12.26

v0.12.25

What's Changed

• Fix SOMA ingestion's registration race condition. by @JohnMoutafis in #643
• Add functions to access new asset listing endpoints. by @thetorpedodog in #642
• Perform HEAD requests to find the correct location to upload. by @thetorpedodog in #645

Full Changelog: v0.12.24...v0.12.25

v0.12.24

What's Changed

• Add feature: Split VCF by @spencerseale in #616
• Use file endpoint, not notebooks, to upload files. by @thetorpedodog in #634
• Fix a comment typo. by @NullHypothesis in #635
• Improve handling of unsorted VCF files by @gspowley in #636
• Update find to use VFS.ls_recursive by @gspowley in #639
• invite_to_organization: fix InvitationOrganizationJoinEmail ctor call by @ryan-williams in #637
• Add registered_name to SOMA ingestion. by @JohnMoutafis in #640

New Contributors

• @ryan-williams made their first contribution in #637

Full Changelog: v0.12.23...v0.12.24

v0.12.23

What's Changed

• Allow passing URIs for asset-related functions. by @thetorpedodog in #627
• SOMA ingestion: Refactor access_credentials_name with acn by @JohnMoutafis in #630
• Unit tests for install_wheel by @spencerseale in #629

Full Changelog: v0.12.22...v0.12.23