Release v1.1.0 by DylanWelzel · Pull Request #445 · biothings/biothings.api

DylanWelzel · 2026-05-26T22:31:25Z

v1.1.0 (2026/05/27)
Highlights:
- Added Python 3.14 support and dropped Python 3.8 support.
- Reworked biothings CLI configuration, pathing, and dataplugin command organization.
- Added MongoDB build cleanup management APIs and commands.

biothings.hub improvements:
    - Added prefix support to DataTransformMDB. ([#411](https://github.com/biothings/biothings.api/pull/411))
    - Added TAR and Zstandard file handling. ([#424](https://github.com/biothings/biothings.api/pull/424), [#428](https://github.com/biothings/biothings.api/pull/428))
    - Added support for custom local uploader and dumper classes in dataplugin manifests. ([#431](https://github.com/biothings/biothings.api/pull/431))
    - Added MongoDB build cleanup validation and deletion tooling. ([#437](https://github.com/biothings/biothings.api/pull/437))

biothings.utils improvements:
    - Fixed dict_sweep handling for NaN-like values, including pandas.NA and pandas.NaT. ([#442](https://github.com/biothings/biothings.api/pull/442))
    - Centralized orjson usage across the library. ([#435](https://github.com/biothings/biothings.api/pull/435))

biothings.web improvements:
    - Removed deprecated Google Analytics event support. ([#439](https://github.com/biothings/biothings.api/pull/439))
    - Removed old doc_type and deprecated Elasticsearch compatibility code.
    - Improved Elasticsearch exception handling and query response behavior.
    - Optimized Elasticsearch memory usage when using scroll API.

biothings.cli improvements:
    - Added CLI config and pathing commands. ([#418](https://github.com/biothings/biothings.api/pull/418), [#422](https://github.com/biothings/biothings.api/pull/422))
    - Added CLI dump mark-success support. ([#423](https://github.com/biothings/biothings.api/pull/423))
    - Fixed Typer/rich_utils loading behavior. ([#426](https://github.com/biothings/biothings.api/pull/426))

Misc improvements:
    - Updated dependencies and package metadata for Python 3.9+, including tornado, typer, pymongo, orjson, and zstandard.
    - Updated GitHub Actions test, build, and publish workflows.

* Interim commit for improving scheduler error messaging * Add ValueError messgaing for scheduler errors * Remove prior comments from the indexer scheduler * Move the tests to the corresponding tests directory * Add formal exception messaging * Add additional exception tests * Format the dataindex module directory * Update the tests * Simplify the exception handling test --------- Co-authored-by: jschaff <jschaff@scripps.edu>

…annot switch

…MongoDB builds

…lds method

… and improve logging

* replace orjson.loads with serializer method * remove direct orjson reference from web * centralize orjson library use; extend serializer `to_json` function to return in byte form if specified

* add zst file handling for Python 3.14 and below * condition reordering

Build Requests Improvement

Build cleanup

dict_sweep's `val in vals` membership test raises a ValueError when val is pandas.NA (or similar NaN-like types) because pandas overloads the == operator to raise instead of returning False. Changes: - Add _is_nan() helper that detects float NaN, pandas.NA, and pandas.NaT via math.isnan and duck-typing (__class__.__name__) without importing numpy or pandas - Call _is_nan() before val in vals at every level in dict_sweep (top-level values, list items, and nested dicts) - Replace list.remove() with filter-and-rebuild to avoid __eq__ calls on NaN-like values during list mutation - Add comprehensive tests covering mock and real pandas/numpy types

Remove deprecated Universal Analytics (UA) support

…ved type checks and tests

fix: handle NaN-like values in dict_sweep

This reverts commit 79cb1fd.

fix: refactor code for codacy

DylanWelzel and others added 30 commits May 28, 2025 23:47

update the unlist and unlist_incexcl functions

e980585

add tests for each function

ab7952f

move unlist helper functions outside

cefeca5

add comments for internal helper functions

fb13da2

Hide cloud credentials when finding snapshots

a3ecb92

added more detailed error logging for when the temporary collection c…

65ec46a

…annot switch

fix: 🐛 an issue when calling load_json

bf9d35d

add postgresql collection class

a2973d0

add tests for postgresql collection class

c5987fb

fix import in test

c638bfa

fix imports

b4ab233

fix codacy issues

dae48c6

add sync_snapshots functionality

0b7f21a

use keyword args

9ce1e9e

fix keyword argument

3774770

use keyword args in cleanup method

4dd03a6

handle undefined environments

772baf8

handle unregistered environment

22ed1f0

update missing environment message

d676d60

move key error catch for both legacy and current formats

bc062f0

add not found err message

aee5e75

use workers

5fd6c12

change sync to validate

8dc859e

update sync to validate in commands

1e7746c

add ignore errors logic

947423d

handle delete_snapshots body args

9b3ceb7

remove f strings from logging messages

9b08b55

handle merge conflict

4854677

fix codacy errors

e05134d

DylanWelzel and others added 28 commits February 17, 2026 12:40

feat: add MongoBuildCleanupManager and related commands for managing …

4a4cde6

…MongoDB builds

refactor: rename API endpoints for MongoDB builds for clarity

0ad2d84

fix: ensure asynchronous closing of database connection in delete_bui…

7095ff2

…lds method

feat: enhance delete_builds method to return deleted collections info…

e42b018

… and improve logging

Centralize orjson usage across library (#435)

970bee7

* replace orjson.loads with serializer method * remove direct orjson reference from web * centralize orjson library use; extend serializer `to_json` function to return in byte form if specified

add zst file handling for Python 3.14 and below (#428)

de9f047

* add zst file handling for Python 3.14 and below * condition reordering

Merge pull request #432 from biothings/build-requests

df09f92

Build Requests Improvement

add validate_mongo_builds method and API endpoint

7d58821

remove excess brackets (#436)

56a1387

Merge pull request #437 from biothings/build-cleanup

c74e044

Build cleanup

remove deprecated Google Analytics support and clean up related code

29b5aab

fix: update NaN handling in dict_sweep and add tests for _val_to_delete

6eb5acb

Merge pull request #439 from biothings/remove-ga-deprication

2775ebf

Remove deprecated Universal Analytics (UA) support

fix: enhance NaN handling in dict_sweep and _val_to_delete with impro…

ec6b8b8

…ved type checks and tests

Merge pull request #442 from biothings/fix/dict-sweep-nan-handling

47c9c49

fix: handle NaN-like values in dict_sweep

build: 📦 updated package version to 1.0.3

c3e40d9

fix: refactor code for codacy

d659399

style: address remaining codacy f-string issues

0903280

test: make any query randomness assertion deterministic

79cb1fd

Revert "test: make any query randomness assertion deterministic"

8460eb4

This reverts commit 79cb1fd.

Merge pull request #446 from biothings/codacy-fixes

5a30fdf

fix: refactor code for codacy

fix: close zst tar resources safely

6c24999

fix: raise specific error for invalid zst tar member

132e503

fix: replace broad common utility exceptions

fb69a24

fix: preserve tar member lookup context

7fc553a

Merge origin/master into 1.1.x for release 1.1.0

69a5955

build: 📦 updated package version to 1.1.0

572048f

DylanWelzel changed the title ~~1.1.x~~ Release v1.1.0 May 27, 2026

DylanWelzel merged commit b863001 into master May 27, 2026
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Release v1.1.0#445

Release v1.1.0#445
DylanWelzel merged 178 commits into
masterfrom
1.1.x

DylanWelzel commented May 26, 2026 •

edited

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DylanWelzel commented May 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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DylanWelzel commented May 26, 2026 •

edited

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