v1.3.0 (2025-09-16)

What's Changed

• build(deps): bump actions/download-artifact from 4 to 5 by @dependabot[bot] in #567
• build(deps): bump actions/checkout from 4 to 5 by @dependabot[bot] in #568
• build(deps): bump the python-packages group with 5 updates by @dependabot[bot] in #571
• build(deps): bump pandas from 2.3.1 to 2.3.2 by @dependabot[bot] in #570
• build(deps): bump sqlalchemy from 2.0.42 to 2.0.43 by @dependabot[bot] in #569
• build(deps-dev): bump types-openpyxl from 3.1.5.20250602 to 3.1.5.20250822 by @dependabot[bot] in #572
• build(deps): bump actions/setup-python from 5 to 6 in /.github/actions/setup-env by @dependabot[bot] in #577
• Enable anndata input and output by @d33bs in #573
• Decrease "small" pytest testing duration time by @d33bs in #579
• Add type hints for all production code by @d33bs in #580
• bump: version 1.2.4 -> 1.3.0 by @d33bs in #581

Full Changelog: v1.2.4...v1.3.0

v1.2.4 (2025-08-06)

What's Changed

• Add large_data_tests marker to help deselect time intensive tests for development by @d33bs in #529
• Update pre-commit-lite conditions by @d33bs in #528
• Return output filepath when output_file is used by core functions by @d33bs in #530
• Update tornado to address CVE-2025-47287 by @d33bs in #531
• Use trusted publishing for PyPI package deployment by @d33bs in #532
• build(deps-dev): bump setuptools from 70.0.0 to 78.1.1 by @dependabot[bot] in #533
• Add docs about versioning by @d33bs in #534
• Alleviate nbsphinx dependency bug for docs builds by @d33bs in #536
• build(deps-dev): bump the python-packages group with 4 updates by @dependabot[bot] in #540
• build(deps): bump sqlalchemy from 2.0.40 to 2.0.41 by @dependabot[bot] in #541
• build(deps-dev): bump types-openpyxl from 3.1.5.20250306 to 3.1.5.20250516 by @dependabot[bot] in #542
• build(deps-dev): bump requests from 2.32.2 to 2.32.4 by @dependabot[bot] in #543
• Add isort to linting checks, apply formatting, and resolve circular imports by @d33bs in #545
• chore: consistent project title casing by @d33bs in #547
• ci: add Almanack to pre-commit checks by @d33bs in #548
• ci: fix poetry install for devcontainer by @d33bs in #550
• build(deps): bump the python-packages group with 6 updates by @dependabot[bot] in #552
• build(deps): bump pandas from 2.2.3 to 2.3.0 by @dependabot[bot] in #554
• build(deps-dev): bump lxml from 5.4.0 to 6.0.0 by @dependabot[bot] in #553
• build(deps): bump aiohttp from 3.10.11 to 3.12.14 by @dependabot[bot] in #557
• build(deps-dev): bump starlette from 0.41.2 to 0.47.2 by @dependabot[bot] in #558
• docs: add CytoTable guidance to readme by @d33bs in #556
• build(deps): bump pandas from 2.3.0 to 2.3.1 by @dependabot[bot] in #562
• build(deps): bump the python-packages group with 4 updates by @dependabot[bot] in #559
• build(deps-dev): bump furo from 2024.8.6 to 2025.7.19 by @dependabot[bot] in #560
• build(deps): bump pyarrow from 20.0.0 to 21.0.0 by @dependabot[bot] in #561
• build(deps): bump sqlalchemy from 2.0.41 to 2.0.42 by @dependabot[bot] in #563
• refactor: transition asserts for production code by @d33bs in #564
• bump: version 1.2.3 -> 1.2.4 by @d33bs in #565

Full Changelog: v1.2.3...v1.2.4

v1.2.3 (2025-05-08)

What's Changed

• fix(cell_locations): modify tests for data updates by @d33bs in #505
• build(deps): bump the python-packages group with 5 updates by @dependabot in #502
• build(deps): bump pyarrow from 18.1.0 to 19.0.0 by @dependabot in #503
• build(deps): bump sqlalchemy from 2.0.36 to 2.0.37 by @dependabot in #504
• ci(cache): use os with arch for cache naming by @d33bs in #508
• ci(runners): bump macos gh actions runner version by @d33bs in #506
• update doi for nature methods pub by @gwaybio in #514
• Remove citation info (keep just pointer) in readme by @gwaybio in #515
• build(deps): bump the python-packages group with 6 updates by @dependabot in #512
• build(deps): bump sqlalchemy from 2.0.37 to 2.0.38 by @dependabot in #513
• build(deps-dev): bump jinja2 from 3.1.5 to 3.1.6 by @dependabot in #516
• build(deps-dev): bump the python-packages group with 8 updates by @dependabot in #517
• build(deps-dev): bump types-openpyxl from 3.1.5.20241225 to 3.1.5.20250306 by @dependabot in #518
• Organize DeepProfiler test data in one spot by @d33bs in #520
• build(deps-dev): bump h11 from 0.14.0 to 0.16.0 by @dependabot in #521
• ci: add pre-commit-update and related updates by @d33bs in #507
• refactor: add plugin configuration to pyproject by @d33bs in #509
• Update docs configuration for virtualenv and poetry bug by @d33bs in #523
• docs(pr): comment block for PR template desc by @d33bs in #496
• build(deps): bump the python-packages group with 5 updates by @dependabot in #524
• build(deps): bump pyarrow from 19.0.1 to 20.0.0 by @dependabot in #525
• Enable Python 3.13 compatibility by @d33bs in #526
• bump: version 1.2.2 -> 1.2.3 by @d33bs in #527

Full Changelog: v1.2.2...v1.2.3

v1.2.2 (2025-01-23)

What's Changed

• build(deps-dev): bump tornado from 6.4.1 to 6.4.2 by @dependabot in #480
• build(deps-dev): bump types-openpyxl from 3.1.5.20240918 to 3.1.5.20241126 by @dependabot in #482
• build(deps-dev): bump pytest-cov from 4.1.0 to 6.0.0 by @dependabot in #483
• build(deps-dev): bump commitizen from 3.30.0 to 4.0.0 by @dependabot in #484
• build(deps-dev): bump furo from 2023.9.10 to 2024.8.6 by @dependabot in #485
• build(deps): bump the python-packages group with 6 updates by @dependabot in #481
• ci(python): bump target python for ci workflows by @d33bs in #486
• ci(pre-commit): add pre-commit lite for auto fixes by @d33bs in #488
• Check if downloaded file is empty by @shntnu in #385
• docs(maintainer): add maintainer governance docs by @d33bs in #487
• build(deps): bump the python-packages group with 7 updates by @dependabot in #490
• build(deps-dev): bump types-openpyxl from 3.1.5.20241126 to 3.1.5.20241225 by @dependabot in #491
• build(deps-dev): bump jinja2 from 3.1.4 to 3.1.5 by @dependabot in #492
• build(deps-dev): bump virtualenv from 20.25.1 to 20.26.6 by @dependabot in #493
• Fix Bug in sample Parameter in feature_select(): Prevent Unintended Row Removal and Dataset Modification by @axiomcura in #495
• bump: version 1.2.1 -> 1.2.2 by @d33bs in #498

Full Changelog: v1.2.1...v1.2.2

v1.2.1 (2024-11-20)

What's Changed

• ci(dependencies): update setup python action dependencies and dependabot settings by @d33bs in #457
• ci(releases): constrain PyPI GitHub Actions release trigger types by @d33bs in #458
• ci(pre-commit): format pyproject.toml with pyproject-fmt by @d33bs in #453
• Modify CITATION.cff to conform to cffconvert formatting by @d33bs in #460
• build(python): bump minimum Python version to 3.9 by @d33bs in #464
• build(deps): bump scikit-learn from 1.3.2 to 1.5.0 by @dependabot in #465
• ci(dependabot): enable auto poetry updates by @d33bs in #463
• build(deps-dev): bump sphinx-autobuild from 2021.3.14 to 2024.10.3 by @dependabot in #467
• build(deps-dev): bump pre-commit from 3.5.0 to 4.0.1 by @dependabot in #468
• build(deps-dev): bump sphinx from 7.1.2 to 7.4.7 by @dependabot in #470
• ci: exclude scipy, sqlachemy, pandas from groups updates by @kenibrewer in #471
• build(deps): bump the python-packages group across 1 directory with 13 updates; retain cytominer-database 0.3.4 by @dependabot in #473
• build(deps): bump sqlalchemy from 1.4.52 to 2.0.36; move to sqlalchemy.text for queries by @dependabot in #469
• build(python): add python 3.12 compatibility by @d33bs in #475
• refactor(collate): deprecationwarning for collate by @d33bs in #462
• build(deps): bump aiohttp from 3.10.2 to 3.10.11 by @dependabot in #479
• build(deps): bump codecov/codecov-action from 4 to 5 by @dependabot in #478
• bump: version 1.2.0 -> 1.2.1 by @d33bs in #461

Full Changelog: v1.2.0...v1.2.1

v1.2.0 (2024-09-30)

What's Changed

• build(docker): add Dockerfile and container image build tests by @d33bs in #362
• fix: SQLite joins should be on ImageNumber,TableNumber and not ImageNumber by @shntnu in #378
• fix: add workspaceDir to git safe directories for devcontainers by @shntnu in #379
• dev: add docker-in-docker feature to devcontainer by @kenibrewer in #381
• refactor: update ruff to 0.3.4 by @kenibrewer in #386
• Refactor/apply isort linting checks by @kenibrewer in #389
• build(docker): add docker hub push capabilities by @d33bs in #377
• refactor: apply bandit checks by @kenibrewer in #387
• fix(ci): docker image push fixes by @d33bs in #395
• fix(ci): docker image push readme updates by @d33bs in #398
• build(deps): bump idna from 3.6 to 3.7 by @dependabot in #403
• refactor(pandas): enable copy_on_write for Pandas by @d33bs in #401
• fix(poetry): add tool.setuptools_scm section by @d33bs in #402
• build(deps): bump aiohttp from 3.9.3 to 3.9.4 by @dependabot in #405
• ci(runners): update macos version for python by @d33bs in #408
• refactor(pd): avoid dataframe fragmentation in agg by @d33bs in #407
• feat(dev): add improved makefile with additional helper commands by @kenibrewer in #391
• ci(runners): specify GitHub Actions Ubuntu runner image by @d33bs in #411
• docs(docker): add docker installation instructions by @d33bs in #409
• fix(pandas): add condition for pandas config by @d33bs in #415
• build(deps-dev): bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in #413
• build(deps-dev): bump requests from 2.31.0 to 2.32.2 by @dependabot in #419
• build(deps-dev): bump tornado from 6.4 to 6.4.1 by @dependabot in #417
• build(deps): bump urllib3 from 1.26.18 to 1.26.19 by @dependabot in #420
• bug(compartments): avoid lowercase compartment strings by @d33bs in #421
• build(deps-dev): bump certifi from 2024.2.2 to 2024.7.4 by @dependabot in #422
• build(deps-dev): bump zipp from 3.18.1 to 3.19.1 by @dependabot in #423
• build(deps-dev): bump setuptools from 69.2.0 to 70.0.0 by @dependabot in #424
• build(deps-dev): bump webob from 1.8.7 to 1.8.8 by @dependabot in #425
• build(deps): bump aiohttp from 3.9.4 to 3.10.2 by @dependabot in #426
• Add dark mode style color for contrast in docs by @d33bs in #429
• ci(codecov): fix errors with automated coverage by @d33bs in #432
• ci(dependabot): enable GitHub Actions updates by @d33bs in #438
• ci(codecov): add codecov token by @d33bs in #446
• ci(codecov): correct codecov key typo by @d33bs in #447
• build(deps): bump pre-commit/action from 3.0.0 to 3.0.1 by @dependabot in #445
• build(deps): bump docker/build-push-action from 5 to 6 by @dependabot in #444
• build(deps): bump peter-evans/dockerhub-description from 3 to 4 by @dependabot in #443
• Improve Documentation for Non-CellProfiler Datasets in Pycytominer by @axiomcura in #430
• Update error message and docs for features argument to clarify CellProfiler default expectations and how to handle non-CellProfiler data by @axiomcura in #448
• ci(mypy): add mypy check and adjust code for types by @d33bs in #439
• Updating pyproject python versioning by @axiomcura in #454
• bump: version 1.1.0 → 1.2.0 by @d33bs in #455

Full Changelog: v1.1.0...v1.2.0

v1.1.0 (2024-03-13)

What's Changed

• Bump pyarrow from 13.0.0 to 14.0.1 by @dependabot in #357
• Bump aiohttp from 3.8.6 to 3.9.0 by @dependabot in #358
• Update Readme with Citation section by @axiomcura in #359
• docs(template): PR template attribution to comment by @d33bs in #363
• Fix Spherize – use SVD, simplify calculations by @shntnu in #320
• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #364
• Bump aiohttp from 3.9.0 to 3.9.2 by @dependabot in #370
• fix(build): add pdv plugin by @kenibrewer in #368
• docs(changelog): add commitizen template by @kenibrewer in #356
• ci: add versioned artifact build action by @kenibrewer in #373
• Apply ruff formatting and linting along with relevant refactoring by @kenibrewer in #371
• bump: version 1.0.1 → 1.1.0 by @d33bs in #374

Full Changelog: v1.0.1...v1.1.0

v1.0.1 (2023-11-09)

What's Changed

• fix(collate): make optional dependency imports localized by @kenibrewer in #351
• fix(docs): add dynamic versioning to docs build by @kenibrewer in #353

Full Changelog: v1.0.0...v1.0.1

v1.0.0 Release

Pycytominer v1.0.0 Release

What's Changed

• Updating __about__.py version and fixing pyPI upload action by @gwaybio in #209
• Use numpy to calculate pearson corr of non NaN matrices by @johnarevalo in #193
• Implementing DeepProfiler single cell output and normalization by @roshankern in #210
• Fix #192 warnings for scipy mad func and other deprecated params by @johnarevalo in #194
• Fix of .merge_single_cells() to Load Single-Cell Data into Dataframes by @bunnech in #219
• Add column numbers to DP locations by @roshankern in #218
• Add to Function Converting SQLite to Pandas DataFrame and Merging of Additional Metadata by @bunnech in #228
• Address Installation Dependency Gaps by @d33bs in #232
• Enable custom image table name for SQLite queries in cells.py by @gwaybio in #235
• Enable flexible pyarrow dependency by @d33bs in #236
• Change drop_outlier default to 500 by @bethac07 in #238
• Added check before dropping well column by @kenibrewer in #241
• Allow column subsetting at the time of loading by @bethac07 in #246
• Reflect updated defaults in collate documentation by @bethac07 in #244
• avoid re-validation for excluded features by @johnarevalo in #243
• Add float_datatype parameter for SingleCells compartment load and merge performance flexibility by @d33bs in #248
• Pin SQLAlchemy below 2 by @bethac07 in #251
• Make AWS obey excludes by @bethac07 in #256
• Implementing parquet loading in load_profiles function by @axiomcura in #262
• pin scipy <1.9 by @ErinWeisbart in #258
• New cyto tool: create cell locations file by @shntnu in #257
• Adding gitpod, codespaces, devcontainer configs along with pre-commit code formatting using black and prettier by @kenibrewer in #264
• make default unique_cut value for variance_threshold consistent with feature_select by @alxndrkalinin in #283
• cell_locations: Writing output to S3 was failing; fixed this by @shntnu in #271
• load_profiles should work with PurePath types by @gwaybio in #285
• Change variance_threshold default to 0.01 by @shntnu in #286
• Update python versions - 3.7 deprecation, 3.10 and 3.11 testing support by @gwaybio in #287
• Github actions pre-commit CI pipeline by @kenibrewer in #279
• Update README in preparation for version 1 release by @gwaybio in #289
• Run pre-commit (black, prettier) on all files by @gwaybio in #291
• Changed function arguments throughout pycytominer from str 'none' to None by @kenibrewer in #293
• Update docs by @gwaybio in #290
• logo touchup by @vincerubinetti in #300
• Add pipeline-examples tutorial by @niranjchandrasekaran in #297
• [Hot Fix] README figure wonk by @gwaybio in #295
• Add issue templates by @jenna-tomkinson in #296
• Add informative merge suffixes for platemap and external metadata column collisions by @kenibrewer in #292
• Adding Pycytominer General Walkthrough Tutorial for RTD Website by @axiomcura in #305
• Add "output_type" parameter to major functions by @jenna-tomkinson in #307
• Make sample argument uniform for normalize and feature_select by @gwaybio in #311
• Switch build from setuptools to Poetry and move tests path by @kenibrewer in #303
• added ipython to rtd requirments file by @axiomcura in #309
• Remove master branch references after migrating to main by @kenibrewer in #324
• Bump urllib3 from 1.26.16 to 1.26.17 by @dependabot in #326
• [Refactor] Migrate dependencies in docs/requirements.txt to pyproject.toml by @kenibrewer in #325
• Bump urllib3 from 1.26.17 to 1.26.18 by @dependabot in #329
• refactor(devcontainer): move vscode settings into devcont config by @kenibrewer in #336
• fix(devcontainer): install poetry via devcontainer feature by @kenibrewer in #337
• docs: update CITATION.cff and pyproject.toml authors by @kenibrewer in #339
• fix(build): fix optional poetry dependencies by @kenibrewer in #338
• feat(build): enable poetry-dynamic-versioning and cz changelog by @kenibrewer in #341
• fix(dev): remove gitpod support and update docs by @kenibrewer in #347
• feat: add commitizen cli and commit standards by @kenibrewer in #340
• feat: refactor integration pipeline and add poetry-dynamic-versioning support by @kenibrewer in #342
• bump: version 0.2.0 → 1.0.0 by @kenibrewer in #348

New Contributors

• @johnarevalo made their first contribution in #193
• @roshankern made their first contribution in #210
• @bunnech made their first contribution in #219
• @axiomcura made their first contribution in #262
• @alxndrkalinin made their first contribution in #283
• @jenna-tomkinson made their first contribution in #296
• @dependabot made their first contribution in #326

Full Changelog: v0.2.0...v1.0.0

Supporting CellProfiler output data collation

Pycytominer now fully supports CellProfiler analyses directly from CellProfiler output files.

What's Changed

• Add collate.py by @shntnu and @bethac07 in #160

Full Changelog: v0.1.5...v0.2.0