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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.2.3...v1.2.4

- Python
Published by d33bs 7 months ago

pycytominer - v1.2.3 (2025-05-08)

What's Changed

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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.2.2...v1.2.3

- Python
Published by d33bs 10 months ago

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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.2.1...v1.2.2

- Python
Published by d33bs about 1 year ago

pycytominer - v1.2.1 (2024-11-20)

What's Changed

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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.2.0...v1.2.1

- Python
Published by d33bs over 1 year ago

pycytominer - v1.2.0 (2024-09-30)

What's Changed

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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.1.0...v1.2.0

- Python
Published by d33bs over 1 year ago

pycytominer - v1.1.0 (2024-03-13)

What's Changed

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

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.0.1...v1.1.0

- Python
Published by d33bs almost 2 years ago

pycytominer - v1.0.1 (2023-11-09)

What's Changed

• fix(collate): make optional dependency imports localized by @kenibrewer in https://github.com/cytomining/pycytominer/pull/351
• fix(docs): add dynamic versioning to docs build by @kenibrewer in https://github.com/cytomining/pycytominer/pull/353

Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.0.0...v1.0.1

- Python
Published by kenibrewer over 2 years ago

pycytominer - v1.0.0 Release

Pycytominer v1.0.0 Release

What's Changed

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

New Contributors

• @johnarevalo made their first contribution in https://github.com/cytomining/pycytominer/pull/193
• @roshankern made their first contribution in https://github.com/cytomining/pycytominer/pull/210
• @bunnech made their first contribution in https://github.com/cytomining/pycytominer/pull/219
• @axiomcura made their first contribution in https://github.com/cytomining/pycytominer/pull/262
• @alxndrkalinin made their first contribution in https://github.com/cytomining/pycytominer/pull/283
• @jenna-tomkinson made their first contribution in https://github.com/cytomining/pycytominer/pull/296
• @dependabot made their first contribution in https://github.com/cytomining/pycytominer/pull/326

Full Changelog: https://github.com/cytomining/pycytominer/compare/v0.2.0...v1.0.0

- Python
Published by kenibrewer over 2 years ago

pycytominer - 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 https://github.com/cytomining/pycytominer/pull/160

Full Changelog: https://github.com/cytomining/pycytominer/compare/v0.1.5...v0.2.0

- Python
Published by gwaybio over 3 years ago

pycytominer - Minor bump to 0.1.5 in preparation for collate-specific release

What's Changed

• Remove codeowners and update install instructions by @gwaybio in https://github.com/cytomining/pycytominer/pull/190
• Upload Logo by @vincerubinetti in https://github.com/cytomining/pycytominer/pull/196
• Improve Memory Performance Within mergesinglecells by @d33bs in https://github.com/cytomining/pycytominer/pull/197

New Contributors

• @vincerubinetti made their first contribution in https://github.com/cytomining/pycytominer/pull/196
• @d33bs made their first contribution in https://github.com/cytomining/pycytominer/pull/197

Full Changelog: https://github.com/cytomining/pycytominer/compare/v0.1...v0.1.5

- Python
Published by gwaybio over 3 years ago

pycytominer - Initial release of pycytominer

Pycytominer release v0.1

Pycytominer is a python package that implements functions for every step of the image-based profiling pipeline.

Processing image-based readouts of cell morphology, we can now:

• aggregate single cells to form bulk profiles
• subsample single cells to form pseudo bulk replicates
• normalize both single cells and bulk profiles
• apply feature selection functions to remove uninformative morphology features
• generate consensus signatures from replicates

The package currently has 98% test coverage and is fully documented with some examples. We hope that you enjoy using pycytominer, and please report bugs, make recommendations, and discuss any ideas you might have.

What's Changed

• Adding Initial Functions by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/1
• Update LICENSE file by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/2
• Adding Travis yml by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/3
• Add normalize function by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/4
• Adding setup.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/7
• Add Cytominer Authors to Setup by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/8
• Add Covariance Functions by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/9
• Adding sparse random projection by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/10
• Adding Whitening Transform Method by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/13
• Adding feature_select.py function by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/15
• Adding Feature Select Testing by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/17
• Updating aggregate to work with sqlite files by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/16
• Adding random state set function in aggregate.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/18
• Add sqlalchemy to setup.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/19
• Adding codecov to travis by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/20
• Adding annotate.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/21
• Updating normalize.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/23
• Updating feature_select.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/24
• Inferring Features in feature_select.py by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/27
• Add Audit by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/33
• Try to coerce string input for subsample_n by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/34
• [hotfix] save quantile in audit by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/35
• [hotfix] make sure to enable audit output! by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/36
• Adding option to compress output data by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/40
• Blacklist features by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/41
• Inferring Cell Painting Features by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/42
• Add whitening by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/43
• Refactor Before PooledCellPainting by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/44
• Adding PooledCellPainting by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/45
• Add Init File in Pooled by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/46
• [Pooled] try to convert columns to numeric by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/47
• Adding MODZ Consensus Signature Operation by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/53
• Fixing MODZ to behave properly when not all metadata columns are specified by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/55
• Add write_gct function by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/56
• Upgrading Audit Functionality by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/60
• Functionality to Drop Outlier Features by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/62
• Fix aggregate dtype bug by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/65
• Remove kwargs everywhere by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/66
• Allowing feature and metadata feature setting in write_gct by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/67
• Add Feature Metadata to writing gct file by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/68
• Adding Robust Normalization by MAD by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/72
• Fix mad_robustize policy on low variance columns by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/74
• Enable cell counting with more than 2 defined strata by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/76
• Add CMAP options to annotate by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/73
• Abstract loading profiles and platemap by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/84
• Adding CSV sniffing for delimiters by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/85
• Fix missing value in variance threshold error by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/86
• Fix write_gct too much strip by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/87
• Switch to "samples='all'" as default and move operations to subfolder by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/88
• Updating whitening implementations by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/91
• clean pycytominer folder base to include core functionality by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/92
• changed whiten_method default by @AdeboyeML in https://github.com/cytomining/pycytominer/pull/97
• Fix gzip sniffer by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/98
• Refactor the consensus.py file to keep consistent API by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/101
• Change whiten nomenclature to spherize by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/102
• increase modularity of infercpfeatures by @hillsbury in https://github.com/cytomining/pycytominer/pull/103
• Setting up auto documentation with sphinx by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/104
• Updating theme and fixing RTD integration by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/105
• Adding pytest to requirements by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/106
• documentation edits by @bethac07 in https://github.com/cytomining/pycytominer/pull/108
• Adding single cell module by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/111
• Updating consensus.py to also work with input files by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/115
• Output compression to ignore timestamps by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/119
• Subsampling at the point of single cell merging by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/121
• Refactoring annotate by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/118
• Fixing sphinx docs by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/124
• [hotfix] rename requirements doc by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/125
• Adding epsilon parameter to spherize by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/132
• Fix aggregate dropping samples by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/134
• Modify aggregate by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/129
• Adding open source guideline documents by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/136
• Update README with Cell Painting paper URL by @shntnu in https://github.com/cytomining/pycytominer/pull/139
• Set default objectfeature to MetadataObjectNumber by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/143
• Adding pipeline figure and boosting README by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/145
• Adding functionality to aggregate and annotate DeepProfiler output by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/78
• Replace travis with github actions by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/151
• Replace aggregate_args by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/148
• Update DeepProfiler Processing by @michaelbornholdt in https://github.com/cytomining/pycytominer/pull/149
• add citation note by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/157
• cells.aggregate_compartment() queries the database in chunks, reducing memory by @sjfleming in https://github.com/cytomining/pycytominer/pull/156
• Add "noise removal" feature selection by @ruifanp in https://github.com/cytomining/pycytominer/pull/153
• fix issue when some samples have replicates and some don't by @bethac07 in https://github.com/cytomining/pycytominer/pull/166
• Image features by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/168
• Add Metadata_ prefix to count features in the image table by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/171
• update pipeline by @michaelbornholdt in https://github.com/cytomining/pycytominer/pull/163
• Remove step where image feature groups are capitalized by @niranjchandrasekaran in https://github.com/cytomining/pycytominer/pull/173
• Citation.cff by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/182
• Fix dataframe reference in SingleCells function by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/183
• Add explicit documentation for variancethreshold freqcut and unique_cut by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/184
• Update doc style by @gwaygenomics in https://github.com/cytomining/pycytominer/pull/185
• Add github action to publish to pypi by @staylorx in https://github.com/cytomining/pycytominer/pull/188

New Contributors

• @gwaygenomics made their first contribution in https://github.com/cytomining/pycytominer/pull/1
• @AdeboyeML made their first contribution in https://github.com/cytomining/pycytominer/pull/97
• @hillsbury made their first contribution in https://github.com/cytomining/pycytominer/pull/103
• @bethac07 made their first contribution in https://github.com/cytomining/pycytominer/pull/108
• @niranjchandrasekaran made their first contribution in https://github.com/cytomining/pycytominer/pull/129
• @shntnu made their first contribution in https://github.com/cytomining/pycytominer/pull/139
• @michaelbornholdt made their first contribution in https://github.com/cytomining/pycytominer/pull/149
• @sjfleming made their first contribution in https://github.com/cytomining/pycytominer/pull/156
• @ruifanp made their first contribution in https://github.com/cytomining/pycytominer/pull/153
• @staylorx made their first contribution in https://github.com/cytomining/pycytominer/pull/188

Full Changelog: https://github.com/cytomining/pycytominer/commits/v0.1

- Python
Published by gwaybio about 4 years ago