- citation: fix citation.cff file formatting (#460)
- collate: deprecationwarning for
collate(#462)
- python: add python 3.12 compatibility (#475)
- python: bump minimum python version to 3.9 (#464)
- pre-commit: format pyproject.toml with pyproject-fmt (#453)
- releases: constrain PyPI GitHub Actions release trigger types (#458)
- dependencies: update setup python action dependencies and dependabot settings (#457)
- dependabot: enable auto poetry updates (#463)
- dev: add improved makefile with additional helper commands (#391)
- pandas: add condition for pandas config (#415)
- poetry: add tool.setuptools_scm section (#402)
- ci: docker image push readme updates (#398, #395)
- ci: fix errors with automated coverage (#432)
- ci: add workspaceDir to git safe directories for devcontainers (#379)
- SQLite: joins should be on ImageNumber, TableNumber, and not ImageNumber (#378)
- compartments: avoid lowercase compartment strings (#421)
- pd: avoid dataframe fragmentation in agg (#407)
- pandas: enable copy_on_write for pandas (#401)
- bandit: apply bandit checks (#387)
- isort: apply isort linting checks (#389)
- ruff: update ruff to 0.3.4 (#386)
- dev: add docker-in-docker feature to devcontainer (#381)
- docker: add Dockerfile and container image build tests (#362)
- docker: add docker hub push capabilities (#377)
- deps: various dependency updates automated by dependabot
- docker: add docker installation instructions (#409)
- docs: improve documentation for non-CellProfiler datasets in Pycytominer (#430)
- docs: update error message and docs for features argument to clarify CellProfiler default expectations (#448)
- ci: update macOS version for Python (#408)
- ci: specify GitHub Actions Ubuntu runner image (#411)
- ci: enable GitHub Actions updates (#438)
- ci: add mypy check and adjust code for types (#439)
- build: fix build versioning
- simplify Spherize transform – epsilon to regularize instead of clip, add additional checks (see #320)
- docs: apply flake8-builtins checks
- dev: apply pyflakes checks
- dev: apply flake8-simplify checks
- add flake8-bandit ignores
- add clarifying comments for cell_loc test
- update cell_loc s3 paths and testing
- update Readme with Citation section
- template: PR template attribution to comment
- changelog: add commitizen template
- add description of ruff linting/formatting
- reorganize style guide
- add versioned artifact build action
- integration-test: add explicit artifact retention time
- add pygrep-hooks and flake8-20202 checks
- swap out black for ruff-format
- apply pyupgrade checks
- devcontainer: add ruff extension
- apply ruff native checks
- apply pycodestyle checks
- add flake8-comprehensions checks
- poetry: make dev dep group optional
- docs: add dynamic versioning to docs build
- collate: move optional dep import to function
- functions now use expect None type as argument where they previously expected a "none" string
- drop_outliers:: change default outlier threshold to 500
- variance_threshold change variance_threshold default to 0.01
- add parquet support for all i/o functions
- annotate: add function to convert SQLite to pandas DataFrame and merge additional metadata
- build: switch to poetry for dependency management and builds
- cells: Enable custom image table name for SQLite queries in cells.py
- deepprofiler: add single cell output and normalization
- dev: standardized dev process and workflows (See CONTRIBUTING.md):
- add vscode devcontainer and codespaces config
- add conventional commit standards and commitizen cli
- add pre-commit hooks for black, prettier, actionlint
- docs: Add detailed single-cell profiling walkthrough
- utils: cell_locations script to append X,Y locations to LoadData
- annotate: add informative merge suffixes to platemap and external_metadata
- annotate: add check before dropping well columns
- build: remove python 3.7 support
- correlation: Use numpy to calculate pearson corr of non NaN matrices
- load_profiles: now works with PurePath types
- collate: support CellProfiler analyses directly from CellProfiler output files
- merge_single_cells - improve memory performance