Pycytominer

[Detailed release notes](https://github.com/cytomining/pycytominer/releases/tag/v1.2.0)

Feat

- **dev**: add improved makefile with additional helper commands (391)

Fix

- **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)

Refactor

- **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)

Build

- **docker**: add Dockerfile and container image build tests (362)
- **docker**: add docker hub push capabilities (377)
- **deps**: various dependency updates automated by dependabot

Docs

- **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

- **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)

[Detailed release notes](https://github.com/cytomining/pycytominer/releases/tag/v1.1.0)

Fix

- **build**: fix build versioning
- simplify Spherize transform – epsilon to regularize instead of clip, add additional checks (see 320)

Refactor

- **docs**: apply flake8-builtins checks
- **dev**: apply pyflakes checks
- **dev**: apply flake8-simplify checks

Test

- add flake8-bandit ignores
- add clarifying comments for cell_loc test
- update cell_loc s3 paths and testing

Docs

- update Readme with Citation section
- **template**: PR template attribution to comment
- **changelog**: add commitizen template
- add description of ruff linting/formatting
- reorganize style guide

CI

- add versioned artifact build action
- **integration-test**: add explicit artifact retention time
- add pygrep-hooks and flake8-20202 checks

Style

- swap out black for ruff-format
- apply pyupgrade checks
- **devcontainer**: add ruff extension
- apply ruff native checks
- apply pycodestyle checks
- add flake8-comprehensions checks

Build

- **poetry**: make dev dep group optional

[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v1.0.1)

Fix

- **docs**: add dynamic versioning to docs build
- **collate**: move optional dep import to function

[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v1.0.0)

BREAKING CHANGE

- 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

Feat

- 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](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](https://pycytominer.readthedocs.io/en/latest/walkthroughs/single_cell_usage.html)
- **utils**: cell_locations script to append X,Y locations to LoadData

Fix

- **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

[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v0.2.0)

Feat

- **collate**: support CellProfiler analyses directly from CellProfiler output files

[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v0.1.5)

Fix

- **merge_single_cells** - improve memory performance