pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "spyglass-neuro"
description = "Neuroscience data analysis framework for reproducible research"
readme = "README.md"
requires-python = ">=3.9,<3.13"
license = { file = "LICENSE" }
authors = [
    { name = "Loren Frank", email = "loren.frank@ucsf.edu" },
    { name = "Kyu Hyun Lee", email = "kyuhyun.lee@ucsf.edu" },
    { name = "Eric Denovellis", email = "eric.denovellis@ucsf.edu" },
    { name = "Ryan Ly", email = "rly@lbl.gov" },
    { name = "Daniel Gramling", email = "daniel.gramling@ucsf.edu" },
    { name = "Chris Brozdowski", email = "chris.broz@ucsf.edu" },
]
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
keywords = [
    "neuroscience",
    "research",
    "electrophysiology",
    "reproducible",
    "data analysis",
    "spike sorting",
    "spikeinterface",
    "datajoint",
    "nwb",
    "kachery",
    "sortingview",
]
dynamic = ["version"]
dependencies = [
    "black[jupyter]",
    "bottleneck",
    "dask",
    "datajoint>=0.14.2",
    # "ghostipy", # removed from list bc M1 users need to install pyfftw first
    "hdmf>=3.4.6",
    "ipympl",
    "matplotlib",
    "ndx_franklab_novela>=0.1.0",
    "non_local_detector",
    "numpy",
    "opencv-python",
    "panel>=1.4.0",                  # panel #6325 resolved
    "position_tools>=0.1.0",
    "pubnub<6.4.0",                  # TODO: remove this when sortingview is updated
    "pydotplus",
    "pynwb>=2.2.0,<3",
    "ripple_detection",
    "seaborn",
    "sortingview>=0.11",
    "spikeinterface>=0.99.1,<0.100",
    "track_linearization>=2.3",
]

[project.optional-dependencies]
dlc = [
    "ffmpeg",
    "deeplabcut[tf]", # removing dlc pin removes need to pin tf/numba
]
test = [
    "click",                  # for CLI subpackage only
    "docker",                 # for tests in a container
    "ghostipy",
    "kachery",                # database access
    "kachery-client",
    "kachery-cloud>=0.4.0",
    "opencv-python-headless", # for headless testing of Qt
    "pre-commit",             # linting
    "pytest",                 # unit testing
    "pytest-cov",             # code coverage
    "pytest-xvfb",            # for headless testing of Qt
]
docs = [
    "hatch",                 # Get version from env
    "jupytext",              # Convert notebooks to .py
    "mike",                  # Docs versioning
    "mkdocs",                # Docs core
    "mkdocs-exclude",        # Docs exclude files
    "mkdocs-exclude-search", # Docs exclude files in search
    "mkdocs-gen-files",      # Docs API generator
    "mkdocs-jupyter",        # Docs render notebooks
    "mkdocs-literate-nav",   # Dynamic page list for API docs
    "mkdocs-material",       # Docs theme
    "mkdocstrings[python]",  # Docs API docstrings
]

[project.scripts]
spyglass_cli = "spyglass.cli:cli"

[project.urls]
"Homepage" = "https://github.com/LorenFrankLab/spyglass"
"Bug Tracker" = "https://github.com/LorenFrankLab/spyglass/issues"

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.hooks.vcs]
# this file is created/updated when the package is installed and used in
# src/spyglass/__init__.py to set `spyglass.__version__`
version-file = "src/spyglass/_version.py"

[tool.hatch.build.targets.sdist]
exclude = [".git_archival.txt"]

[tool.hatch.build.targets.wheel]
packages = ["src/spyglass"]
exclude = []

[tool.black]
line-length = 80

[tool.codespell]
skip = '.git,*.pdf,*.svg,*.ipynb,./docs/site/**,temp*'
ignore-words-list = 'nevers'
# Nevers - name in Citation

[tool.pytest.ini_options]
minversion = "7.0"
addopts = [
    "-s", # no capture
    # "-v", # verbose output
    # "--sw", # stepwise: resume with next test after failure
    # "--pdb", # drop into debugger on failure
    "-p no:warnings",
    # "--no-teardown", # don't teardown the database after tests
    # "--quiet-spy",   # don't show logging from spyglass
    # "--no-dlc",      # don't run DLC tests
    "--show-capture=no",
    "--pdbcls=IPython.terminal.debugger:TerminalPdb", # use ipython debugger
    "--doctest-modules",                              # run doctests in all modules
    "--cov=spyglass",
    "--cov-report=term-missing",
    "--no-cov-on-fail",
]
testpaths = ["tests"]
log_level = "INFO"
env = [
    "QT_QPA_PLATFORM = offscreen", # QT fails headless without this
    "DISPLAY = :0",                # QT fails headless without this
    "TF_ENABLE_ONEDNN_OPTS = 0",   # TF disable approx calcs
    "TF_CPP_MIN_LOG_LEVEL = 2",    # Disable TF warnings
]

[tool.coverage.run]
source = ["*/src/spyglass/*"]
omit = [ # which submodules have no tests
    "*/__init__.py",
    "*/_version.py",
    "*/cli/*",
    # "*/common/*",
    "*/data_import/*",
    "*/decoding/*",
    "*/figurl_views/*",
    # "*/lfp/*",
    # "*/linearization/*",
    "*/lock/*",
    "*/mua/*",
    # "*/position/*",
    "*/ripple/*",
    "*/sharing/*",
    "*/spikesorting/v0/*",
    # "*/spikesorting/*",
    # "*/utils/*",
    "settings.py",
]

[tool.ruff] # CB: Propose replacing flake8 with ruff to delete setup.cfg
line-length = 80

[tool.ruff.lint]
ignore = ["F401", "E402", "E501"]