pyproject.toml

[build-system]
build-backend = "hatchling.build"

requires = [ "hatch-vcs", "hatchling" ]

[project]
name = "spyglass-neuro"
description = "Neuroscience data analysis framework for reproducible research"
readme = "README.md"
keywords = [
  "data analysis",
  "datajoint",
  "electrophysiology",
  "kachery",
  "neuroscience",
  "nwb",
  "reproducible",
  "research",
  "sortingview",
  "spike sorting",
  "spikeinterface",
]
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" },
  { name = "Samuel Bray", email = "sam.bray@ucsf.edu" },
]
requires-python = ">=3.10,<3.13"
classifiers = [
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]
dynamic = [ "version" ]
dependencies = [
  "black[jupyter]>26",
  "bottleneck",
  "dask",
  "datajoint>=0.14.5,<2.0",
  # "ghostipy", # removed from list bc M1 users need to install pyfftw first
  "hdmf>=3.4.6",
  "ipympl",
  "matplotlib",
  "ndx-franklab-novela>=0.2.4",
  "ndx-optogenetics==0.3.0",
  "ndx-ophys-devices",
  "ndx-pose",
  "non-local-detector",
  "numpy",
  "opencv-python",
  "panel>=1.4",
  "position-tools>=0.1",
  "probeinterface<0.3",            # Bc some probes fail space checks
  "pubnub<6.4",                    # TODO: remove this when sortingview is updated
  "pydotplus",
  "pynwb>=3.1.3",
  "ripple-detection",
  "seaborn",
  "sortingview>=0.11",
  "spikeinterface>=0.99.1,<0.100",
  "track-linearization>=2.3",
]

optional-dependencies.dlc = [
  "deeplabcut[tf]", # removing dlc pin removes need to pin tf/numba
  "ffmpeg",
]
optional-dependencies.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
  "mkdocs-mermaid2-plugin", # Docs mermaid diagrams
  "mkdocstrings[python]",   # Docs API docstrings
]
optional-dependencies.kachery-cloud = [
  "kachery",
  "kachery-client",
  "kachery-cloud>=0.4",
]
optional-dependencies.moseq-cpu = [
  "jax[cpu]",
  "jax-moseq",
  "keypoint-moseq",
]
optional-dependencies.moseq-gpu = [
  "jax[cuda12]",
  "jax-moseq[cuda12]",
  "keypoint-moseq",
]
optional-dependencies.test = [
  "codecov",                # for code coverage badge
  "docker",                 # for tests in a container
  "ghostipy",
  "kachery",                # database access
  "kachery-client",
  "kachery-cloud>=0.4",
  "netcdf4",                # for decoding mocking
  "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
]
urls."Bug Tracker" = "https://github.com/LorenFrankLab/spyglass/issues"
urls."Homepage" = "https://github.com/LorenFrankLab/spyglass"

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

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

[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
]
filterwarnings = [
  "ignore::ResourceWarning:.*",
  "ignore::DeprecationWarning:.*",
  "ignore::UserWarning:.*",
  "ignore::FutureWarning:.*",
  "ignore::PerformanceWarning:.*",
  "ignore::MissingRequiredBuildWarning:.*",
  # DLC training ends by cancelling a TF enqueue thread; expected, not a bug
  "ignore::pytest.PytestUnhandledThreadExceptionWarning",
]
markers = [
  # Speed-based markers (based on total time: setup + call + teardown)
  "fast: Tests that complete in <1 second",
  "medium: Tests that complete in 1-10 seconds",
  "slow: Tests that complete in 10-60 seconds",
  "very_slow: Tests that complete in >60 seconds (top bottlenecks)",

  # Type-based markers
  "unit: Pure unit tests with no I/O dependencies",
  "integration: Integration tests involving multiple components",
  "io_heavy: I/O-intensive tests (database and/or NWB files)",
  "database: Tests requiring database operations",
  "nwb: Tests requiring NWB file I/O",

  # Special markers
  "serial: Tests that must run serially (not parallel-safe)",
]

[tool.coverage.run] # NOTE: changes need to be mirrored in tests/.coveragerc
source = [ "*/src/spyglass/*" ]
omit = [ # which submodules have no tests
  "*/__init__.py",
  "*/_version.py",
  # "*/behavior/*",
  # "*/common/*",
  "*/data_import/*",
  "*/decoding/v0/*",
  # "*/decoding/*",
  "*/figurl_views/*",
  # "*/lfp/*",
  # "*/linearization/*",
  "*/lock/*",
  "*/mua/*",
  # "*/position/*",
  "*/ripple/*",
  "*/sharing/*",
  # "*/spikesorting/*",
  # "*/utils/*",
  "settings.py",
]