pyproject.toml

[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "nemos"
version = "0.1.6"
authors = [{name = "nemos authors"}]
description = "NEural MOdelS, a statistical modeling framework for neuroscience."
readme = "README.md"
requires-python = ">=3.10"
keywords = ["neuroscience", "Poisson-GLM"]
license = { file = "LICENSE" }
classifiers = [
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12"
]

# Define dependencies for the project
dependencies = [
    "jax>=0.4.28",                     # Numerical computing library
    "jaxopt>=0.6",                  # Optimization library built on JAX
    "numpy>1.20",                   # Numerical computing library
    "scipy>=1.10",                  # Scientific computing library
    "typing_extensions>=4.6",       # Typing extensions for Python
    "pynapple>=0.6.6",
]



# Configure package discovery for setuptools
[tool.setuptools.packages.find]
where = ["src"]     # The directory where package modules are located
include = ["nemos"] # The specific package(s) to include in the distribution


# Define optional dependencies for the project
[project.optional-dependencies]
dev = [
    "black",                        # Code formatter
    "isort",                        # Import sorter
    "pip-tools",                    # Dependency management
    "pytest",                       # Testing framework
    "pytest-xdist",                 # Parallelize pytest
    "flake8",                       # Code linter
    "coverage",                     # Test coverage measurement
    "pytest-cov",                   # Test coverage plugin for pytest
    "statsmodels",                  # Used to compare model pseudo-r2 in testing
    "scikit-learn",                 # Testing compatibility with CV & pipelines
    "matplotlib>=3.7",              # Needed by doctest to run docstrings examples
    "pooch",                        # Required by doctest for fetch module
    "dandi",                        # Required by doctest for fetch module
    "seaborn",                      # Required by doctest for _documentation_utils module
]
docs = [
    "mkdocs",                       # Documentation generator
    "mkdocstrings[python]",         # Python-specific plugin for mkdocs
    "mkdocs-section-index",         # Plugin for generating a section index in mkdocs
    "mkdocs-gen-files",             # Plugin for generating additional files in mkdocs
    "mkdocs-literate-nav>=0.6.1",   # Plugin for literate-style navigation in mkdocs
    "mkdocs-gallery",               # Plugin for adding image galleries to mkdocs
    "mkdocs-material",              # Material theme for mkdocs
    "mkdocs-autorefs>=0.5",
    "mkdocs-linkcheck",             # Check relative links
    "scikit-learn",
    "dandi",
    "matplotlib>=3.7",
    "seaborn",
    "pooch",
]
examples = [
    "scikit-learn",
    "dandi",
    "matplotlib>=3.7",
    "seaborn",
    "pooch",
    "fsspec",
]


[tool.black]
target-version = ['py38', 'py39', 'py310']
skip-string-normalization = false
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.md
    | \.toml
    | \.cfg
    | \.txt
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
    | examples))'''

# Configure isort
[tool.isort]
multi_line_output = 3             # Use three-line style for multi-line imports
include_trailing_comma = true     # Include trailing comma in multi-line imports
profile = "black"

# Configure pytest
[tool.pytest.ini_options]
testpaths = ["tests"]             # Specify the directory where test files are located
addopts = "-n auto"

[tool.coverage.run]
omit = [
    "src/nemos/fetch/*",
    "src/nemos/_documentation_utils/*",
]

[tool.coverage.report]
exclude_lines = [
    "@abc.abstractmethod",
    "if __name__ == .__main__.:"
]