pyproject.toml

[tool.poetry]
name = "pyrovelocity"
version = "0.3.0"
packages = [{ include = "pyrovelocity", from = "src" }]
description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
authors = ["pyrovelocity team"]
license = "AGPL-3.0-only"
readme = "README.md"
homepage = "https://docs.pyrovelocity.net"
repository = "https://github.com/pinellolab/pyrovelocity"
documentation = "https://docs.pyrovelocity.net"
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: GNU Affero General Public License v3",
  "Natural Language :: English",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]

[tool.poetry.urls]
Changelog = "https://github.com/pinellolab/pyrovelocity/releases"

[tool.poetry.dependencies]
python = ">=3.11, <3.13"
adjusttext = ">=1.1.1"
altair = ">=5.3.0"
anndata = ">=0.10.5"
anyio = ">=4.3.0"
appdirs = ">=1.4.4"
# 0.18.0 adds a dependency on dm-tree = ">=0.1.8"
# whose build is broken and wheel attempts to 
# dlopen an undeclared or broken shared library
# on Darwin
arviz = ">=0.17.1"
astropy = ">=6.1.2"
beartype = ">=0.18.5"
# pinning chex>=0.1.82 may be required to avoid
# dm-tree = ">=0.1.8"
# whose build is broken on Darwin
# https://github.com/NixOS/nixpkgs/blob/4e44fb9c2673c5b58c44deb7e05bcf312a5862cf/pkgs/development/python-modules/dm-tree/default.nix#L52
chex = ">=0.1.7"
click = ">=8.1.7"
colorlog = ">=6.7.0"
daft = ">=0.1.2"
diffrax = ">=0.5.0"
diskcache = ">=5.6.1"
duckdb = ">=1.0.0"
einops = ">=0.7.0"
# requires python 3.11
expression = ">=5.0.2"
flax = ">=0.8.1"
frozenlist = { version = ">=1.1.1", python = "<3.12" }
# frozenlist = [
#   { version = ">=1.1.1", python = "<3.12" },
#   { version = ">=1.4.1", python = ">=3.12" },
# ]
fsspec = ">=2024.3.0"
greenlet = ">=3.0.3"
httpx = ">=0.27.0"
h5py = ">=3.9.0"
ibis-framework = { extras = ["duckdb"], version = ">=9.2.0" }
jax = ">=0.4.23"
jaxlib = ">=0.4.23"
jaxtyping = ">=0.2.25"
leidenalg = ">=0.9.1"
llvmlite = { version = ">=0.41.1", python = "<3.12" }
# llvmlite = [
#   { version = ">=0.41.1", python = "<3.12" },
#   { version = ">=0.42.0", python = ">=3.12" },
# ]
# Temporarily pin yanked matplotlib 3.9.1
# https://github.com/matplotlib/matplotlib/issues/28551
# for usage with pip installs
matplotlib = ">=3.9.1"
mlflow = ">=2.13.0"
numpyro = ">=0.15.0"
pandas = ">=2.0.0"
plumbum = ">=1.8.2"
polars = ">=0.20.17"
pyarrow = ">=14.0.2"
pydantic = ">=2.8.0"
pyro-ppl = ">=1.9.1"
lightning = ">=2.0.0"
pytorch-lightning = ">=2.0.0"
pyyaml = ">=6.0.1"
returns = ">=0.23.0"
rich = ">=13.7.1"
scanpy = ">=1.10.1"
scikit-learn = ">=1.3.1"
scipy = ">=1.10.1,<1.14.0"
scvelo = ">=0.3.2"
# scvelo = { git = "https://github.com/theislab/scvelo.git", rev = "3fbce6ff6d644a44911091f498efa0c69f6b85b0" }
scvi-tools = ">=1.1.1"
seaborn = ">=0.13.2"
sparse = ">=0.15.4"
statsmodels = ">=0.14.2"
sympy = ">=1.12"
termcolor = ">=2.2.0"
tiledb = ">=0.31.1"
torch = { version = ">=2.1.2", python = "<3.12" }
# torch = [
#   { version = ">=2.1.2", python = "<3.12" },
#   { version = ">=2.2.0", python = ">=3.12" },
# ]
torchmetrics = ">=1.2.1"
trio = ">=0.26.0"
validators = ">=0.33.0"
vegafusion = ">=1.6.9"
vegafusion-python-embed = ">=1.6.9"
vl-convert-python = ">=1.6.0"
zstandard = ">=0.23.0"
# removed from library at
# cospar = { version = ">=0.1.9", source = "pypi" }
# scikit-misc = ">=0.1.4"

# extras
# annoy = { version = "^1.17.3", optional = true }
black = { version = ">=23.3.0", optional = true }
coverage = { extras = ["toml"], version = ">=6.2", optional = true }
# darglint = { version = ">=1.8.1", optional = true }
dataclasses-json = { version = ">=0.5.7", optional = true }
# dparse = { version = ">=0.5.2", optional = true }
# dvc = { version = ">=3.0", optional = true }
# dvc-gs = { version = ">=2.22.1", optional = true }
dulwich = { version = ">=0.21.7", optional = true }
# flake8 = { version = ">=4.0.1", optional = true }
# flake8-bandit = { version = ">=2.1.2", optional = true, source = "pypi" }
# flake8-bugbear = { version = ">=21.9.2", optional = true }
# flake8-docstrings = { version = ">=1.6.0", optional = true }
# flake8-rst-docstrings = { version = ">=0.2.5", optional = true }
flytekit = { version = ">=1.13.3", optional = true }
furo = { version = ">=2023.5.20", optional = true }
google-api-python-client = { version = ">=2.79.0", optional = true }
hydra-core = { version = ">=1.3.2", optional = true }
hydra-zen = { version = ">=0.12.1", optional = true }
hypothesis = { version = ">=6.71.0", optional = true }
ipython = { version = ">=8.11.0", optional = true }
ipywidgets = { version = ">=8.0.0", optional = true }
# isort = { version = ">=5.10.1", optional = true }
jupyter-cache = { version = ">=0.6.1", optional = true }
# see https://jupyterlab-contrib.github.io/migrate_from_classical.html for extensions
jupyterlab = { version = ">=4.0.9", optional = true }
jupytext = { version = ">=1.16.0", optional = true }
mashumaro = { version = ">=3.10", optional = true }
matplotlib-venn = { version = ">=0.11.9", optional = true }
mypy = { version = ">=0.930", optional = true }
myst-parser = { version = ">=2.0.0", optional = true }
nbconvert = { version = ">=7.14.0", optional = true }
nbformat = { version = ">=5.9.2", optional = true }
nbsphinx = { version = ">=0.9.3", optional = true }
omegaconf = { version = ">=2.3.0", optional = true }
# orjson =  { version = ">=3.9.15", optional = true }
papermill = { version = ">=2.4.0", optional = true }
# pep8-naming = { version = ">=0.12.1", optional = true }
# poethepoet = { version = ">=0.16.0", optional = true, source = "pypi" }
pre-commit = { version = ">=2.16.0", optional = true }
pre-commit-hooks = { version = ">=4.1.0", optional = true }
pyensembl = { version = ">=2.3.12", optional = true }
pyfaidx = { version = ">=0.8.1.1", optional = true }
pygments = { version = ">=2.15.0", optional = true }
pytest = { version = ">=6.2.5", optional = true }
pytest-asyncio = { version = ">=0.21.1", optional = true }
pytest-cov = { version = ">=4.0.0", optional = true }
pytest-mock = { version = ">=3.10.0", optional = true }
python-dotenv = { version = ">=1.0.0", optional = true }
# pyupgrade = { version = ">=2.29.1", optional = true }
# pyvis = { version = ">=0.3.2", optional = true }
rich-click = { version = ">=1.7.3", optional = true }
ruff = { version = ">=0.1.5", optional = true }
# safety = { version = ">=1.10.3", optional = true }
sphinx = { version = ">=7.0.1", optional = true }
sphinx-autobuild = { version = ">=2021.3.14", optional = true }
sphinx-autodoc-typehints = { version = ">=1.23.3", optional = true }
sphinx-click = { version = ">=4.4.0", optional = true }
sphinx-copybutton = { version = ">=0.5.2", optional = true }
sphinx-markdown-builder = { version = ">=0.6.6", optional = true }
quartodoc = { version = ">=0.7.2", optional = true }
# statannotations = { version = ">=0.6.0", optional = true }
# typeguard = { version = ">=2.13.3", optional = true }
xdoctest = { extras = ["colors"], version = ">=0.15.10", optional = true }

# Enable with make lock-pip-cpu
# [[tool.poetry.source]]
# name = "pytorch"
# url = "https://download.pytorch.org/whl/cpu"
# priority = "supplemental"

# [tool.poetry.group.cpu]
# optional = true

# [tool.poetry.group.cpu.dependencies]
# # requirements-cpu.txt
# # torch==1.13.1+cpu ; python_version >= ">=3.10" and python_version < "3.11" and (sys_platform == "linux" or platform_system == "Linux")
# # torch==1.13.1 ; python_version >= ">=3.10" and python_version < "3.11" and (sys_platform == "darwin" or platform_system == "Darwin")
# torch = [
#   {platform = "linux", version = ">=1.13.1+cpu", source = "pytorch"},
#   {platform = "darwin", version = ">=1.13.1", source = "pypi"},
# ]

[tool.poetry.group.lint]
optional = true

[tool.poetry.group.lint.dependencies]
black = { version = ">=23.3.0", extras = ["jupyter"] }
mypy = ">=1.5.1"
pre-commit = ">=2.16.0"
pre-commit-hooks = ">=4.1.0"
pyright = ">=1.1.347"
ruff = ">=0.1.5"
docformatter = { version = ">=1.7.5", extras = ["tomli"] }


[tool.poetry.group.test]
optional = true

[tool.poetry.group.test.dependencies]
coverage = { version = ">=6.2", extras = ["toml"] }
hypothesis = ">=6.72.1"
ipython = ">=8.11.0"
# poethepoet = ">=0.19.0"
pygments = ">=2.15.0"
pytest = ">=7.3.1"
pytest-asyncio = ">=0.21.1"
pytest-cov = ">=4.0.0"
pytest-mock = ">=3.10.0"
requests-mock = ">=1.11.0"
xdoctest = ">=1.1.1"


[tool.poetry.group.docs]
optional = true

[tool.poetry.group.docs.dependencies]
furo = ">=2023.5.20"
jupyter-cache = ">=0.6.1"
jupyterlab = ">=4.0.9"
jupytext = ">=1.16.0"
myst-parser = ">=2.0.0"
nbsphinx = ">=0.9.3"
sphinx-autobuild = ">=2021.3.14"
sphinx-autodoc-typehints = ">=1.23.3"
sphinx-click = ">=4.4.0"
sphinx-copybutton = ">=0.5.2"
sphinx-markdown-builder = ">=0.6.6"
sphinx = ">=7.0.1"
quartodoc = ">=0.7.2"

[tool.poetry.group.workflows]
optional = true

[tool.poetry.group.workflows.dependencies]
dataclasses-json = ">=0.5.7"
dulwich = ">=0.21.7"
flytekit = ">=1.13.0"
google-api-python-client = ">=2.79.0"
google-cloud-storage = ">=2.14.0"
hydra-core = ">=1.3.2"
hydra-zen = ">=0.12.1"
ipywidgets = ">=8.0.0"
jupytext = ">=1.16.0"
mashumaro = ">=3.10"
nbconvert = ">=7.14.0"
nbformat = ">=5.9.2"
omegaconf = ">=2.3.0"
# orjson = ">=3.9.15"
papermill = ">=2.4.0"
pyperclip = ">=1.8.2"
python-dotenv = ">=1.0.0"
rich-click = ">=1.7.3"

[tool.poetry.group.bioinformatics]
optional = true

[tool.poetry.group.bioinformatics.dependencies]
pyensembl = ">=2.3.12"
pyfaidx = ">=0.8.1.1"

[tool.poetry.extras]
bioinformatics = ["pyensembl", "pyfaidx"]

lint = [
  "black",
  "docformatter",
  "mypy",
  "pre-commit-hooks",
  "pre-commit",
  "pygments",
  "pyright",
  "ruff",
]

test = [
  "coverage",
  "hypothesis",
  "ipython",
  # "poethepoet",
  "pygments",
  "pytest",
  "pytest-asyncio",
  "pytest-cov",
  "pytest-mock",
  "requests-mock",
  "xdoctest",
]

docs = [
  "furo",
  "jupyter-cache",
  "jupyterlab",
  "jupytext",
  "myst-parser",
  "nbsphinx",
  "quartodoc",
  "sphinx-autobuild",
  "sphinx-autodoc-typehints",
  "sphinx-click",
  "sphinx-copybutton",
  "sphinx-markdown-builder",
  "sphinx",
]

plotting = [
  # "annoy",
  "matplotlib-venn",
  "statannotations",
]

workflows = [
  "dataclasses-json",
  "dulwich",
  "flytekit",
  "google-api-python-client",
  "hydra-core",
  "hydra-zen",
  "ipywidgets",
  "jupytext",
  "mashumaro",
  "nbconvert",
  "nbformat",
  "omegaconf",
  # "orjson",
  "papermill",
  "pyperclip",
  "python-dotenv",
  "rich-click",
]


[tool.conda-lock]
channels = ['nodefaults', 'pytorch', 'nvidia', 'conda-forge', 'bioconda']
platforms = [
  'linux-64',
  # 'linux-aarch64',
  # 'osx-arm64',
  # 'osx-amd64'
]
conda_executor = "mamba"
log_level = "INFO"
virtual_package_spec = "conda/virtual-packages.yml"

[tool.conda-lock.dependencies]
python = ">=3.11, <3.12"
pip = ">=23.2"
fmt = ">=10.2.1,<11.0"
# jax "<0.4.27" required
# when using conda-lock
# due to https://github.com/google/jax/issues/21116
# fixed in jax 0.4.29 but not available on conda-forge
jax = ">=0.4.23,<0.4.27"
jaxlib = ">=0.4.23,<0.4.27"
pydantic = ">=2.1.1"
# scikit-learn requires an upper bound of
# 1.2.0 when using conda-lock due to inconsistent
# dependency bounds on conda-forge and pypi
# scikit-learn = "<1.2.0"
scikit-learn = "<1.2.0"
# poethepoet = { source = "pypi" }

[tool.poe.tasks.conda-lock]
# This assumes conda-lock has been installed
# using pipx since conda-lock is not available
# to the nix flake and has undesirable dependency
# constraints for inclusion with the main package.
cmd = """
  $HOME/.local/bin/conda-lock \
  --conda mamba \
  --kind lock \
  --kind env \
  --no-dev-dependencies \
  --filter-categories \
  --category test \
  --category workflows \
  --virtual-package-spec conda/virtual-packages.yml \
  --filename-template "conda/conda-{platform}.lock" \
  --lockfile conda/conda-lock.yml \
  -f pyproject.toml
"""
help = "Runs conda-lock to generate a conda environment lock file derived from package dependencies."

# WORKAROUND: see EOF
# only on Linux and Windows
# https://github.com/python-poetry/poetry/issues/2613#issuecomment-799693903
[tool.poe.tasks.force-cuda11]
cmd = """
  python -m \
  pip install \
  torch==1.13.1+cu111 \
  --extra-index-url https://download.pytorch.org/whl/cu111
"""
help = "Force install torch 1.13.1+cu111 on Linux and Windows."

[tool.poetry.scripts]
pyrovelocity = "pyrovelocity.workflows.cli:main"
pyrovelocity-notebooks = "pyrovelocity.workflows.notebooks:cli"

# Change log_level to "DEBUG" and consider redirecting output to a searchable
# syntax-highlighted file to see all log messages, e.g.
# $ pytest > test.log.py
[tool.pytest.ini_options]
log_level = "INFO"
# We exclude markers associated with slow tests by default
# but run them in CI with the make target `test-cov-xml`
# which overrides this behavior.
addopts = """ 
-m "not slow and not pyensembl"
-rA
--xdoctest
--disable-warnings
--cov=src/pyrovelocity/
--cov-report=term-missing
--durations=0
"""
asyncio_mode = "strict"
norecursedirs = ["bazel-*", ".direnv", "reproducibility", "scripts"]
markers = [
  "pyensembl: Tests that require pyensembl to run.",
  "slow: Tests that are slow and should be run separately.",
  "integration: Tests that use many library components.",
]

[tool.coverage.paths]
source = ["src/pyrovelocity"]
tests = ["src/pyrovelocity/tests"]

[tool.coverage.run]
source_pkgs = ["pyrovelocity"]
branch = true
parallel = true
omit = [
  "scripts/**",
  "src/pyrovelocity/**/__init__.py",
  "src/pyrovelocity/__main__.py",
  "src/pyrovelocity/tests/**",
  "src/pyrovelocity/workflows/**",
]

[tool.coverage.report]
show_missing = true
exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]

[tool.docformatter]
black = true
wrap-summaries = 80
wrap-descriptions = 80
recursive = true
in-place = true
diff = true
make-summary-multi-line = true
pre-summary-newline = true

[tool.ruff]
target-version = "py39"
line-length = 80
exclude = ["app", "bazel-*", "reproducibility", "scripts", ".direnv", ".github"]
# select = []
select = [
  # "B",   # flake8-bugbear
  # "BLE", # flake8-blind-except
  # "C4",  # comprehensions
  # "D",   # pydocstyle
  # "E", # pycodestyle
  # "EXE", # flake8-executable
  # "F", # pyflakes
  # "FA",  # flake8-future-annotations
  # "G",   # flake8-logging-format
  # "FLY", # flynt (format string conversion)
  # "I",   # isort
  # "ICN", # flake8-import-conventions
  # "INP", # flake8-no-pep420 (implicit namespace packages)
  # "ISC", # flake8-implicit-str-concat
  # "PGH", # pygrep-hooks
  # "PIE", # flake8-pie
  # "PL",  # pylint
  # "RET", # flake8-return
  # "RUF", # ruff-specific rules
  # "SIM", # flake8-simplify
  # "T10", # flake8-debugger
  # "T20", # flake8-print
  # "TCH", # flake8-type-checking
  # "TID", # flake8-tidy-imports
  # "UP",  # pyupgrade
  # "W", # pycodestyle
  # "YTT", # flake8-2020
]
ignore = [
  "B028",    # required stacklevel argument to warn
  "B904",    # raise from e or raise from None in exception handlers
  "C408",    # dict(...) as literal
  "D100",    # public module
  "D101",    # public class
  "D102",    # public method
  "D103",    # public function
  "D104",    # public package
  "D105",    # magic methods
  "D106",    # nested class
  "D107",    # init
  "D202",    # blank lines after function docstring
  "D203",    # blank line before class docstring
  "D213",    # Multi-line docstring summary should start at the second line
  "D401",    # Imperative mood
  "D402",    # First line should not be the function's signature
  "D413",    # Blank line required after last section
  "E501",    # line-too-long, this is automatically enforced by ruff format
  "E731",    # lambda-assignment
  "ISC001",  # single line implicit string concat, handled by ruff format
  "PGH003",  # blanket-type-ignore
  "PLC0105", # covariant type parameters should have a _co suffix
  "PLR0124", # name compared with self, e.g., a == a
  "PLR0911", # too many return statements
  "PLR0912", # too many branches
  "PLR0913", # too many arguments
  "PLR0915", # too many statements
  "PLR2004", # forces everything to be a constant
  "PLW2901", # overwriting loop variable
  "RET504",  # unnecessary-assign, these are useful for debugging
  "RET505",  # superfluous-else-return, stylistic choice
  "RET506",  # superfluous-else-raise, stylistic choice
  "RET507",  # superfluous-else-continue, stylistic choice
  "RET508",  # superfluous-else-break, stylistic choice
  "RUF005",  # splat instead of concat
  "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
  "SIM102",  # nested ifs
  "SIM108",  # convert everything to ternary operator
  "SIM114",  # combine `if` branches using logical `or` operator
  "SIM116",  # dictionary instead of `if` statements
  "SIM117",  # nested with statements
  "SIM118",  # remove .keys() calls from dictionaries
  "SIM300",  # yoda conditions
  "UP007",   # Optional[str] -> str | None
]
unfixable = [
  "T201",   # print statements
  "F401",   # unused imports
  "RUF100", # unused noqa comments
  "F841",   # unused variables
]

[tool.ruff.isort]
known-first-party = ["pyrovelocity"]

[tool.ruff.flake8-tidy-imports]
ban-relative-imports = "all"

[tool.ruff.per-file-ignores]
# Tests can use magic values, assertions, and relative imports
"src/pyrovelocity/tests/**/*" = ["PLR2004", "S101", "TID252"]

[tool.pyright]
include = ["src"]
exclude = ["**/node_modules", "**/__pycache__", "**/.hypothesis", "**/docs"]
reportUnnecessaryTypeIgnoreComment = true
reportUnnecessaryIsInstance = false

[tool.isort]
profile = "black"
force_single_line = true
lines_after_imports = 2

[tool.mypy]
python_version = ">=3.11"

[[tool.mypy.overrides]]
module = [""]
ignore_missing_imports = true
warn_unreachable = true
pretty = true
show_column_numbers = true
# show_error_codes = true
show_error_context = true

[tool.pydeps]
max_bacon = 3
cluster = true
max_cluster_size = 10
min_cluster_size = 2
keep_target_cluster = true
rankdir = "TB"
no_show = true
show_dot = true
start_color = 15
rmprefix = "pyrovelocity."
exclude = [
  "pyrovelocity.workflows.configuration",
  "pyrovelocity.logging",
  "pyrovelocity.__main__",
  "pyrovelocity.tests.*",
  "pyrovelocity.workflows.cli",
]

[build-system]
requires = ["poetry-core>=1.6.0"]
build-backend = "poetry.core.masonry.api"