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pyproject.toml
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[project]
name = "skema"
authors = [
{name="Keith Alcock", email="[email protected]"},
{name="Tito Ferra", email="[email protected]"},
{name="Clayton Morrison", email="[email protected]"},
{name="Enrique Noriega", email="[email protected]"},
{name = "Adarsh Pyarelal", email="[email protected]"},
{name="Vincent Raymond", email="[email protected]"},
]
description = "Scientific Knowledge Extraction and Model Analysis"
version = "0.1.0"
dependencies=[
"Cython",
"numpy",
"dill==0.3.7",
"networkx==2.8.8",
"PyYAML==6.*",
"tree-sitter==0.20.4",
"neo4j==5.14.1",
"requests",
"beautifulsoup4==4.12.*", # used to remove comments etc from pMML before sending to MORAE
"typing_extensions", # see https://github.com/pydantic/pydantic/issues/5821#issuecomment-1559196859
"fastapi~=0.100.0",
"starlette",
"httpx",
"pydantic>=2.0.0",
"uvicorn",
"python-multipart",
"func_timeout==4.3.5"
]
# The Python program analysis pipeline does not currently work with Python 3.9
# or 3.10. This may change in the future.
requires-python = "==3.8.*"
license = {text="MIT"}
dynamic = ["readme"]
[project.optional-dependencies]
# Dev dependencies.
# - pytest: for running tests
# - black: Autoformatting
# - pygraphviz: for creating function network visualizations for debugging.
# Pygraphviz is often tricky to install, so we reserve it for the dev extras
# list.
# - six: Required by auto-generated Swagger models
dev = ["pytest", "pytest-cov", "pytest-xdist", "pytest-asyncio", "pytest-mock", "black", "mypy", "coverage", "pygraphviz", "six"]
demo = ["notebook"]
# ISA dependencies.
isa = [
"pydot==1.4.2",
"graphviz==0.20.1",
"graspologic==3.2.0", # NOTE: this depends on rust when installing on an M1/ARM64 machine
"Levenshtein==0.21.1",
"sentence_transformers==2.2.2"
]
# shared ML dependencies
ml = ["torch==2.0.1", "torchvision==0.15.2", "beartype==0.15.0", "huggingface_hub"]
# Im2MML dependencies. The img2mml service converts equation images to MathML.
# See the skema/img2mml directory.
img2mml = ["skema[ml]", "lxml==4.9.3", "Pillow==10.0.1"]
# dependencies for METAL utilities.
metal = ["skema[ml]",
"fire==0.5.0",
"pyarrow==13.0.0",
"transformers==4.33.2",
"sentence_transformers==2.2.2",
"mock",
"askem_extractions[all]@git+https://github.com/ml4ai/ASKEM-TA1-DataModel"]
# for llm use in skema
llms = ["langchain==0.0.325", "openai==0.28.0"]
# dependencies for text reading utilities.
tr = ["skema[ml]", "pyarrow==13.0.0",
"tqdm",
"pandas==2.0.3"]
# project documentation generation
doc = ["mkdocs==1.2.3", "pdoc3==0.10.0", "mkdocs-git-snippet==0.1.1", "mkdocs-git-revision-date-localized-plugin==0.11.1", "mkdocs-git-authors-plugin==0.6.3", "mkdocs-rtd-dropdown==1.0.2", "jinja2<3.1.0"]
core = ["skema[img2mml]", "skema[isa]", "skema[tr]", "skema[metal]", "skema[llms]"]
# see skema/img2mml/render_mml/mathpix_annotator
annotations = ["matplotlib", "notebook"]
# all extras
all = ["skema[core]", "skema[dev]", "skema[doc]", "skema[demo]", "skema[annotations]"]
[tool.setuptools.package-dir]
"skema.gromet" = "skema/gromet"
"skema.img2mml" = "skema/img2mml"
"skema.isa" = "skema/isa"
"skema.model_assembly" = "skema/model_assembly"
"skema.program_analysis" = "skema/program_analysis"
"skema.rest" = "skema/rest"
"skema.skema_py" = "skema/skema_py"
"skema.utils" = "skema/utils"
"skema.data" = "skema/data"
# re-map skema/text_reading/python to skema.text_reading
#"skema.text_reading" = "skema/text_reading/python"
"skema.metal.model_linker" = "skema/metal/model_linker/skema_model_linker"
# [tool.setuptools.packages]
# find = {} # Scan the project directory with the default parameters
[tool.setuptools.package-data]
# needed to ensure models are included in package/discoverable
"*" = ["*.json", "*vocab.txt", "*.pt", "*.png", "*.html", "*.yml", "*.yaml", "*.zip"]
[tool.setuptools.dynamic]
readme = {file = ["README.md"], content-type = "text/markdown"}
# runnables
[project.scripts]
#skema-tree-sitter-build-fortran-grammar = "skema.program_analysis.CAST.fortran.build_tree_sitter_fortran:main"
link_amr = "skema.metal.model_linker.link_amr:main"
#parquet2json = "skema.text_reading.cosmos_integration:main"
# Minimum requirements for the build system to execute.
[build-system]
requires = ["setuptools>=67", "wheel"]
build-backend = "setuptools.build_meta"
# pytest
[tool.pytest.ini_options]
markers = [
"ci_only: marks tests to only be run in CI (deselect with '-m \"not ci_only\"')"
]
minversion = "7.0"
addopts = "-v --cov=skema --cov-report html:docs/coverage/python"
testpaths = [
# NOTE: There are currently a couple of test ordering dependencies that should be maintained or could cause CI failures
# 1. skema/img2mm/tests needs be run first to generate model files
# 2. program_analysis/tests needs to be run before skema/gromet/execution_engine and any test that may build the python primitive map
"skema/img2mml/tests",
"skema/program_analysis/tests",
"skema/program_analysis/comment_extractor/tests",
"skema/program_analysis/tree_sitter_parsers/tests",
"skema/program_analysis/CAST/matlab/tests",
# TODO: Fix fortran tests
"skema/program_analysis/CAST/fortran/tests",
#"skema/program_analysis/CAST/python/tests"
"skema/gromet/execution_engine/tests",
"skema/rest/tests",
"skema/skema_py/tests",
]
# Configuration for Black.
# NOTE: you have to use single-quoted strings in TOML for regular expressions.
# It's the equivalent of r-strings in Python. Multiline strings are treated as
# verbose regular expressions by Black. Use [ ] to denote a significant space
# character.
[tool.black]
line-length = 88
target-version = ['py38']
include = '\.pyi?$'
extend-exclude = '''
/(
# The following are specific to Black, you probably don't want those.
| blib2to3
| tests/data
| profiling
)/
'''