From 9f9b59fee02389494c7596cfce218947dc727a53 Mon Sep 17 00:00:00 2001
From: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>
Date: Tue, 13 Feb 2024 21:17:34 -0500
Subject: [PATCH] Add pyproject.toml

---
 pyproject.toml | 157 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 157 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..ae31e029d
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,157 @@
+# https://peps.python.org/pep-0517/
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+# https://peps.python.org/pep-0621/
+[project]
+name = "dacapo-ml"
+description = "Framework for easy composition of volumetric machine learning jobs."
+readme = "README.md"
+requires-python = ">=3.8"
+# license = { text = "BSD 3-Clause License" }
+authors = [
+    { email = "rhoadesj@hhmi.org", name = "Jeff Rhoades" },
+    { email = "pattonw@janelia.hhmi.org", name = "Will Patton" },
+    { email = "zouinkhim@hhmi.org", name = "Marwan Zouinkhi" },
+    { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Typing :: Typed",
+]
+dynamic = ["version"]
+dependencies = [
+        "numpy==1.22.3",
+        "pyyaml",
+        "zarr",
+        "cattrs",
+        "pymongo",
+        "tqdm",
+        "simpleitk",
+        "lazy-property",
+        "neuroglancer",
+        "torch",
+        "fibsem_tools",
+        "attrs",
+        "bokeh",
+        "numpy-indexed>=0.3.7",
+        "daisy>=1.0",
+        "funlib.math>=0.1",
+        "funlib.geometry>=0.2",
+        "mwatershed>=0.1",
+        "funlib.persistence @ git+https://github.com/janelia-cellmap/funlib.persistence",
+        "funlib.evaluate @ git+https://github.com/pattonw/funlib.evaluate",
+        "gunpowder>=1.3",
+        # "lsds>=0.1.3",
+        "lsds @ git+https://github.com/funkelab/lsd",
+        "xarray",
+        "cattrs",
+        "numpy-indexed",
+        "click",]
+
+# extras
+# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
+[project.optional-dependencies]
+test = ["pytest==7.4.4", "pytest-cov", "pytest-lazy-fixture"]
+dev = [
+    "black",
+    "ipython",
+    "mypy",
+    "pdbpp",
+    "pre-commit",
+    "pytest-cov",
+    "pytest",
+    "rich",
+    "ruff",
+]
+
+[project.urls]
+homepage = "https://github.com/janelia-cellmap/dacapo"
+repository = "https://github.com/janelia-cellmap/dacapo"
+
+# https://hatch.pypa.io/latest/config/metadata/
+[tool.hatch.version]
+source = "vcs"
+
+# https://hatch.pypa.io/latest/config/build/#file-selection
+# [tool.hatch.build.targets.sdist]
+# include = ["/src", "/tests"]
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+only-include = ["dacapo"]
+sources = ["dacapo"]
+
+# https://github.com/charliermarsh/ruff
+[tool.ruff]
+line-length = 88
+target-version = "py38"
+src = ["dacapo"]
+# https://beta.ruff.rs/docs/rules/
+select = [
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "D",    # pydocstyle
+    "I",    # isort
+    "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
+    "B",    # flake8-bugbear
+    "A001", # flake8-builtins
+    "RUF",  # ruff-specific rules
+]
+
+[tool.ruff.per-file-ignores]
+"tests/*.py" = ["D", "S"]
+
+# https://docs.pytest.org/en/6.2.x/customize.html
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+filterwarnings = ["error"]
+
+# https://mypy.readthedocs.io/en/stable/config_file.html
+[tool.mypy]
+files = "dacapo/**/"
+strict = true
+disallow_any_generics = false
+disallow_subclassing_any = false
+show_error_codes = true
+pretty = true
+
+# # module specific overrides
+# [[tool.mypy.overrides]]
+# module = ["numpy.*",]
+# ignore_errors = true
+
+
+# https://coverage.readthedocs.io/en/6.4/config.html
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "@overload",
+    "except ImportError",
+    "\\.\\.\\.",
+    "raise NotImplementedError()",
+]
+[tool.coverage.run]
+source = ["dacapo"]
+
+# https://github.com/mgedmin/check-manifest#configuration
+[tool.check-manifest]
+ignore = [
+    ".github_changelog_generator",
+    ".pre-commit-config.yaml",
+    ".ruff_cache/**/*",
+    "tests/**/*",
+]