Add license, complete pyproject.toml and configure pre-commit

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/crate-ci/typos
+    rev: dictgen-v0.3.1
+    hooks:
+      - id: typos
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.6
+    hooks:
+      - id: ruff
+        args: [--fix]
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        # # you have to add the things you want to type check against here
+        # additional_dependencies:
+        #   - numpy

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Funke lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyproject.toml

@@ -4,20 +4,112 @@ version = "0.1.0"
 description = "Reference implementation of the Graph Exchange File Format"
 readme = "README.md"
 requires-python = ">=3.10"
+license = { text = "MIT License" }
 dependencies = [
-    "spatial-graph",
+    "spatial-graph @ git+https://github.com/funkelab/spatial_graph.git@d02b691e4fa0f184871939a89c6f964bfd0f5e39",
     "zarr<3.0.0",
 ]
 
-[dependency-groups]
+[project.optional-dependencies]
 dev = [
     "pytest>=8.3.4",
-    "pytest-cov"
+    "pytest-cov",
+    "mypy",
+    "pre-commit",
+    "ruff"
 ]
 
-[tool.uv.sources]
-spatial-graph = { git = "https://github.com/funkelab/spatial_graph", rev = "d02b691e4fa0f184871939a89c6f964bfd0f5e39" }
-
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
+
+[tool.hatch.metadata]
+# Enables installing from git commit
+allow-direct-references = true
+
+# https://github.com/charliermarsh/ruff
+[tool.ruff]
+line-length = 100
+target-version = "py38"
+# https://beta.ruff.rs/docs/rules/
+extend-select = [
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "I",    # isort
+    "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
+    "B",    # flake8-bugbear
+    "A001", # flake8-builtins
+    "RUF",  # ruff-specific rules
+    "TID",  # tidy imports
+    "TCH",  # type checking
+    # "D",    # pydocstyle
+]
+# I do this to get numpy-style docstrings AND retain
+# D417 (Missing argument descriptions in the docstring)
+# otherwise, see:
+# https://beta.ruff.rs/docs/faq/#does-ruff-support-numpy-or-google-style-docstrings
+# https://github.com/charliermarsh/ruff/issues/2606
+extend-ignore = [
+    "D100", # Missing docstring in public module
+    "D107", # Missing docstring in __init__
+    "D203", # 1 blank line required before class docstring
+    "D212", # Multi-line docstring summary should start at the first line
+    "D213", # Multi-line docstring summary should start at the second line
+    "D401", # First line should be in imperative mood
+    "D413", # Missing blank line after last section
+    "D416", # Section name should end with a colon
+]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[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"]
+pythonpath = [
+  "tests"
+]
+
+# https://mypy.readthedocs.io/en/stable/config_file.html
+[tool.mypy]
+files = "src/**/"
+# 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()",
+    "pass",
+]
+[tool.coverage.run]
+source = ["traccuracy"]
+
+# https://github.com/mgedmin/check-manifest#configuration
+# [tool.check-manifest]
+# ignore = [
+#     ".github_changelog_generator",
+#     ".pre-commit-config.yaml",
+#     ".ruff_cache/**/*",
+#     "tests/**/*",
+# ]