add formatting config

nwb_linkml/pyproject.toml

@@ -43,6 +43,11 @@ tests = [
     "pytest-profiling<2.0.0,>=1.7.0",
     "sybil<6.0.0,>=5.0.3",
 ]
+dev = [
+    "nwb-linkml[tests]",
+    "ruff>=0.5.0",
+    "black>=24.4.2",
+]
 
 [tool.pdm]
 distribution = true

pdm.lock

@@ -5,7 +5,7 @@
 groups = ["default", "dev"]
 strategy = ["cross_platform", "inherit_metadata"]
 lock_version = "4.4.2"
-content_hash = "sha256:f11ad9b7b3e0d83f13c208abbc38ae91609f617a3ceae75b7dd951553900ef24"
+content_hash = "sha256:3113d2345a99f9287c2a8a545bcfeb5d34b99f44377f211dab8652e78d2f551d"
 
 [[package]]
 name = "alabaster"
@@ -146,6 +146,38 @@ files = [
     {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
 ]
 
+[[package]]
+name = "black"
+version = "24.4.2"
+requires_python = ">=3.8"
+summary = "The uncompromising code formatter."
+groups = ["dev"]
+dependencies = [
+    "click>=8.0.0",
+    "mypy-extensions>=0.4.3",
+    "packaging>=22.0",
+    "pathspec>=0.9.0",
+    "platformdirs>=2",
+    "tomli>=1.1.0; python_version < \"3.11\"",
+    "typing-extensions>=4.0.1; python_version < \"3.11\"",
+]
+files = [
+    {file = "black-24.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dd1b5a14e417189db4c7b64a6540f31730713d173f0b63e55fabd52d61d8fdce"},
+    {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"},
+    {file = "black-24.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063"},
+    {file = "black-24.4.2-cp310-cp310-win_amd64.whl", hash = "sha256:7768a0dbf16a39aa5e9a3ded568bb545c8c2727396d063bbaf847df05b08cd96"},
+    {file = "black-24.4.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:257d724c2c9b1660f353b36c802ccece186a30accc7742c176d29c146df6e474"},
+    {file = "black-24.4.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:bdde6f877a18f24844e381d45e9947a49e97933573ac9d4345399be37621e26c"},
+    {file = "black-24.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e151054aa00bad1f4e1f04919542885f89f5f7d086b8a59e5000e6c616896ffb"},
+    {file = "black-24.4.2-cp311-cp311-win_amd64.whl", hash = "sha256:7e122b1c4fb252fd85df3ca93578732b4749d9be076593076ef4d07a0233c3e1"},
+    {file = "black-24.4.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:accf49e151c8ed2c0cdc528691838afd217c50412534e876a19270fea1e28e2d"},
+    {file = "black-24.4.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:88c57dc656038f1ab9f92b3eb5335ee9b021412feaa46330d5eba4e51fe49b04"},
+    {file = "black-24.4.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:be8bef99eb46d5021bf053114442914baeb3649a89dc5f3a555c88737e5e98fc"},
+    {file = "black-24.4.2-cp312-cp312-win_amd64.whl", hash = "sha256:415e686e87dbbe6f4cd5ef0fbf764af7b89f9057b97c908742b6008cc554b9c0"},
+    {file = "black-24.4.2-py3-none-any.whl", hash = "sha256:d36ed1124bb81b32f8614555b34cc4259c3fbc7eec17870e8ff8ded335b58d8c"},
+    {file = "black-24.4.2.tar.gz", hash = "sha256:c872b53057f000085da66a19c55d68f6f8ddcac2642392ad3a355878406fbd4d"},
+]
+
 [[package]]
 name = "blosc2"
 version = "2.7.0"
@@ -1240,6 +1272,17 @@ files = [
     {file = "msgpack-1.0.8.tar.gz", hash = "sha256:95c02b0e27e706e48d0e5426d1710ca78e0f0628d6e89d5b5a5b91a5f12274f3"},
 ]
 
+[[package]]
+name = "mypy-extensions"
+version = "1.0.0"
+requires_python = ">=3.5"
+summary = "Type system extensions for programs checked with the mypy type checker."
+groups = ["dev"]
+files = [
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
+]
+
 [[package]]
 name = "myst-nb"
 version = "1.1.1"
@@ -1460,8 +1503,8 @@ dependencies = [
     "myst-nb @ git+https://github.com/executablebooks/MyST-NB.git",
     "myst-parser>=2.0.0",
     "nptyping>=2.5.0",
-    "nwb-linkml",
+    "nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml",
-    "nwb-schema-language",
+    "nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language",
     "sphinx-autobuild>=2021.3.14",
     "sphinx-design>=0.5.0",
     "sphinx-togglebutton>=0.3.2",
@@ -1542,6 +1585,17 @@ files = [
     {file = "partd-1.4.2.tar.gz", hash = "sha256:d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c"},
 ]
 
+[[package]]
+name = "pathspec"
+version = "0.12.1"
+requires_python = ">=3.8"
+summary = "Utility library for gitignore style pattern matching of file paths."
+groups = ["dev"]
+files = [
+    {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
+    {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
+]
+
 [[package]]
 name = "pexpect"
 version = "4.9.0"
@@ -2301,6 +2355,33 @@ files = [
     {file = "ruamel.yaml.clib-0.2.8.tar.gz", hash = "sha256:beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512"},
 ]
 
+[[package]]
+name = "ruff"
+version = "0.5.0"
+requires_python = ">=3.7"
+summary = "An extremely fast Python linter and code formatter, written in Rust."
+groups = ["dev"]
+files = [
+    {file = "ruff-0.5.0-py3-none-linux_armv6l.whl", hash = "sha256:ee770ea8ab38918f34e7560a597cc0a8c9a193aaa01bfbd879ef43cb06bd9c4c"},
+    {file = "ruff-0.5.0-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:38f3b8327b3cb43474559d435f5fa65dacf723351c159ed0dc567f7ab735d1b6"},
+    {file = "ruff-0.5.0-py3-none-macosx_11_0_arm64.whl", hash = "sha256:7594f8df5404a5c5c8f64b8311169879f6cf42142da644c7e0ba3c3f14130370"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:adc7012d6ec85032bc4e9065110df205752d64010bed5f958d25dbee9ce35de3"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:d505fb93b0fabef974b168d9b27c3960714d2ecda24b6ffa6a87ac432905ea38"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9dc5cfd3558f14513ed0d5b70ce531e28ea81a8a3b1b07f0f48421a3d9e7d80a"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:db3ca35265de239a1176d56a464b51557fce41095c37d6c406e658cf80bbb362"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:b1a321c4f68809fddd9b282fab6a8d8db796b270fff44722589a8b946925a2a8"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2c4dfcd8d34b143916994b3876b63d53f56724c03f8c1a33a253b7b1e6bf2a7d"},
+    {file = "ruff-0.5.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81e5facfc9f4a674c6a78c64d38becfbd5e4f739c31fcd9ce44c849f1fad9e4c"},
+    {file = "ruff-0.5.0-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:e589e27971c2a3efff3fadafb16e5aef7ff93250f0134ec4b52052b673cf988d"},
+    {file = "ruff-0.5.0-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:d2ffbc3715a52b037bcb0f6ff524a9367f642cdc5817944f6af5479bbb2eb50e"},
+    {file = "ruff-0.5.0-py3-none-musllinux_1_2_i686.whl", hash = "sha256:cd096e23c6a4f9c819525a437fa0a99d1c67a1b6bb30948d46f33afbc53596cf"},
+    {file = "ruff-0.5.0-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:46e193b36f2255729ad34a49c9a997d506e58f08555366b2108783b3064a0e1e"},
+    {file = "ruff-0.5.0-py3-none-win32.whl", hash = "sha256:49141d267100f5ceff541b4e06552e98527870eafa1acc9dec9139c9ec5af64c"},
+    {file = "ruff-0.5.0-py3-none-win_amd64.whl", hash = "sha256:e9118f60091047444c1b90952736ee7b1792910cab56e9b9a9ac20af94cd0440"},
+    {file = "ruff-0.5.0-py3-none-win_arm64.whl", hash = "sha256:ed5c4df5c1fb4518abcb57725b576659542bdbe93366f4f329e8f398c4b71178"},
+    {file = "ruff-0.5.0.tar.gz", hash = "sha256:eb641b5873492cf9bd45bc9c5ae5320648218e04386a5f0c264ad6ccce8226a1"},
+]
+
 [[package]]
 name = "setuptools"
 version = "70.2.0"

pyproject.toml

@@ -8,6 +8,8 @@ dev = [
     '-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
     '-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
     '-e docs @ file:///${PROJECT_ROOT}/docs',
+    "ruff>=0.5.0",
+    "black>=24.4.2",
 ]
 
 [tool.codespell]
@@ -16,3 +18,73 @@ skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/n
 check-hidden = true
 # ignore-regex = ''
 # ignore-words-list = ''
+
+[tool.ruff]
+target-version = "py311"
+include = ["nwb_linkml/**/*.py", "nwb_schema_language/src/**/*.py", "pyproject.toml"]
+exclude = [
+    "docs",
+    "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py",
+    "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py",
+    "nwb_linkml/src/nwb_linkml/models/**/*.py"
+]
+line-length = 100
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # annotations
+    "ANN",
+    ## ----------
+    # pydocstyle
+    # undocumented public objects
+    "D100", "D101", "D102", "D103", "D104", "D106", "D107",
+    # indentation
+    "D207", "D208",
+    # whitespace
+    "D210", "D211",
+    # emptiness
+    "D419",
+]
+ignore = [
+    "ANN101", "ANN102", "ANN401", "ANN204",
+    # explicit strict arg for zip
+    "B905",
+    # builtin type annotations
+    "UP006", "UP035",
+    # | for Union types (only supported >=3.10
+    "UP007", "UP038",
+    # docstrings for __init__
+    "D107",
+]
+
+fixable = ["ALL"]
+
+[tool.mypy]
+plugins = [
+    "pydantic.mypy"
+]
+packages = [
+    "miniscope_io"
+]
+exclude = [
+    '.*vendor.*'
+]
+follow_imports = "silent"
+warn_unreachable = true
+
+[tool.black]
+target-version = ['py38', 'py39', 'py310', 'py311']
+include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$"
+line-length = 100