diff --git a/.github/workflows/model_rebuild.yml b/.github/workflows/model_rebuild.yml new file mode 100644 index 0000000..86a18e7 --- /dev/null +++ b/.github/workflows/model_rebuild.yml @@ -0,0 +1,46 @@ +name: Model Rebuild + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + build_models: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.11" + cache: pip + cache-dependency-path: | + nwb_linkml/pyproject.toml + nwb_schema_language/pyproject.toml + - name: Install packages + run: | + python -m pip install -e ./nwb_schema_language + python -m pip install -e ./nwb_linkml + python -m pip install -e ./nwb_models + - name: Build models + run: | + python ./scripts/generate_core.py + python ./scripts/generate_core.py --hdmf + - name: Test for uncommitted changes + run: | + if [ -z "$(git status --porcelain)" ]; + then + echo "No changes detected" + exit 0 + else + echo "Changes to models detected" + echo "$(git status)" + echo "$(git diff)" + exit 1 + fi + diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ce2fffc..a11fff9 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -18,7 +18,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Install system libraries run: | @@ -26,7 +26,7 @@ jobs: sudo apt install -y libhdf5-dev hdf5-tools - name: Set up python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} cache: 'pip' diff --git a/docs/pyproject.toml b/docs/pyproject.toml index 73f84a0..833f2e8 100644 --- a/docs/pyproject.toml +++ b/docs/pyproject.toml @@ -29,7 +29,7 @@ build-backend = "pdm.backend" [tool.codespell] # Ref: https://github.com/codespell-project/codespell#using-a-config-file -skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema' +skip = '.git*,*.lock,*.css,./nwb_models/src/nwb_models/models,./nwb_linkml/src/nwb_linkml/schema' check-hidden = true # ignore-regex = '' # ignore-words-list = '' diff --git a/nwb_linkml/pdm.lock b/nwb_linkml/pdm.lock index bea21e9..7627014 100644 --- a/nwb_linkml/pdm.lock +++ b/nwb_linkml/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "dev", "plot", "tests"] strategy = ["inherit_metadata"] lock_version = "4.5.0" -content_hash = "sha256:d9e9b2a7f48f3db3e59cd58907a18aa69f91595d07eca53be0bf53b5fb2ba990" +content_hash = "sha256:3223b7fb1c0ac9877a6d8af33e55f10e54fe8eb3a8b4fa053d3e7082863260ac" [[metadata.targets]] requires_python = ">=3.10,<3.13" @@ -512,7 +512,7 @@ version = "3.0.3" requires_python = ">=3.7" summary = "Lightweight in-process concurrent programming" groups = ["default"] -marker = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\"" +marker = "(platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\") and python_version < \"3.13\"" files = [ {file = "greenlet-3.0.3-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:9da2bd29ed9e4f15955dd1595ad7bc9320308a3b766ef7f837e23ad4b4aac31a"}, {file = "greenlet-3.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d353cadd6083fdb056bb46ed07e4340b0869c305c8ca54ef9da3421acbdf6881"}, @@ -1038,6 +1038,22 @@ files = [ {file = "numpydantic-1.3.3.tar.gz", hash = "sha256:1cc2744f7b5fbcecd51a64fafaf8c9a564bb296336a566a16be97ba7b1c28698"}, ] +[[package]] +name = "nwb-models" +version = "0.1.0" +requires_python = ">=3.10" +summary = "Pydantic/LinkML models for Neurodata Without Borders" +groups = ["default"] +dependencies = [ + "numpydantic>=1.3.3", + "pandas>=2.2.2", + "pydantic>=2.3.0", +] +files = [ + {file = "nwb_models-0.1.0-py3-none-any.whl", hash = "sha256:d485422865f6762586e8f8389d67bce17a3e66d07f6273385a751145afbbbfea"}, + {file = "nwb_models-0.1.0.tar.gz", hash = "sha256:3c3ccfc6c2ac03dffe26ba7f180aecc650d6593c05d4f306f84b90fabc3ff2b8"}, +] + [[package]] name = "nwb-schema-language" version = "0.1.3" @@ -1758,7 +1774,7 @@ version = "0.2.8" requires_python = ">=3.6" summary = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" groups = ["default"] -marker = "platform_python_implementation == \"CPython\"" +marker = "platform_python_implementation == \"CPython\" and python_version < \"3.13\"" files = [ {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b42169467c42b692c19cf539c38d4602069d8c1505e97b86387fcf7afb766e1d"}, {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_13_0_arm64.whl", hash = "sha256:07238db9cbdf8fc1e9de2489a4f68474e70dffcb32232db7c08fa61ca0c7c462"}, @@ -1789,29 +1805,29 @@ files = [ [[package]] name = "ruff" -version = "0.5.7" +version = "0.6.0" requires_python = ">=3.7" summary = "An extremely fast Python linter and code formatter, written in Rust." groups = ["dev"] files = [ - 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"--ignore=src/nwb_linkml/models", "--ignore=src/nwb_linkml/schema" ] markers = [ diff --git a/nwb_linkml/src/nwb_linkml/includes/hdmf.py b/nwb_linkml/src/nwb_linkml/includes/hdmf.py index 19bbf34..8bc9107 100644 --- a/nwb_linkml/src/nwb_linkml/includes/hdmf.py +++ b/nwb_linkml/src/nwb_linkml/includes/hdmf.py @@ -34,7 +34,7 @@ from pydantic import ( ) if TYPE_CHECKING: # pragma: no cover - from nwb_linkml.models import VectorData, VectorIndex + from nwb_models.models import VectorData, VectorIndex T = TypeVar("T", bound=NDArray) T_INJECT = 'T = TypeVar("T", bound=NDArray)' diff --git a/nwb_linkml/src/nwb_linkml/io/hdf5.py b/nwb_linkml/src/nwb_linkml/io/hdf5.py index 387e4a6..ade89d9 100644 --- a/nwb_linkml/src/nwb_linkml/io/hdf5.py +++ b/nwb_linkml/src/nwb_linkml/io/hdf5.py @@ -37,10 +37,9 @@ from tqdm import tqdm from nwb_linkml.maps.hdf5 import ReadPhases, ReadQueue, flatten_hdf -# from nwb_linkml.models.core_nwb_file import NWBFile if TYPE_CHECKING: - from nwb_linkml.models import NWBFile from nwb_linkml.providers.schema import SchemaProvider + from nwb_models.models import NWBFile if sys.version_info.minor >= 11: from typing import Never diff --git a/nwb_linkml/src/nwb_linkml/providers/git.py b/nwb_linkml/src/nwb_linkml/providers/git.py index 8219aaf..77afc59 100644 --- a/nwb_linkml/src/nwb_linkml/providers/git.py +++ b/nwb_linkml/src/nwb_linkml/providers/git.py @@ -117,7 +117,11 @@ class GitRepo: path (:class:`pathlib.Path`): A directory to clone to - if ``None``, use :attr:`~.Config.git_dir` / :attr:`.NamespaceRepo.name` """ - self._temp_directory = path + if path is None: + self._base_directory = Config().git_dir + else: + self._base_directory = Path(path) + self._temp_directory = None self.namespace = namespace self._commit = commit @@ -135,8 +139,7 @@ class GitRepo: Temporary directory where this repository will be cloned to """ if self._temp_directory is None: - git_dir = Config().git_dir - self._temp_directory = git_dir / self.namespace.name + self._temp_directory = self._base_directory / self.namespace.name if not self._temp_directory.exists(): self._temp_directory.mkdir(parents=True) diff --git a/nwb_linkml/src/nwb_linkml/providers/provider.py b/nwb_linkml/src/nwb_linkml/providers/provider.py index ea48b76..87f6567 100644 --- a/nwb_linkml/src/nwb_linkml/providers/provider.py +++ b/nwb_linkml/src/nwb_linkml/providers/provider.py @@ -94,7 +94,7 @@ class Provider(ABC): namespace_path = self.path / namespace_module if not namespace_path.exists() and namespace in ("core", "hdmf-common") and allow_repo: # return builtins - module_path = Path(importlib.util.find_spec("nwb_linkml").origin).parent + module_path = Path(importlib.util.find_spec("nwb_models").origin).parent if self.PROVIDES == "linkml": namespace_path = module_path / "schema" / "linkml" / namespace @@ -131,7 +131,7 @@ class Provider(ABC): # first get any builtins provided by the package itself # these get overwritten by - module_path = Path(importlib.util.find_spec("nwb_linkml").origin).parent + module_path = Path(importlib.util.find_spec("nwb_models").origin).parent builtin_namespaces = [] if self.PROVIDES == "linkml": namespace_path = module_path / "schema" / "linkml" diff --git a/nwb_linkml/src/nwb_linkml/providers/pydantic.py b/nwb_linkml/src/nwb_linkml/providers/pydantic.py index f02a2c8..3e379dd 100644 --- a/nwb_linkml/src/nwb_linkml/providers/pydantic.py +++ b/nwb_linkml/src/nwb_linkml/providers/pydantic.py @@ -234,7 +234,7 @@ class PydanticProvider(Provider): e.g.:: - nwb_linkml.models.pydantic.{namespace}.{version} + nwb_models.models.pydantic.{namespace}.{version} """ name_pieces = [ "nwb_linkml", @@ -296,7 +296,7 @@ class PydanticProvider(Provider): Get the imported module for a given namespace and version. A given namespace will be stored in :data:`sys.modules` as - ``nwb_linkml.models.{namespace}``, + ``nwb_models.models.{namespace}``, so first check if there is any already-imported module, and return that if so. Then we check in the temporary directory for an already-built ``namespace.py`` file @@ -306,12 +306,12 @@ class PydanticProvider(Provider): Notes: The imported modules shadow the "actual" - ``nwb_linkml.models`` module as would be imported from the usual location + ``nwb_models.models`` module as would be imported from the usual location within the package directory. This is intentional, as models can then be used as if they were integrated parts of the package, and also so the active version of a namespace can be cleanly accessed - (ie. without ``from nwb_linkml.models.core import v2_2_0 as core`` ). + (ie. without ``from nwb_models.models.core import v2_2_0 as core`` ). Accordingly, we assume that people will only be using a single version of NWB in a given Python session. @@ -324,7 +324,7 @@ class PydanticProvider(Provider): version (Optional[str]): Version to import. If ``None``, get the most recently build module allow_repo (bool): Allow getting modules provided within - :mod:`nwb_linkml.models.pydantic` + :mod:`nwb_models.models.pydantic` Returns: The imported :class:`types.ModuleType` object that has all the built @@ -367,7 +367,7 @@ class PydanticProvider(Provider): repo_base = Path(__file__).parents[1] deletes = [] for k, v in sys.modules.items(): - if not k.startswith("nwb_linkml.models.pydantic"): + if not k.startswith("nwb_models.models.pydantic"): continue try: Path(v.__file__).relative_to(repo_base) @@ -428,7 +428,7 @@ class EctopicModelFinder(MetaPathFinder): """ - MODEL_STEM = "nwb_linkml.models.pydantic" + MODEL_STEM = "nwb_models.models.pydantic" def __init__(self, path: Path, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/nwb_linkml/tests/test_includes/conftest.py b/nwb_linkml/tests/test_includes/conftest.py index 67011ec..53e3a39 100644 --- a/nwb_linkml/tests/test_includes/conftest.py +++ b/nwb_linkml/tests/test_includes/conftest.py @@ -3,7 +3,7 @@ from typing import Tuple import numpy as np import pytest -from nwb_linkml.models import ( +from nwb_models.models import ( Device, DynamicTableRegion, ElectricalSeries, diff --git a/nwb_linkml/tests/test_includes/test_hdmf.py b/nwb_linkml/tests/test_includes/test_hdmf.py index cb2b974..920e8b4 100644 --- a/nwb_linkml/tests/test_includes/test_hdmf.py +++ b/nwb_linkml/tests/test_includes/test_hdmf.py @@ -15,7 +15,7 @@ from nwb_linkml.includes.hdmf import ( ) # FIXME: Make this just be the output of the provider by patching into import machinery -from nwb_linkml.models.pydantic.core.v2_7_0.namespace import ( +from nwb_models.models.pydantic.core.v2_7_0.namespace import ( ElectrodeGroup, ) diff --git a/nwb_models/.gitignore b/nwb_models/.gitignore new file mode 100644 index 0000000..3a8816c --- /dev/null +++ b/nwb_models/.gitignore @@ -0,0 +1,162 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm-project.org/#use-with-ide +.pdm.toml +.pdm-python +.pdm-build/ + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. 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nwb_models/src/nwb_models/__init__.py diff --git a/nwb_linkml/src/nwb_linkml/models/__init__.py b/nwb_models/src/nwb_models/models/__init__.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/__init__.py rename to nwb_models/src/nwb_models/models/__init__.py diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/__init__.py b/nwb_models/src/nwb_models/models/pydantic/__init__.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/pydantic/core/__init__.py rename to nwb_models/src/nwb_models/models/pydantic/__init__.py diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/__init__.py b/nwb_models/src/nwb_models/models/pydantic/core/__init__.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/pydantic/hdmf_common/__init__.py rename to nwb_models/src/nwb_models/models/pydantic/core/__init__.py diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/__init__.py b/nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/__init__.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/__init__.py rename to nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/__init__.py diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py b/nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_base.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_base.py rename to nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_base.py diff --git a/nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_behavior.py b/nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_behavior.py similarity index 100% rename from nwb_linkml/src/nwb_linkml/models/pydantic/core/v2_2_0/core_nwb_behavior.py rename to nwb_models/src/nwb_models/models/pydantic/core/v2_2_0/core_nwb_behavior.py diff --git 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a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/hdmf-common.sparse.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/hdmf-common.sparse.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/hdmf-common.sparse.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/hdmf-common.sparse.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/hdmf-common.table.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/hdmf-common.table.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/hdmf-common.table.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/hdmf-common.table.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_6_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.base.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.base.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.base.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.base.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.sparse.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.sparse.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.sparse.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.sparse.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.table.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.table.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/hdmf-common.table.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.table.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_7_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.base.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.base.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.base.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.base.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.sparse.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.sparse.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.sparse.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.sparse.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.table.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.table.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/hdmf-common.table.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.table.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_common/v1_8_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.experimental.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.experimental.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.experimental.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.experimental.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/hdmf-experimental.resources.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_1_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_1_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.experimental.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.experimental.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.experimental.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.experimental.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.resources.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.resources.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.resources.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/hdmf-experimental.resources.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_2_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_2_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.experimental.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.experimental.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.experimental.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.experimental.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.resources.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.resources.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.resources.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/hdmf-experimental.resources.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_3_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_3_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.experimental.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.experimental.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.experimental.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.experimental.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.resources.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.resources.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.resources.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/hdmf-experimental.resources.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_4_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_4_0/namespace.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.experimental.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.experimental.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.experimental.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.experimental.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.nwb.language.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.nwb.language.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.nwb.language.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.nwb.language.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.resources.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.resources.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.resources.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.resources.yaml diff --git a/nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/namespace.yaml b/nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/namespace.yaml similarity index 100% rename from nwb_linkml/src/nwb_linkml/schema/linkml/hdmf_experimental/v0_5_0/namespace.yaml rename to nwb_models/src/nwb_models/schema/linkml/hdmf_experimental/v0_5_0/namespace.yaml diff --git a/nwb_models/tests/__init__.py b/nwb_models/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/pyproject.toml b/pyproject.toml index b8723db..99b5e1f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,6 +7,7 @@ requires-python = "<3.13,>=3.10" dev = [ '-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml', '-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language', + '-e nwb-models @ file:///${PROJECT_ROOT/nwb_models', '-e docs @ file:///${PROJECT_ROOT}/docs', "ruff>=0.5.0", "black>=24.4.2", @@ -14,7 +15,7 @@ dev = [ [tool.codespell] # Ref: https://github.com/codespell-project/codespell#using-a-config-file -skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema' +skip = '.git*,*.lock,*.css,./nwb_models/src/nwb_models/models,./nwb_models/src/nwb_models/schema' check-hidden = true # ignore-regex = '' # ignore-words-list = '' @@ -24,11 +25,10 @@ target-version = "py311" include = ["nwb_linkml/**/*.py", "nwb_schema_language/src/**/*.py", "pyproject.toml"] exclude = [ "docs", - "nwb_linkml/src/nwb_linkml/models/**/*.py", + "nwb_models/src/nwb_models/models/**/*.py", "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py", "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py", "tests/__tmp__/**/*" - # "nwb_linkml/src/nwb_linkml/models/**/*.py" ] line-length = 100 @@ -82,7 +82,7 @@ fixable = ["ALL"] [tool.ruff.lint.per-file-ignores] "**/tests/**.py" = ["D", "ANN", "E501", "F841", "F722"] -"nwb_linkml/src/nwb_linkml/models/**/*.py" = ["ANN202", "E501", "D", "F722", "UP036", "F403"] +"nwb_models/src/nwb_models/models/**/*.py" = ["ANN202", "E501", "D", "F722", "UP036", "F403"] [tool.mypy] plugins = [ @@ -101,5 +101,5 @@ warn_unreachable = true target-version = ['py38', 'py39', 'py310', 'py311'] enable-unstable-feature = ["string_processing"] preview = true -include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$" +include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$|nwb_models/.*\\.py$" line-length = 100 \ No newline at end of file diff --git a/scripts/generate_core.py b/scripts/generate_core.py index ea037f9..ad593cf 100644 --- a/scripts/generate_core.py +++ b/scripts/generate_core.py @@ -50,6 +50,18 @@ def generate_core_pydantic(yaml_path: Path, output_path: Path, dry_run: bool = F pfile.write(gen_pydantic) +def make_tmp_dir(clear: bool = False) -> Path: + # use a directory underneath this one as the temporary directory rather than + # the default hidden one + tmp_dir = Path(__file__).parent / "__tmp__" + if tmp_dir.exists() and clear: + for p in tmp_dir.iterdir(): + if p.is_dir() and not p.name == "git": + shutil.rmtree(tmp_dir) + tmp_dir.mkdir(exist_ok=True) + return tmp_dir + + def generate_versions( yaml_path: Path, pydantic_path: Path, @@ -64,12 +76,7 @@ def generate_versions( # repo.clone(force=True) repo.clone() - # use a directory underneath this one as the temporary directory rather than - # the default hidden one - tmp_dir = Path(__file__).parent / "__tmp__" - if tmp_dir.exists(): - shutil.rmtree(tmp_dir) - tmp_dir.mkdir() + tmp_dir = make_tmp_dir() linkml_provider = LinkMLProvider(path=tmp_dir, verbose=False) pydantic_provider = PydanticProvider(path=tmp_dir, verbose=False) @@ -199,13 +206,13 @@ def parser() -> ArgumentParser: "--yaml", help="directory to export linkML schema to", type=Path, - default=Path(__file__).parent.parent / "nwb_linkml" / "src" / "nwb_linkml" / "schema", + default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "schema", ) parser.add_argument( "--pydantic", help="directory to export pydantic models", type=Path, - default=Path(__file__).parent.parent / "nwb_linkml" / "src" / "nwb_linkml" / "models", + default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "models", ) parser.add_argument("--hdmf", help="Only generate the HDMF namespaces", action="store_true") parser.add_argument( @@ -227,10 +234,15 @@ def parser() -> ArgumentParser: def main(): args = parser().parse_args() + + tmp_dir = make_tmp_dir(clear=True) + git_dir = tmp_dir / "git" + git_dir.mkdir(exist_ok=True) + if args.hdmf: - repo = GitRepo(HDMF_COMMON_REPO) + repo = GitRepo(HDMF_COMMON_REPO, path=git_dir) else: - repo = GitRepo(NWB_CORE_REPO) + repo = GitRepo(NWB_CORE_REPO, path=git_dir) if not args.dry_run: args.yaml.mkdir(exist_ok=True)