From a7a935d508a4cda6dae8e4b79ed079081fc154ee Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Thu, 15 Aug 2024 23:31:40 -0700 Subject: [PATCH] initial refactor --- docs/pyproject.toml | 2 +- nwb_linkml/pyproject.toml | 2 +- nwb_linkml/src/nwb_linkml/includes/hdmf.py | 2 +- nwb_linkml/src/nwb_linkml/io/hdf5.py | 3 +- .../src/nwb_linkml/providers/pydantic.py | 14 +- nwb_linkml/tests/test_includes/conftest.py | 2 +- nwb_linkml/tests/test_includes/test_hdmf.py | 2 +- nwb_models/.gitignore | 162 +++++++++++ nwb_models/README.md | 1 + nwb_models/pdm.lock | 263 ++++++++++++++++++ nwb_models/pyproject.toml | 23 ++ .../src/nwb_models}/__init__.py | 0 .../src/nwb_models}/models/__init__.py | 0 .../nwb_models/models/pydantic}/__init__.py | 0 .../models/pydantic/core}/__init__.py | 0 .../models/pydantic/core/v2_2_0/__init__.py | 0 .../pydantic/core/v2_2_0/core_nwb_base.py | 0 .../pydantic/core/v2_2_0/core_nwb_behavior.py | 0 .../pydantic/core/v2_2_0/core_nwb_device.py | 0 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nwb_models/src/nwb_models}/schema/linkml/hdmf_experimental/v0_5_0/hdmf-experimental.resources.yaml (100%) rename {nwb_linkml/src/nwb_linkml => nwb_models/src/nwb_models}/schema/linkml/hdmf_experimental/v0_5_0/namespace.yaml (100%) create mode 100644 nwb_models/tests/__init__.py 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/pyproject.toml b/nwb_linkml/pyproject.toml index f603a55..9c8e2af 100644 --- a/nwb_linkml/pyproject.toml +++ b/nwb_linkml/pyproject.toml @@ -9,6 +9,7 @@ license = {text = "AGPL-3.0"} readme = "README.md" requires-python = "<3.13,>=3.10" dependencies = [ + "nwb-models>=0.1.0", "pyyaml>=6.0", "linkml-runtime>=1.7.7", "nwb-schema-language>=0.1.3", @@ -64,7 +65,6 @@ addopts = [ "--cov-config=.coveragerc", "-p no:doctest", "--ignore=tests/__tmp__", - "--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..dad4be9 100644 --- a/nwb_linkml/src/nwb_linkml/io/hdf5.py +++ b/nwb_linkml/src/nwb_linkml/io/hdf5.py @@ -37,9 +37,8 @@ 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_models.models import NWBFile from nwb_linkml.providers.schema import SchemaProvider if sys.version_info.minor >= 11: 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. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ diff --git a/nwb_models/README.md b/nwb_models/README.md new file mode 100644 index 0000000..cc36d0a --- /dev/null +++ b/nwb_models/README.md @@ -0,0 +1 @@ +# nwb-models diff --git a/nwb_models/pdm.lock b/nwb_models/pdm.lock new file mode 100644 index 0000000..1dc8eb6 --- /dev/null +++ b/nwb_models/pdm.lock @@ -0,0 +1,263 @@ +# This file is @generated by PDM. +# It is not intended for manual editing. + +[metadata] +groups = ["default"] +strategy = ["inherit_metadata"] +lock_version = "4.5.0" +content_hash = "sha256:f063699fe8934d23fa0a10d71f005d8eaea6c714442adf664f94e8d3cad25b00" + +[[metadata.targets]] +requires_python = ">=3.10" + +[[package]] +name = "annotated-types" +version = "0.7.0" +requires_python = ">=3.8" +summary = "Reusable constraint types to use with typing.Annotated" +groups = ["default"] +dependencies = [ + "typing-extensions>=4.0.0; python_version 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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..30d5e43 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 = [ diff --git a/scripts/generate_core.py b/scripts/generate_core.py index ea037f9..620d9d4 100644 --- a/scripts/generate_core.py +++ b/scripts/generate_core.py @@ -199,13 +199,13 @@ 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(