Merge pull request #8 from p2p-ld/separate-nwb-models

Separate models into `nwb_models` package

.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
+          

.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'

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 = ''

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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+    {file = "ruff-0.6.0-py3-none-linux_armv6l.whl", hash = "sha256:92dcce923e5df265781e5fc76f9a1edad52201a7aafe56e586b90988d5239013"},
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+    {file = "ruff-0.6.0-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:31b90ff9dc79ed476c04e957ba7e2b95c3fceb76148f2079d0d68a908d2cfae7"},
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+    {file = "ruff-0.6.0-py3-none-macosx_11_0_arm64.whl", hash = "sha256:6d834a9ec9f8287dd6c3297058b3a265ed6b59233db22593379ee38ebc4b9768"},
-    {file = "ruff-0.5.7-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a01c34400097b06cf8a6e61b35d6d456d5bd1ae6961542de18ec81eaf33b4cb8"},
+    {file = "ruff-0.6.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f2089267692696aba342179471831a085043f218706e642564812145df8b8d0d"},
-    {file = "ruff-0.5.7-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:fcc8054f1a717e2213500edaddcf1dbb0abad40d98e1bd9d0ad364f75c763eea"},
+    {file = "ruff-0.6.0-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:aa62b423ee4bbd8765f2c1dbe8f6aac203e0583993a91453dc0a449d465c84da"},
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+    {file = "ruff-0.6.0.tar.gz", hash = "sha256:272a81830f68f9bd19d49eaf7fa01a5545c5a2e86f32a9935bb0e4bb9a1db5b8"},
 ]
 
 [[package]]

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 = [

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)'

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

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 = self._base_directory / self.namespace.name
-            self._temp_directory = git_dir / self.namespace.name
             if not self._temp_directory.exists():
                 self._temp_directory.mkdir(parents=True)
 

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"

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)

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,

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,
 )
 

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.
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nwb_models/README.md

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nwb_models/pdm.lock

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nwb_models/pyproject.toml

@@ -0,0 +1,23 @@
+[project]
+name = "nwb-models"
+version = "0.1.0"
+description = "Pydantic/LinkML models for Neurodata Without Borders"
+authors = [
+    {name = "sneakers-the-rat", email = "sneakers-the-rat@protonmail.com"},
+]
+dependencies = [
+    "pydantic>=2.3.0",
+    "numpydantic>=1.3.3",
+    "pandas>=2.2.2"
+]
+requires-python = ">=3.10"
+readme = "README.md"
+license = {text = "AGPL-3.0"}
+
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
+
+
+[tool.pdm]
+distribution = true