some baseline tests, fixing imports, coverage reports

.github/workflows/tests.yml

@@ -4,7 +4,7 @@ on:
   push:
 
 jobs:
-  build:
+  test:
     strategy:
       matrix:
         python-version: [3.11]
@@ -20,7 +20,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: pip install .[tests] pytest-md pytest-emoji
+        run: pip install .[tests]
         working-directory: nwb_linkml
 
       - uses: pavelzw/pytest-action@v2
@@ -29,3 +29,8 @@ jobs:
           emoji: true
           verbose: true
           job-summary: true
+
+      - working-directory: nwb_linkml
+        run: "coveralls --service=github"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

nwb_linkml/poetry.lock

@@ -212,6 +212,87 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "coverage"
+version = "6.5.0"
+description = "Code coverage measurement for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "coverage-6.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef8674b0ee8cc11e2d574e3e2998aea5df5ab242e012286824ea3c6970580e53"},
+    {file = "coverage-6.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:784f53ebc9f3fd0e2a3f6a78b2be1bd1f5575d7863e10c6e12504f240fd06660"},
+    {file = "coverage-6.5.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b4a5be1748d538a710f87542f22c2cad22f80545a847ad91ce45e77417293eb4"},
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+    {file = "coverage-6.5.0-cp39-cp39-win32.whl", hash = "sha256:d9ecf0829c6a62b9b573c7bb6d4dcd6ba8b6f80be9ba4fc7ed50bf4ac9aecd72"},
+    {file = "coverage-6.5.0-cp39-cp39-win_amd64.whl", hash = "sha256:fc2af30ed0d5ae0b1abdb4ebdce598eafd5b35397d4d75deb341a614d333d987"},
+    {file = "coverage-6.5.0-pp36.pp37.pp38-none-any.whl", hash = "sha256:1431986dac3923c5945271f169f59c45b8802a114c8f548d611f2015133df77a"},
+    {file = "coverage-6.5.0.tar.gz", hash = "sha256:f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84"},
+]
+
+[package.extras]
+toml = ["tomli"]
+
+[[package]]
+name = "coveralls"
+version = "3.3.1"
+description = "Show coverage stats online via coveralls.io"
+optional = true
+python-versions = ">= 3.5"
+files = [
+    {file = "coveralls-3.3.1-py2.py3-none-any.whl", hash = "sha256:f42015f31d386b351d4226389b387ae173207058832fbf5c8ec4b40e27b16026"},
+    {file = "coveralls-3.3.1.tar.gz", hash = "sha256:b32a8bb5d2df585207c119d6c01567b81fba690c9c10a753bfe27a335bfc43ea"},
+]
+
+[package.dependencies]
+coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0"
+docopt = ">=0.6.1"
+requests = ">=1.0.0"
+
+[package.extras]
+yaml = ["PyYAML (>=3.10)"]
+
 [[package]]
 name = "curies"
 version = "0.6.0"
@@ -344,6 +425,16 @@ wrapt = ">=1.10,<2"
 [package.extras]
 dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
+[[package]]
+name = "docopt"
+version = "0.6.2"
+description = "Pythonic argument parser, that will make you smile"
+optional = true
+python-versions = "*"
+files = [
+    {file = "docopt-0.6.2.tar.gz", hash = "sha256:49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491"},
+]
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
@@ -1372,6 +1463,24 @@ pluggy = ">=0.12,<2.0"
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pytest-cov"
+version = "4.1.0"
+description = "Pytest plugin for measuring coverage."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
+    {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
+]
+
+[package.dependencies]
+coverage = {version = ">=5.2.1", extras = ["toml"]}
+pytest = ">=4.6"
+
+[package.extras]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+
 [[package]]
 name = "pytest-depends"
 version = "1.0.1"
@@ -1389,6 +1498,20 @@ future-fstrings = "*"
 networkx = "*"
 pytest = ">=3"
 
+[[package]]
+name = "pytest-emoji"
+version = "0.2.0"
+description = "A pytest plugin that adds emojis to your test result report"
+optional = false
+python-versions = ">=3.4"
+files = [
+    {file = "pytest-emoji-0.2.0.tar.gz", hash = "sha256:e1bd4790d87649c2d09c272c88bdfc4d37c1cc7c7a46583087d7c510944571e8"},
+    {file = "pytest_emoji-0.2.0-py3-none-any.whl", hash = "sha256:6e34ed21970fa4b80a56ad11417456bd873eb066c02315fe9df0fafe6d4d4436"},
+]
+
+[package.dependencies]
+pytest = ">=4.2.1"
+
 [[package]]
 name = "pytest-logging"
 version = "2015.11.4"
@@ -1402,6 +1525,20 @@ files = [
 [package.dependencies]
 pytest = ">=2.8.1"
 
+[[package]]
+name = "pytest-md"
+version = "0.2.0"
+description = "Plugin for generating Markdown reports for pytest results"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pytest-md-0.2.0.tar.gz", hash = "sha256:3b248d5b360ea5198e05b4f49c7442234812809a63137ec6cdd3643a40cf0112"},
+    {file = "pytest_md-0.2.0-py3-none-any.whl", hash = "sha256:4c4cd16fea6d1485e87ee254558712c804a96d2aa9674b780e7eb8fb6526e1d1"},
+]
+
+[package.dependencies]
+pytest = ">=4.2.1"
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.2"
@@ -2186,9 +2323,9 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [extras]
 dev = []
 plot = ["dash", "dash-cytoscape"]
-tests = ["pytest", "pytest-depends"]
+tests = ["coverage", "pytest", "pytest-cov", "pytest-depends", "pytest-emoji", "pytest-md"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "4b3073d732a5ddcc84db255baea64e2df0414967995d20bd902f83a39de0bc10"
+content-hash = "2d93043f4c9a191ba4a48ffed4739d027cc9b10f26b1f882326d1e385af462cb"

nwb_linkml/pyproject.toml

@@ -17,17 +17,25 @@ linkml-runtime = "^1.5.6"
 #nwb_schema_language = { path = './nwb_schema_language', develop = true, optional = true }
 rich = "^13.5.2"
 linkml = "^1.5.7"
-pytest = { version="^7.4.0", optional=true}
-pytest-depends = {version="^1.0.1", optional=true}
-dash = {version="^2.12.1", optional=true}
-dash-cytoscape = {version="^0.3.0", optional=true}
 nptyping = "^2.5.0"
 pydantic = "^2.3.0"
 h5py = "^3.9.0"
+dash = {version="^2.12.1", optional=true}
+dash-cytoscape = {version="^0.3.0", optional=true}
+pytest = { version="^7.4.0", optional=true}
+pytest-depends = {version="^1.0.1", optional=true}
+coverage = {version = "^6.1.1", optional = true}
+pytest-md = {version = "^0.2.0", optional = true}
+pytest-emoji = {version="^0.2.0", optional = true}
+pytest-cov = {version = "^4.1.0", optional = true}
+coveralls = {version = "^3.3.1", optional = true}
 
 [tool.poetry.extras]
 dev = ["nwb_schema_language"]
-tests = ["pytest", "pytest-depends"]
+tests = [
+    "pytest",       "pytest-depends", "coverage", "pytest-md",
+    "pytest-emoji", "pytest-cov"
+]
 plot = ["dash", "dash-cytoscape"]
 
 
@@ -37,6 +45,10 @@ optional = true
 [tool.poetry.group.tests.dependencies]
 pytest = "^7.4.0"
 pytest-depends = "^1.0.1"
+coverage = "^6.1.1"
+pytest-md = "^0.2.0"
+pytest-emoji = "^0.2.0"
+pytest-cov = "^4.1.0"
 
 [tool.poetry.group.plot]
 optional = true
@@ -51,3 +63,21 @@ build-backend = "poetry.core.masonry.api"
 
 
 [tool.pytest.ini_options]
+addopts = [
+    "--cov",
+    "--cov-append"
+]
+testpaths = [
+    "tests"
+]
+
+[tool.coverage.run]
+branch = true
+source = [
+"src/nwb_linkml"
+]
+omit = [
+    "*/nwb_schema_language/*",
+    "*/nwb_linkml/models/*"
+]
+

nwb_linkml/src/nwb_linkml/__init__.py

@@ -1 +1 @@
-from nwb_linkml.src.nwb_linkml.maps import preload
+from nwb_linkml.maps import preload

nwb_linkml/src/nwb_linkml/adapters/__init__.py

@@ -1 +1,4 @@
-from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.adapters.classes import ClassAdapter
+from nwb_linkml.adapters.group import GroupAdapter
+from nwb_linkml.adapters.schema import SchemaAdapter

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -7,7 +7,7 @@ from typing import List, Optional
 from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, DTypeType
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
-from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.maps import QUANTITY_MAP
 
 CAMEL_TO_SNAKE = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')
 """

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -11,7 +11,7 @@ from pydantic import PrivateAttr
 from nwb_schema_language import Dataset, ReferenceDtype, CompoundDtype, DTypeType
 from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
 from nwb_linkml.adapters.adapter import BuildResult
-from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.maps import QUANTITY_MAP
 
 class DatasetAdapter(ClassAdapter):
     cls: Dataset

nwb_linkml/src/nwb_linkml/adapters/group.py

@@ -9,7 +9,7 @@ from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, D
 from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
 from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.adapter import BuildResult
-from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.maps import QUANTITY_MAP
 
 class GroupAdapter(ClassAdapter):
     cls: Group

nwb_linkml/src/nwb_linkml/generators/__init__.py

@@ -0,0 +1 @@
+from nwb_linkml.generators.pydantic import PydanticGenerator

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -25,7 +25,7 @@ from types import ModuleType
 from copy import deepcopy
 import warnings
 
-from nwb_linkml.src.nwb_linkml.maps import flat_to_npytyping
+from nwb_linkml.maps import flat_to_npytyping
 from linkml.generators import PydanticGenerator
 from linkml_runtime.linkml_model.meta import (
     Annotation,

nwb_linkml/src/nwb_linkml/io/__init__.py

@@ -0,0 +1 @@
+from nwb_linkml.io import schema

nwb_linkml/src/nwb_linkml/io/git.py

@@ -1,6 +1,8 @@
 """
 Define and manage NWB namespaces in external repositories
 """
+import pdb
+from typing import Optional
 import warnings
 from pathlib import Path
 import tempfile
@@ -50,7 +52,7 @@ class GitRepo:
     def __init__(self, namespace:NamespaceRepo, commit:str|None=None):
         self._temp_directory = None
         self.namespace = namespace
-        self.commit = commit
+        self._commit = commit
 
     def _git_call(self, *args) -> subprocess.CompletedProcess:
         res = subprocess.run(
@@ -68,9 +70,7 @@ class GitRepo:
         """
         if self._temp_directory is None:
             self._temp_directory = Path(tempfile.gettempdir()) / f'nwb_linkml__{self.namespace.name}'
-            if self._temp_directory.exists():
+            if not self._temp_directory.exists():
-                warnings.warn(f'Temporary directory already exists! {self._temp_directory}')
-            else:
                 self._temp_directory.mkdir(parents=True)
 
         return self._temp_directory
@@ -99,6 +99,23 @@ class GitRepo:
         """
         return self.temp_directory / self.namespace.path
 
+    @property
+    def commit(self) -> Optional[str]:
+        """
+        The intended commit to check out.
+
+        If ``None``, should be the latest commit when the repo was checked out
+
+        Should match :prop:`.active_commit`, differs semantically in that it is used to
+        set the active_commit, while :prop:`.active_commit` reads what commit is actually checked out
+        """
+        return self._commit
+
+    @commit.setter
+    def commit(self, commit:str):
+        self._git_call('checkout', commit)
+        self._commit = commit
+
     def check(self) -> bool:
         """
         Check if the repository is already cloned and checked out
@@ -120,7 +137,7 @@ class GitRepo:
             return False
 
         # Check that the remote matches
-        if self.remote.strip('.git') != self.namespace.repository:
+        if self.remote != str(self.namespace.repository):
             warnings.warn(f'Repository exists, but has the wrong remote URL.\nExpected: {self.namespace.repository}\nGot:{self.remote.strip(".git")}')
             return False
 
@@ -164,6 +181,8 @@ class GitRepo:
             self.cleanup()
 
         res = subprocess.run(['git', 'clone', str(self.namespace.repository), str(self.temp_directory)])
+        if self.commit:
+            self.commit = self.commit
         if res.returncode != 0:
             raise GitError(f'Could not clone repository:\n{res.stderr}')
 

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -4,15 +4,14 @@ Loading/saving NWB Schema yaml files
 from pathlib import Path
 from typing import Optional
 from pprint import pprint
-import warnings
 
 from linkml_runtime.loaders import yaml_loader
 import yaml
 
 from nwb_schema_language import Namespaces,  Group, Dataset
-from nwb_linkml.namespaces import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
+from nwb_linkml.io.git import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
-from nwb_linkml.src.nwb_linkml.map import PHASES, Map
+from nwb_linkml.map import PHASES, Map
-from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
 
 
@@ -32,12 +31,9 @@ def load_namespaces(path:Path|NamespaceRepo) -> Namespaces:
 
     ns_dict = load_yaml(path)
 
-
     namespaces = yaml_loader.load(ns_dict, target_class=Namespaces)
     return namespaces
 
-
-
 def load_schema_file(path:Path, yaml:Optional[dict] = None) -> SchemaAdapter:
     if yaml is not None:
         source = yaml
@@ -89,7 +85,7 @@ def load_namespace_schema(namespace: Namespaces, path:Path=Path('..')) -> Namesp
     for ns in namespace.namespaces:
         for schema in ns.schema_:
             if schema.source is None:
-                warnings.warn(f"No source specified for {schema}")
+                # this is normal, we'll resolve later
                 continue
             yml_file = (path / schema.source).resolve()
             sch.append(load_schema_file(yml_file))

nwb_linkml/src/nwb_linkml/lang_elements.py

@@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import \
     TypeDefinition,\
     Prefix,\
     PermissibleValue
-from nwb_linkml.src.nwb_linkml.maps import flat_to_linkml
+from nwb_linkml.maps import flat_to_linkml
 
 
 FlatDType = EnumDefinition(
@@ -20,34 +20,6 @@ FlatDType = EnumDefinition(
     permissible_values=[PermissibleValue(p) for p in FlatDtype_source.__members__.keys()],
 )
 
-# DimNameSlot = SlotDefinition(
-#     name="dim_name",
-#     range="string",
-#     description="The name of a dimension"
-# )
-# DimShapeSlot = SlotDefinition(
-#     name="dim_shape",
-#     range="integer",
-#     required=False
-# )
-# DimClass = ClassDefinition(
-#     name="Dimension",
-#     slots=[DimNameSlot.name, DimShapeSlot.name],
-#     description="A single dimension within a shape"
-# )
-# DimSlot = SlotDefinition(
-#     name="dim",
-#     range=DimClass.name,
-#     multivalued=True,
-#     description="Slot representing the dimensions that a Shape can have"
-# )
-
-# ShapeClass = ClassDefinition(
-#     name="Shape",
-#     description="A possible shape for an array-like dataset",
-#     slots=[DimSlot.name]
-# )
-
 DTypeTypes = []
 for nwbtype, linkmltype in flat_to_linkml.items():
     amin = None
@@ -85,7 +57,6 @@ NwbLangSchema = SchemaDefinition(
     id='nwb.language',
     description="Adapter objects to mimic the behavior of elements in the nwb-schema-language",
     enums=[FlatDType],
-    # slots=[DimNameSlot, DimShapeSlot, DimSlot],
     classes=[Arraylike, AnyType],
     types=DTypeTypes,
     imports=['linkml:types'],

nwb_linkml/src/nwb_linkml/maps/__init__.py

@@ -1,3 +1,4 @@
 # Import everything so it's defined, but shoudlnt' necessarily be used from here
-from nwb_linkml.src.nwb_linkml.maps import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
+from nwb_linkml.maps.preload import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
-from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.maps.quantity import QUANTITY_MAP
+from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_npytyping

nwb_linkml/src/nwb_linkml/maps/preload.py

@@ -2,7 +2,7 @@
 Maps to change the loaded .yaml from nwb schema before it's given to the nwb_schema_language models
 """
 
-from nwb_linkml.src.nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
+from nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
 
 MAP_HDMF_DATATYPE_DEF = KeyMap(
     source="\'data_type_def\'",

nwb_linkml/src/nwb_linkml/plot.py

@@ -10,7 +10,7 @@ import dash_cytoscape as cyto
 cyto.load_extra_layouts()
 
 from nwb_schema_language import Namespace, Group, Dataset
-from nwb_linkml.src.nwb_linkml.io import load_nwb_core
+from nwb_linkml.io import load_nwb_core
 
 if TYPE_CHECKING:
     from nwb_linkml.adapters import NamespacesAdapter

nwb_linkml/src/nwb_linkml/translate.py

@@ -12,9 +12,9 @@ import h5py
 from linkml_runtime.dumpers import yaml_dumper
 
 from nwb_schema_language import Namespaces
-from nwb_linkml.src.nwb_linkml.io import load_schema_file
+from nwb_linkml.io.schema import load_schema_file
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
-from nwb_linkml.src.nwb_linkml.map import apply_preload
+from nwb_linkml.map import apply_preload
 from nwb_linkml.adapters import SchemaAdapter, NamespacesAdapter
 
 def make_namespace_adapter(schema: dict) -> NamespacesAdapter:

nwb_linkml/tests/fixtures.py

@@ -1,7 +1,7 @@
 import pytest
 
-from nwb_linkml.src.nwb_linkml import io
+from nwb_linkml.io import schema as io
-from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.adapters.namespaces import NamespacesAdapter
 import shutil
 from pathlib import Path
 

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -1,5 +1,5 @@
 import pytest
-from .fixtures import nwb_core_fixture
+from ..fixtures import nwb_core_fixture
 
 from nwb_schema_language import Dataset, Group, Schema
 
@@ -20,3 +20,9 @@ def test_walk_types(nwb_core_fixture, walk_class, known_number):
     # pdb.set_trace()
 
 
+def test_build_result_add():
+    """
+    Build results can
+    Returns:
+
+    """

nwb_linkml/tests/test_adapters/test_adapter_group.py

@@ -1,4 +1,4 @@
 import pytest
 
-from .fixtures import nwb_core_fixture
+from ..fixtures import nwb_core_fixture
 

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -1,5 +1,7 @@
 import pytest
-from .fixtures import nwb_core_fixture
+from ..fixtures import nwb_core_fixture
+from nwb_schema_language import Dataset, Group
+from nwb_linkml.adapters import SchemaAdapter
 
 @pytest.mark.parametrize(
     ['class_name','schema_file','namespace_name'],
@@ -17,4 +19,17 @@ def test_find_type_source(nwb_core_fixture, class_name, schema_file, namespace_n
 
 
 def test_populate_imports(nwb_core_fixture):
-    nwb_core_fixture.populate_imports()
+    nwb_core_fixture.populate_imports()
+    schema: SchemaAdapter
+    assert len(nwb_core_fixture.schemas) > 0
+    for schema in nwb_core_fixture.schemas:
+        need_imports = [nwb_core_fixture.find_type_source(cls.neurodata_type_def).namespace for cls in schema.created_classes if cls.neurodata_type_inc is not None]
+        need_imports = [i for i in need_imports if i != schema.namespace]
+        for i in need_imports:
+            assert i in schema.imports
+
+
+
+
+def test_build(nwb_core_fixture):
+    pass

nwb_linkml/tests/test_adapters/test_adapter_schema.py

@@ -1,5 +1,5 @@
 import pytest
-from .fixtures import nwb_core_fixture
+from ..fixtures import nwb_core_fixture
 
 from nwb_schema_language import Dataset, Group, Schema
 

nwb_linkml/tests/test_generate.py

@@ -5,7 +5,6 @@ import warnings
 
 from .fixtures import nwb_core_fixture, tmp_output_dir
 from linkml_runtime.dumpers import yaml_dumper
-from linkml.generators import PydanticGenerator
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 
 from nwb_linkml.lang_elements import NwbLangSchema

nwb_linkml/tests/test_io/test_io_git.py

@@ -0,0 +1,94 @@
+import pytest
+import tempfile
+import shutil
+
+import yaml
+from nwb_linkml.io.git import GitRepo, GitError, NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
+from nwb_schema_language import Namespaces
+
+@pytest.mark.parametrize(
+    ['source', 'commit'],
+    [
+        (NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4'),
+        (HDMF_COMMON_REPO, '660b6ac0780dd9d2cb1e56fea8b62c671ca5e2c8')
+    ]
+)
+def test_gitrepo(source, commit):
+    """
+    Basic functionality of GitRepo
+    """
+    repo = GitRepo(source)
+
+    # make a temp directory that exists
+    first_dir = repo.temp_directory
+    assert repo.temp_directory.exists()
+
+    # find the same repository when it's deleted
+    shutil.rmtree(str(repo.temp_directory))
+    repo._temp_directory = None
+    second_dir = repo.temp_directory
+    assert first_dir == second_dir
+
+    # successfully clone the repository after its deleted
+    assert not any(repo.temp_directory.iterdir())
+    repo.clone()
+    # check that the namespace file exists and has some expected fields
+    assert repo.namespace_file.exists()
+    with open(repo.namespace_file, 'r') as nsfile:
+        ns = yaml.safe_load(nsfile)
+    # correct model instantiation confirms the repo was cloned successfully
+    ns_model = Namespaces(**ns)
+
+    # setting commit should change the active commit
+    prior_commit = repo.active_commit
+    repo.commit = commit
+    assert prior_commit != repo.active_commit
+    assert repo.active_commit == commit
+    assert repo.commit == commit
+
+    # remote is gotten correctly
+    assert repo.remote == str(source.repository)
+
+    # cleanup should remove files
+    repo.cleanup()
+    assert not any(repo.temp_directory.iterdir())
+
+@pytest.mark.parametrize(
+    ['source', 'commit'],
+    [
+        (NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4')
+    ]
+)
+def test_gitrepo_check(source, commit):
+    """
+    Our check method should flag common problems with the repo
+    """
+    repo = GitRepo(NWB_CORE_REPO, commit=commit)
+    # cleanup is tested separately
+    repo.cleanup()
+
+    # check should fail without warning when the repo is empty
+    assert not repo.check()
+
+    repo.clone()
+    assert repo.check()
+
+    # check should fail when repo is at wrong commit
+    assert repo.active_commit == commit
+    repo._git_call('checkout', 'HEAD~10')
+    with pytest.warns(UserWarning, match=".*wrong commit.*"):
+        assert not repo.check()
+    repo.commit = commit
+    assert repo.active_commit == commit
+    assert repo.check()
+
+    # check should fail on repo namespace mismatch
+    old_repo = repo.namespace.repository
+    repo.namespace.repository = "https://example.com/a/git/repository"
+    with pytest.warns(UserWarning, match='.*wrong remote.*'):
+        assert not repo.check()
+    repo.namespace.repository = old_repo
+    assert repo.check()
+
+
+

nwb_linkml/tests/test_maps.py

@@ -0,0 +1,42 @@
+import pytest
+import shutil
+
+import tempfile
+import yaml
+from yaml import CDumper as Dumper
+from pathlib import Path
+from nwb_linkml.io.schema import load_yaml
+
+def test_preload_maps():
+    hdmf_style_naming = {
+        'groups': [
+            {
+                'data_type_def': 'Container',
+                'data_type_inc': 'MainClass',
+                'doc': 'Demo group',
+                'datasets': [
+                    {
+                        'data_type_inc': 'Data'
+                    }
+                ]
+            }
+        ]
+    }
+
+    temp, temp_name = tempfile.mkstemp(suffix='.yaml')
+
+    with open(temp_name, 'w') as temp_f:
+        yaml.dump(hdmf_style_naming, temp_f, Dumper=Dumper)
+    loaded = load_yaml(Path(temp_name))
+
+    assert 'neurodata_type_def' in loaded['groups'][0].keys()
+    assert 'data_type_def' not in loaded['groups'][0].keys()
+    assert 'neurodata_type_inc' in loaded['groups'][0].keys()
+    assert 'data_type_inc' not in loaded['groups'][0].keys()
+    assert 'neurodata_type_inc' in loaded['groups'][0]['datasets'][0].keys()
+    assert 'data_type_inc' not in loaded['groups'][0]['datasets'][0].keys()
+
+    shutil.rmtree(temp_name)
+
+
+

pytest.ini

@@ -1,4 +0,0 @@
-[pytest]
-
-testpaths =
-    nwb_linkml/tests