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copy and overwrite rather than shutil.move in generate

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sneakers-the-rat 2024-08-27 20:49:53 -07:00
parent 798b92de6b
commit fac18ab147
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
6 changed files with 860 additions and 994 deletions
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.gitignore vendored
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@ -167,4 +167,5 @@ jupyter_execute
.pdm-python
.venv*
requests-cache.sqlite
requests-cache.sqlite
*.pstats

217
nwb_linkml/pdm.lock
View file

@ -5,7 +5,7 @@
groups = ["default", "dev", "plot", "tests"]
strategy = ["inherit_metadata"]
lock_version = "4.5.0"
content_hash = "sha256:3223b7fb1c0ac9877a6d8af33e55f10e54fe8eb3a8b4fa053d3e7082863260ac"
content_hash = "sha256:f219083028bd024c53bc55626c8b6088d6eb5c2ade56bd694a7a112098aa9bfc"
[[metadata.targets]]
requires_python = ">=3.10,<3.13"
@ -582,18 +582,18 @@ files = [
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requires_python = ">=3.5"
version = "3.8"
requires_python = ">=3.6"
summary = "Internationalized Domain Names in Applications (IDNA)"
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requires_python = ">=3.8"
summary = "Read metadata from Python packages"
groups = ["plot"]
@ -602,8 +602,8 @@ dependencies = [
"zipp>=0.5",
]
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@ -809,7 +809,7 @@ version = "0.0.0"
requires_python = "<4.0.0,>=3.8.1"
git = "https://github.com/sneakers-the-rat/linkml"
ref = "nwb-linkml"
revision = "0a6578bff4713688260f64b3076b197bd6decce9"
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@ -822,7 +822,7 @@ dependencies = [
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@ -860,7 +860,7 @@ files = [
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version = "1.8.2"
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groups = ["default"]
@ -880,8 +880,8 @@ dependencies = [
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3
nwb_linkml/pyproject.toml
View file

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"rich>=13.5.2",
#"linkml>=1.7.10",
"linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
# until recursive imports gets released
"linkml-runtime @ git+https://github.com/linkml/linkml-runtime@main",
"linkml-runtime>=1.8.2",
"pydantic>=2.3.0",
"h5py>=3.9.0",
"pydantic-settings>=2.0.3",

1588
pdm.lock
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File diff suppressed because it is too large Load diff

5
pyproject.toml
View file

@ -7,12 +7,15 @@ 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:///${PROJECT_ROOT/nwb_models',
'-e nwb-models @ file:///${PROJECT_ROOT}/nwb_models',
'-e docs @ file:///${PROJECT_ROOT}/docs',
"ruff>=0.5.0",
"black>=24.4.2",
]
[tool.pdm.scripts]
build-models = "python scripts/generate_core.py"
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.lock,*.css,./nwb_models/src/nwb_models/models,./nwb_models/src/nwb_models/schema'

38
scripts/generate_core.py
View file

@ -166,29 +166,17 @@ def generate_versions(
pydantic_task = None
if not dry_run:
if hdmf_only:
shutil.rmtree(yaml_path / "linkml" / "hdmf_common")
shutil.rmtree(yaml_path / "linkml" / "hdmf_experimental")
shutil.rmtree(pydantic_path / "pydantic" / "hdmf_common")
shutil.rmtree(pydantic_path / "pydantic" / "hdmf_experimental")
shutil.move(tmp_dir / "linkml" / "hdmf_common", yaml_path / "linkml")
shutil.move(tmp_dir / "linkml" / "hdmf_experimental", yaml_path / "linkml")
shutil.move(tmp_dir / "pydantic" / "hdmf_common", pydantic_path / "pydantic")
shutil.move(tmp_dir / "pydantic" / "hdmf_experimental", pydantic_path / "pydantic")
else:
shutil.rmtree(yaml_path / "linkml")
shutil.rmtree(pydantic_path / "pydantic")
shutil.move(tmp_dir / "linkml", yaml_path)
shutil.move(tmp_dir / "pydantic", pydantic_path)
shutil.copytree(tmp_dir / "linkml", yaml_path, dirs_exist_ok=True)
shutil.copytree(tmp_dir / "pydantic", pydantic_path, dirs_exist_ok=True)
shutil.rmtree(tmp_dir / "linkml")
shutil.rmtree(tmp_dir / "pydantic")
# import the most recent version of the schemaz we built
latest_version = sorted(
(pydantic_path / "pydantic" / "core").glob("v*"), key=os.path.getmtime
)[-1]
latest_version = sorted((pydantic_path / "core").glob("v*"), key=os.path.getmtime)[-1]
# make inits to use the schema! we don't usually do this in the
# provider class because we directly import the files there.
with open(pydantic_path / "pydantic" / "__init__.py", "w") as initfile:
with open(pydantic_path / "__init__.py", "w") as initfile:
initfile.write(" ")
with open(pydantic_path / "__init__.py", "w") as initfile:
@ -208,13 +196,23 @@ def parser() -> ArgumentParser:
"--yaml",
help="directory to export linkML schema to",
type=Path,
default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "schema",
default=Path(__file__).parent.parent
/ "nwb_models"
/ "src"
/ "nwb_models"
/ "schema"
/ "linkml",
)
parser.add_argument(
"--pydantic",
help="directory to export pydantic models",
type=Path,
default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "models",
default=Path(__file__).parent.parent
/ "nwb_models"
/ "src"
/ "nwb_models"
/ "models"
/ "pydantic",
)
parser.add_argument("--hdmf", help="Only generate the HDMF namespaces", action="store_true")
parser.add_argument(