copy and overwrite rather than shutil.move in generate

This commit is contained in:
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

3
.gitignore vendored
View file

@ -167,4 +167,5 @@ jupyter_execute
.pdm-python
.venv*
requests-cache.sqlite
requests-cache.sqlite
*.pstats

View file

@ -5,7 +5,7 @@
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View file

@ -16,8 +16,7 @@ dependencies = [
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"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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@ -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'

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@ -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(