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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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@ -168,3 +168,4 @@ jupyter_execute
.venv* .venv*
requests-cache.sqlite requests-cache.sqlite
*.pstats

217
nwb_linkml/pdm.lock
View file

@ -5,7 +5,7 @@
groups = ["default", "dev", "plot", "tests"] groups = ["default", "dev", "plot", "tests"]
strategy = ["inherit_metadata"] strategy = ["inherit_metadata"]
lock_version = "4.5.0" lock_version = "4.5.0"
content_hash = "sha256:3223b7fb1c0ac9877a6d8af33e55f10e54fe8eb3a8b4fa053d3e7082863260ac" content_hash = "sha256:f219083028bd024c53bc55626c8b6088d6eb5c2ade56bd694a7a112098aa9bfc"
[[metadata.targets]] [[metadata.targets]]
requires_python = ">=3.10,<3.13" requires_python = ">=3.10,<3.13"
@ -582,18 +582,18 @@ files = [
[[package]] [[package]]
name = "idna" name = "idna"
version = "3.7" version = "3.8"
requires_python = ">=3.5" requires_python = ">=3.6"
summary = "Internationalized Domain Names in Applications (IDNA)" summary = "Internationalized Domain Names in Applications (IDNA)"
groups = ["default", "dev", "plot", "tests"] groups = ["default", "dev", "plot", "tests"]
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[[package]] [[package]]
name = "importlib-metadata" name = "importlib-metadata"
version = "8.2.0" version = "8.4.0"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Read metadata from Python packages" summary = "Read metadata from Python packages"
groups = ["plot"] groups = ["plot"]
@ -602,8 +602,8 @@ dependencies = [
"zipp>=0.5", "zipp>=0.5",
] ]
files = [ files = [
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[[package]] [[package]]
@ -809,7 +809,7 @@ version = "0.0.0"
requires_python = "<4.0.0,>=3.8.1" requires_python = "<4.0.0,>=3.8.1"
git = "https://github.com/sneakers-the-rat/linkml" git = "https://github.com/sneakers-the-rat/linkml"
ref = "nwb-linkml" ref = "nwb-linkml"
revision = "0a6578bff4713688260f64b3076b197bd6decce9" revision = "0247c0b1e1a87366e0e047449e604881870c4e98"
summary = "Linked Open Data Modeling Language" summary = "Linked Open Data Modeling Language"
groups = ["default"] groups = ["default"]
dependencies = [ dependencies = [
@ -822,7 +822,7 @@ dependencies = [
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"linkml-dataops", "linkml-dataops",
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"openpyxl", "openpyxl",
"parse", "parse",
"prefixcommons>=0.1.7", "prefixcommons>=0.1.7",
@ -860,7 +860,7 @@ files = [
[[package]] [[package]]
name = "linkml-runtime" name = "linkml-runtime"
version = "1.8.0" version = "1.8.2"
requires_python = "<4.0,>=3.8" requires_python = "<4.0,>=3.8"
summary = "Runtime environment for LinkML, the Linked open data modeling language" summary = "Runtime environment for LinkML, the Linked open data modeling language"
groups = ["default"] groups = ["default"]
@ -880,8 +880,8 @@ dependencies = [
"requests", "requests",
] ]
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@ -984,42 +984,45 @@ files = [
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files = [ files = [
{file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"}, {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"},
{file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"}, {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"},
] ]
[[package]] [[package]]
@ -2161,11 +2164,11 @@ files = [
[[package]] [[package]]
name = "zipp" name = "zipp"
version = "3.20.0" version = "3.20.1"
requires_python = ">=3.8" requires_python = ">=3.8"
summary = "Backport of pathlib-compatible object wrapper for zip files" summary = "Backport of pathlib-compatible object wrapper for zip files"
groups = ["plot"] groups = ["plot"]
files = [ files = [
{file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"}, {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
{file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"}, {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
] ]

3
nwb_linkml/pyproject.toml
View file

@ -16,8 +16,7 @@ dependencies = [
"rich>=13.5.2", "rich>=13.5.2",
#"linkml>=1.7.10", #"linkml>=1.7.10",
"linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml", "linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
# until recursive imports gets released "linkml-runtime>=1.8.2",
"linkml-runtime @ git+https://github.com/linkml/linkml-runtime@main",
"pydantic>=2.3.0", "pydantic>=2.3.0",
"h5py>=3.9.0", "h5py>=3.9.0",
"pydantic-settings>=2.0.3", "pydantic-settings>=2.0.3",

1588
pdm.lock
View file

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 = [ dev = [
'-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml', '-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
'-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language', '-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
'-e nwb-models @ file:///${PROJECT_ROOT/nwb_models', '-e nwb-models @ file:///${PROJECT_ROOT}/nwb_models',
'-e docs @ file:///${PROJECT_ROOT}/docs', '-e docs @ file:///${PROJECT_ROOT}/docs',
"ruff>=0.5.0", "ruff>=0.5.0",
"black>=24.4.2", "black>=24.4.2",
] ]
[tool.pdm.scripts]
build-models = "python scripts/generate_core.py"
[tool.codespell] [tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file # 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' 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 pydantic_task = None
if not dry_run: if not dry_run:
if hdmf_only: shutil.copytree(tmp_dir / "linkml", yaml_path, dirs_exist_ok=True)
shutil.rmtree(yaml_path / "linkml" / "hdmf_common") shutil.copytree(tmp_dir / "pydantic", pydantic_path, dirs_exist_ok=True)
shutil.rmtree(yaml_path / "linkml" / "hdmf_experimental") shutil.rmtree(tmp_dir / "linkml")
shutil.rmtree(pydantic_path / "pydantic" / "hdmf_common") shutil.rmtree(tmp_dir / "pydantic")
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)
# import the most recent version of the schemaz we built # import the most recent version of the schemaz we built
latest_version = sorted( latest_version = sorted((pydantic_path / "core").glob("v*"), key=os.path.getmtime)[-1]
(pydantic_path / "pydantic" / "core").glob("v*"), key=os.path.getmtime
)[-1]
# make inits to use the schema! we don't usually do this in the # make inits to use the schema! we don't usually do this in the
# provider class because we directly import the files there. # 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(" ") initfile.write(" ")
with open(pydantic_path / "__init__.py", "w") as initfile: with open(pydantic_path / "__init__.py", "w") as initfile:
@ -208,13 +196,23 @@ def parser() -> ArgumentParser:
"--yaml", "--yaml",
help="directory to export linkML schema to", help="directory to export linkML schema to",
type=Path, 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( parser.add_argument(
"--pydantic", "--pydantic",
help="directory to export pydantic models", help="directory to export pydantic models",
type=Path, 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("--hdmf", help="Only generate the HDMF namespaces", action="store_true")
parser.add_argument( parser.add_argument(