mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-14 10:44:28 +00:00
252 lines
8.8 KiB
Python
252 lines
8.8 KiB
Python
import shutil
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import os
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import sys
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import traceback
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from pdb import post_mortem
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import subprocess
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from argparse import ArgumentParser
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from pathlib import Path
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from linkml_runtime.dumpers import yaml_dumper
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from rich.live import Live
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from rich.panel import Panel
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from rich.console import Group
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from rich.progress import Progress, SpinnerColumn, BarColumn, TextColumn, Column
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from rich import print
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from nwb_linkml.generators.pydantic import NWBPydanticGenerator
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from nwb_linkml.providers import LinkMLProvider, PydanticProvider
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from nwb_linkml.providers.git import NWB_CORE_REPO, HDMF_COMMON_REPO, GitRepo
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from nwb_linkml.io import schema as io
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def generate_core_yaml(output_path: Path, dry_run: bool = False, hdmf_only: bool = False):
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"""Just build the latest version of the core schema"""
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core = io.load_nwb_core(hdmf_only=hdmf_only)
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built_schemas = core.build().schemas
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for schema in built_schemas:
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output_file = output_path / (schema.name + ".yaml")
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if not dry_run:
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yaml_dumper.dump(schema, output_file)
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def generate_core_pydantic(yaml_path: Path, output_path: Path, dry_run: bool = False):
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"""Just generate the latest version of the core schema"""
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for schema in yaml_path.glob("*.yaml"):
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python_name = schema.stem.replace(".", "_").replace("-", "_")
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pydantic_file = (output_path / python_name).with_suffix(".py")
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generator = NWBPydanticGenerator(
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str(schema),
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pydantic_version="2",
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emit_metadata=True,
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gen_classvars=True,
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gen_slots=True,
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)
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gen_pydantic = generator.serialize()
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if not dry_run:
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with open(pydantic_file, "w") as pfile:
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pfile.write(gen_pydantic)
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def make_tmp_dir(clear: bool = False) -> Path:
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# use a directory underneath this one as the temporary directory rather than
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# the default hidden one
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tmp_dir = Path(__file__).parent / "__tmp__"
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if tmp_dir.exists() and clear:
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for p in tmp_dir.iterdir():
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if p.is_dir() and not p.name == "git":
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shutil.rmtree(p)
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tmp_dir.mkdir(exist_ok=True)
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return tmp_dir
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def generate_versions(
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yaml_path: Path,
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pydantic_path: Path,
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dry_run: bool = False,
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repo: GitRepo = NWB_CORE_REPO,
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hdmf_only=False,
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pdb=False,
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):
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"""
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Generate linkml models for all versions
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"""
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# repo.clone(force=True)
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repo.clone()
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tmp_dir = make_tmp_dir()
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linkml_provider = LinkMLProvider(path=tmp_dir, verbose=False)
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pydantic_provider = PydanticProvider(path=tmp_dir, verbose=False)
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failed_versions = {}
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overall_progress = Progress()
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overall_task = overall_progress.add_task("All Versions", total=len(NWB_CORE_REPO.versions))
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build_progress = Progress(
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TextColumn(
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"[bold blue]{task.fields[name]} - [bold green]{task.fields[action]}",
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table_column=Column(ratio=1),
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),
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BarColumn(table_column=Column(ratio=1), bar_width=None),
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)
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panel = Panel(Group(build_progress, overall_progress))
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try:
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with Live(panel) as live:
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# make pbar tasks
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linkml_task = None
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pydantic_task = None
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for version in repo.namespace.versions:
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# build linkml
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try:
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# check out the version (this should also refresh the hdmf-common schema)
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linkml_task = build_progress.add_task(
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"", name=version, action="Checkout Version", total=3
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)
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repo.tag = version
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build_progress.update(linkml_task, advance=1, action="Load Namespaces")
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if repo.namespace == NWB_CORE_REPO:
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# first load HDMF common
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hdmf_common_ns = io.load_namespace_adapter(
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repo.temp_directory / "hdmf-common-schema" / "common" / "namespace.yaml"
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)
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# then load nwb core
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core_ns = io.load_namespace_adapter(
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repo.namespace_file, imported=[hdmf_common_ns]
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)
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else:
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# otherwise just load HDMF
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core_ns = io.load_namespace_adapter(repo.namespace_file)
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build_progress.update(linkml_task, advance=1, action="Build LinkML")
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linkml_res = linkml_provider.build(core_ns)
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build_progress.update(linkml_task, advance=1, action="Built LinkML")
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# build pydantic
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ns_files = [res.namespace for res in linkml_res.values()]
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pydantic_task = build_progress.add_task(
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"", name=version, action="", total=len(ns_files)
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)
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for schema in ns_files:
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pbar_string = schema.parts[-3]
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build_progress.update(pydantic_task, action=pbar_string)
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pydantic_provider.build(
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schema, versions=core_ns.versions, split=True, parallel=True
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)
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build_progress.update(pydantic_task, advance=1)
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build_progress.update(pydantic_task, action="Built Pydantic")
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except Exception as e:
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if pdb:
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live.stop()
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post_mortem()
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sys.exit(1)
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build_progress.stop_task(linkml_task)
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if linkml_task is not None:
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build_progress.update(linkml_task, action="[bold red]LinkML Build Failed")
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build_progress.stop_task(linkml_task)
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if pydantic_task is not None:
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build_progress.update(pydantic_task, action="[bold red]LinkML Build Failed")
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build_progress.stop_task(pydantic_task)
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failed_versions[version] = traceback.format_exception(e)
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finally:
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overall_progress.update(overall_task, advance=1)
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linkml_task = None
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pydantic_task = None
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if not dry_run:
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shutil.copytree(tmp_dir / "linkml", yaml_path, dirs_exist_ok=True)
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shutil.copytree(tmp_dir / "pydantic", pydantic_path, dirs_exist_ok=True)
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shutil.rmtree(tmp_dir / "linkml")
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shutil.rmtree(tmp_dir / "pydantic")
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# make inits to use the schema! we don't usually do this in the
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# provider class because we directly import the files there.
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with open(pydantic_path / "__init__.py", "w") as initfile:
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initfile.write(" ")
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subprocess.run(["black", "."])
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finally:
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if len(failed_versions) > 0:
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print("Failed Building Versions:")
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print(failed_versions)
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def parser() -> ArgumentParser:
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parser = ArgumentParser("Generate all available versions of NWB core schema")
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parser.add_argument(
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"--yaml",
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help="directory to export linkML schema to",
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type=Path,
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default=Path(__file__).parent.parent
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/ "nwb_models"
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/ "src"
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/ "nwb_models"
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/ "schema"
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/ "linkml",
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)
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parser.add_argument(
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"--pydantic",
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help="directory to export pydantic models",
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type=Path,
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default=Path(__file__).parent.parent
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/ "nwb_models"
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/ "src"
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/ "nwb_models"
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/ "models"
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/ "pydantic",
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)
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parser.add_argument("--hdmf", help="Only generate the HDMF namespaces", action="store_true")
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parser.add_argument(
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"--latest",
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help="Only generate the latest version of the core schemas.",
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action="store_true",
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)
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parser.add_argument(
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"--dry-run",
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help=(
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"Generate schema and pydantic models without moving them into the target directories,"
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" for testing purposes"
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),
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action="store_true",
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)
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parser.add_argument("--pdb", help="Launch debugger on an error", action="store_true")
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return parser
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def main():
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args = parser().parse_args()
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tmp_dir = make_tmp_dir(clear=True)
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git_dir = tmp_dir / "git"
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git_dir.mkdir(exist_ok=True)
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if args.hdmf:
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repo = GitRepo(HDMF_COMMON_REPO, path=git_dir)
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else:
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repo = GitRepo(NWB_CORE_REPO, path=git_dir)
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if not args.dry_run:
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args.yaml.mkdir(exist_ok=True)
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args.pydantic.mkdir(exist_ok=True)
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if args.latest:
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generate_core_yaml(args.yaml, args.dry_run, args.hdmf)
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generate_core_pydantic(args.yaml, args.pydantic, args.dry_run)
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else:
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generate_versions(args.yaml, args.pydantic, args.dry_run, repo, args.hdmf, pdb=args.pdb)
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if __name__ == "__main__":
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main()
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