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Upgrade to pydantic v2 (GSI 338) (#68)
* Update template files * Change imports of BaseSettings * Update ModSettings and yaml_settings_actory Remove settings param from yaml_settings_factory Convert Config class in ModSettings to model_config + method * Remove unused ignores * Actually add pydantic_settings to reqs * Update template files * Silence mypy * Update minor documentation Change pydantic.BaseSettings -> pydantic_settings.BaseSettings * Tweak doc for config_from_yaml * Use ConfigDict/SettingsConfigDict * Use model_json_schema instead of deprecated schema * Update other uses of .json, .copy, .schema * Bump version to 0.11.0 * Fix typos and raise error on empty file path --------- Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| [paths] | ||
| source = | ||
| src | ||
| /workspace/src | ||
| **/lib/python*/site-packages |
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14 changes: 8 additions & 6 deletions
14
.github/workflows/unit_and_int_tests.yaml → .github/workflows/tests.yaml
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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env python3 | ||
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| # Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln | ||
| # for the German Human Genome-Phenome Archive (GHGA) | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| # | ||
| """Check capped dependencies for newer versions.""" | ||
| import sys | ||
| from collections.abc import Sequence | ||
| from pathlib import Path | ||
| from typing import Any, NamedTuple | ||
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| import httpx | ||
| from packaging.requirements import Requirement | ||
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| from script_utils import cli, deps, lock_deps | ||
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| REPO_ROOT_DIR = Path(__file__).parent.parent.resolve() | ||
| PYPROJECT_TOML_PATH = REPO_ROOT_DIR / "pyproject.toml" | ||
| DEV_DEPS_PATH = REPO_ROOT_DIR / "requirements-dev.in" | ||
| LOCK_FILE_PATH = REPO_ROOT_DIR / "requirements-dev.txt" | ||
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| class OutdatedDep(NamedTuple): | ||
| """Encapsulates data of an outdated dependency""" | ||
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| name: str | ||
| specified_version: str | ||
| pypi_version: str | ||
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| def get_main_deps_pyproject(modified_pyproject: dict[str, Any]) -> list[Requirement]: | ||
| """Get a list of the dependencies from pyproject.toml""" | ||
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| dependencies: list[str] = [] | ||
| if "dependencies" in modified_pyproject["project"]: | ||
| dependencies = modified_pyproject["project"]["dependencies"] | ||
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| return [Requirement(dependency) for dependency in dependencies] | ||
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| def get_optional_deps_pyproject( | ||
| modified_pyproject: dict[str, Any] | ||
| ) -> list[Requirement]: | ||
| """Get a list of the optional dependencies from pyproject.toml""" | ||
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| dependencies: list[str] = [] | ||
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| if "optional-dependencies" in modified_pyproject["project"]: | ||
| for optional_dependency_list in modified_pyproject["project"][ | ||
| "optional-dependencies" | ||
| ]: | ||
| dependencies.extend( | ||
| modified_pyproject["project"]["optional-dependencies"][ | ||
| optional_dependency_list | ||
| ] | ||
| ) | ||
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| return [Requirement(dependency) for dependency in dependencies] | ||
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| def get_deps_dev() -> list[Requirement]: | ||
| """Get a list of raw dependency strings from requirements-dev.in""" | ||
| with open(DEV_DEPS_PATH, encoding="utf-8") as dev_deps: | ||
| dependencies = [ | ||
| line | ||
| for line in (line.strip() for line in dev_deps) | ||
| if line # skip empty lines | ||
| and not line.startswith("#") # skip comments | ||
| and "requirements-dev-common.in" not in line # skip inclusion line | ||
| ] | ||
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| return [Requirement(dependency) for dependency in dependencies] | ||
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| def get_version_from_pypi(package_name: str, client: httpx.Client) -> str: | ||
| """Make a call to PyPI to get the version information about `package_name`.""" | ||
| try: | ||
| response = client.get(f"https://pypi.org/pypi/{package_name}/json") | ||
| body = response.json() | ||
| version = body["info"]["version"] | ||
| except (httpx.RequestError, KeyError): | ||
| cli.echo_failure(f"Unable to retrieve information for package '{package_name}'") | ||
| sys.exit(1) | ||
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| return version | ||
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| def get_outdated_deps( | ||
| requirements: list[Requirement], strip: bool = False | ||
| ) -> list[OutdatedDep]: | ||
| """Determine which packages have updates available outside of pinned ranges.""" | ||
| outdated: list[OutdatedDep] = [] | ||
| with httpx.Client(timeout=10) as client: | ||
| for requirement in requirements: | ||
| pypi_version = get_version_from_pypi(requirement.name, client) | ||
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| specified = str(requirement.specifier) | ||
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| # Strip the specifier symbols from the front of the string if desired | ||
| if strip: | ||
| specified = specified.lstrip("<=>!~") | ||
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| # append package name, specified version, and latest available version | ||
| if not requirement.specifier.contains(pypi_version): | ||
| outdated.append(OutdatedDep(requirement.name, specified, pypi_version)) | ||
| outdated.sort() | ||
| return outdated | ||
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| def print_table( | ||
| rows: Sequence[tuple[str, ...]], | ||
| headers: tuple[str, ...], | ||
| delimiter: str = " | ", | ||
| ): | ||
| """ | ||
| List outdated dependencies in a formatted table. | ||
| Args: | ||
| `outdated`: A sequence of tuples containing strings. | ||
| `headers`: A tuple containing the header strings for the table columns. | ||
| """ | ||
| if rows and len(rows[0]) != len(headers): | ||
| raise RuntimeError("Number of headers doesn't match number of columns") | ||
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| header_lengths = [len(header) for header in headers] | ||
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| # Find the maximum length of each column | ||
| col_widths = [max(len(str(cell)) for cell in col) for col in zip(*rows)] | ||
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| # Create a row format based on the maximum column widths | ||
| row_format = delimiter.join( | ||
| f"{{:<{max(width, header_len)}}}" | ||
| for width, header_len in zip(col_widths, header_lengths) | ||
| ) | ||
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| print(" " + row_format.format(*headers)) | ||
| for dependency in rows: | ||
| print(" " + row_format.format(*dependency)) | ||
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| def main(transitive: bool = False): | ||
| """Check capped dependencies for newer versions. | ||
| Examine `pyproject.toml` and `requirements-dev.in` for capped dependencies. | ||
| Make a call to PyPI to see if any newer versions exist. | ||
| Use `transitive` to show outdated transitive dependencies. | ||
| """ | ||
| modified_pyproject: dict[str, Any] = deps.get_modified_pyproject( | ||
| PYPROJECT_TOML_PATH | ||
| ) | ||
| main_dependencies = get_main_deps_pyproject(modified_pyproject) | ||
| optional_dependencies = get_optional_deps_pyproject(modified_pyproject) | ||
| dev_dependencies = get_deps_dev() | ||
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| outdated_main = get_outdated_deps(main_dependencies) | ||
| outdated_optional = get_outdated_deps(optional_dependencies) | ||
| outdated_dev = get_outdated_deps(dev_dependencies) | ||
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| found_outdated = any([outdated_main, outdated_optional, outdated_dev]) | ||
| transitive_headers = ("PACKAGE", "SPECIFIED", "AVAILABLE") | ||
| if outdated_main: | ||
| location = PYPROJECT_TOML_PATH.name + " - dependencies" | ||
| cli.echo_failure(f"Outdated dependencies from {location}:") | ||
| print_table(outdated_main, transitive_headers) | ||
| if outdated_optional: | ||
| location = PYPROJECT_TOML_PATH.name + " - optional-dependencies" | ||
| cli.echo_failure(f"Outdated dependencies from {location}:") | ||
| print_table(outdated_optional, transitive_headers) | ||
| if outdated_dev: | ||
| cli.echo_failure(f"Outdated dependencies from {DEV_DEPS_PATH.name}:") | ||
| print_table(outdated_dev, transitive_headers) | ||
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| if not found_outdated: | ||
| cli.echo_success("All top-level dependencies up to date.") | ||
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| if transitive: | ||
| top_level: set[str] = { | ||
| item.name for item in outdated_main + outdated_optional + outdated_dev | ||
| } | ||
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| print("\nRetrieving transitive dependency information...") | ||
| transitive_dependencies = lock_deps.get_lock_file_deps( | ||
| LOCK_FILE_PATH, exclude=top_level | ||
| ) | ||
| outdated_transitive = get_outdated_deps(transitive_dependencies, strip=True) | ||
|
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| if outdated_transitive: | ||
| transitive_headers = ("PACKAGE", "PINNED", "AVAILABLE") | ||
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| cli.echo_failure("Outdated transitive dependencies:") | ||
| print_table(outdated_transitive, transitive_headers) | ||
| else: | ||
| cli.echo_success("All transitive dependencies up to date.") | ||
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| if __name__ == "__main__": | ||
| cli.run(main) |
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