From 1ed119a77b59b3e3048bf22d305fa1e9b18a56b2 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Tue, 19 Dec 2023 23:40:12 -0500 Subject: [PATCH] :sparkles: Add `gradients` command to `cpac` --- .github/workflows/test_cpac.yml | 2 +- .pre-commit-config.yaml | 5 +- CHANGELOG.rst | 2 + poetry.lock | 2007 +++++++++++++++++++++++++++---- pyproject.toml | 10 +- src/cpac/__init__.py | 2 +- src/cpac/__main__.py | 6 + src/cpac/utils/__init__.py | 3 +- src/cpac/utils/bare_wrap.py | 208 ++++ src/cpac/utils/utils.py | 6 + 10 files changed, 2040 insertions(+), 211 deletions(-) create mode 100644 src/cpac/utils/bare_wrap.py diff --git a/.github/workflows/test_cpac.yml b/.github/workflows/test_cpac.yml index 185c6c94..11168b32 100644 --- a/.github/workflows/test_cpac.yml +++ b/.github/workflows/test_cpac.yml @@ -22,7 +22,7 @@ jobs: platform: [docker] tag: [latest, nightly] go: [1.14] - python: [3.7, 3.8, 3.9, '3.10', 3.11] + python: [3.8, 3.9, '3.10', 3.11, 3.12] singularity: [3.6.4] steps: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 627fb479..beca33fd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,8 +14,9 @@ repos: - id: mypy additional_dependencies: - types-tabulate + - types-toml - types-PyYAML - args: [--ignore-missing-imports] + args: [--python-version=3.8, --ignore-missing-imports] - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks rev: v2.11.0 hooks: @@ -31,7 +32,7 @@ repos: - --no-sort - repo: https://github.com/python-poetry/poetry - rev: 1.5.1 + rev: 1.6.0 hooks: - id: poetry-check - id: poetry-lock diff --git a/CHANGELOG.rst b/CHANGELOG.rst index de55b263..2607ed2d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,6 +11,8 @@ Changelog * Replaces ``setup.cfg`` with ``pyproject.toml`` * Replaces ``setuptools`` with ``poetry`` * Adds pre-commit hooks for linting and formatting +* Require Python ≥ 3.8 +* Wrap ``cmi-dair/ba_timeseries_gradients`` as ``gradients`` command `Version 0.5.0: Parse Resources `_ ======================================================================================== diff --git a/poetry.lock b/poetry.lock index a08c0697..e9eb6b00 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.0 and should not be changed by hand. 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+python = ">=3.8" docker = ">=4.2.1" dockerpty = "*" docker-pycreds = "*" importlib_metadata = {version = "*", markers = "python_version < '3.8'"} pandas = ">=0.23.4" -spython = ">=0.0.81" +poetry = "*" pyyaml = "*" rich = "*" semver = "*" +spython = ">=0.0.81" tabulate = ">=0.8.6" +toml = {version = "*", markers = "python_version < '3.11'"} tornado = "*" websocket-client = "*" alabaster = {version = "*", optional = true} +ba_timeseries_gradients = {git = "https://github.com/cmi-dair/ba-timeseries-gradients.git", optional = true, markers = "python_version >= '3.11' and python_version < '3.12'"} coveralls = {version = "*", optional = true} imagesize = {version = "*", optional = true} pytest = {version = "*", optional = true} @@ -55,6 +58,7 @@ sphinx = {version = "*", optional = true} [tool.poetry.extras] dev = ["coveralls", "pytest", "pytest-remotedata", "pytest-runner", "sphinx"] +gradients = ["ba_timeseries_gradients"] testing = ["alabaster", "imagesize", "pytest", "pytest-cov", "pytest-runner", "sphinx"] [tool.poetry.scripts] @@ -75,7 +79,7 @@ testpaths = ["tests"] [tool.ruff] extend-exclude = ["docs/conf.py"] extend-select = ["A", "C4", "D", "G", "I", "ICN", "NPY", "PL", "RET", "RSE", "RUF", "Q", "W"] -target-version = "py37" +target-version = "py38" [tool.ruff.lint.per-file-ignores] "CPAC/func_preproc/func_preproc.py" = ["E402"] diff --git a/src/cpac/__init__.py b/src/cpac/__init__.py index 561930b8..f59415ec 100644 --- a/src/cpac/__init__.py +++ b/src/cpac/__init__.py @@ -3,7 +3,7 @@ try: from importlib.metadata import PackageNotFoundError, distribution except ModuleNotFoundError: - from importlib_metadata import PackageNotFoundError, distribution + from importlib_metadata import PackageNotFoundError, distribution # type: ignore DIST_NAME = __name__ try: diff --git a/src/cpac/__main__.py b/src/cpac/__main__.py index 46490bea..ed7b4b9e 100644 --- a/src/cpac/__main__.py +++ b/src/cpac/__main__.py @@ -13,6 +13,7 @@ from cpac import __version__ from cpac.backends import Backends from cpac.helpers import TODOs, cpac_parse_resources as parse_resources +from cpac.utils.bare_wrap import WRAPPED, add_bare_wrapper, call _logger = logging.getLogger(__name__) @@ -194,6 +195,8 @@ def _parser(): formatter_class=argparse.ArgumentDefaultsHelpFormatter, ) + add_bare_wrapper(subparsers, "gradients") + subparsers.add_parser( "pull", add_help=True, @@ -408,6 +411,9 @@ def run(): if command is None: parser.print_help() parser.exit() + if command in WRAPPED: + # directly call external package and exit on completion or failure + call(command, args) reordered_args = [] option_value_setting = False for i, arg in enumerate(args.copy()): diff --git a/src/cpac/utils/__init__.py b/src/cpac/utils/__init__.py index 12cd2f2b..84339462 100644 --- a/src/cpac/utils/__init__.py +++ b/src/cpac/utils/__init__.py @@ -1,8 +1,9 @@ from .checks import check_version_at_least -from .utils import LocalsToBind, PermissionMode, Volume, Volumes +from .utils import LocalsToBind, PermissionMode, Volume, Volumes, get_project_root __all__ = [ "check_version_at_least", + "get_project_root", "LocalsToBind", "PermissionMode", "Volume", diff --git a/src/cpac/utils/bare_wrap.py b/src/cpac/utils/bare_wrap.py new file mode 100644 index 00000000..c4a1d9e3 --- /dev/null +++ b/src/cpac/utils/bare_wrap.py @@ -0,0 +1,208 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +"""Wrap another Python package without any modifications.""" +from argparse import REMAINDER, ArgumentParser, _SubParsersAction +from dataclasses import dataclass +from logging import ERROR, WARNING, log +from shutil import which +from subprocess import CalledProcessError, call as sub_call +from sys import exit as sys_exit, version_info +from typing import Any, Literal, Optional, TypedDict + +if version_info.minor < 9: # noqa: PLR2004 + from typing import Dict +else: + Dict = dict # type: ignore + +from packaging.markers import Marker + +try: + import tomllib +except (ImportError, ModuleNotFoundError): + import toml + +try: + from ba_timeseries_gradients.parser import get_parser as gradients_parser +except (ImportError, ModuleNotFoundError): + gradients_parser = None + +from cpac.utils import get_project_root + +WRAPPED = {} +"""memoization of wrapped packages""" + + +class ScriptInfo(TypedDict): + """Info needed for bare package wrapping.""" + + command: str + helpstring: Optional[str] + url: str + + +@dataclass +class WrappedBare: + """Info needed for bare package wrapping.""" + + name: str + command: str + _helpstring: Optional[str] + url: str + + @property + def helpstring(self): + """Get the helpstring.""" + if self._helpstring is None: + return f"Extra script {self.command} not found. See {self.url} for more information, or run `pip install cpac[{self.name}]` to install it." + return self._helpstring + + +def add_bare_wrapper(parser: _SubParsersAction, command: str) -> None: + """Add a bare wrapper to the parser. + + Parameters + ---------- + parser : _SubParsersAction + The subparsers to add the wrapper to + + command : str + The command to wrap + """ + from cpac.__main__ import ExtendAction + + bare_parser: ArgumentParser = parser.add_parser( + command, usage=get_wrapped(command).helpstring + ) + bare_parser.add_argument("args", nargs=REMAINDER) + bare_parser.register("action", "extend", ExtendAction) + + +def call(name: str, command: list) -> None: + """Call a bare-wrapped command. + + Parameters + ---------- + name : str + The name of the package to call + + command : list + The command to run + """ + if version_info.minor < 11: # noqa: PLR2004 + pyproject = toml.load(get_project_root() / "pyproject.toml") + else: + with open(get_project_root() / "pyproject.toml", "rb") as _f: + pyproject = tomllib.load(_f) + script = get_wrapped(name) + try: + package_info = get_nested( + pyproject, ["tool", "poetry", "dependencies", script.command] + ) + except KeyError as ke: + raise KeyError(f"Package {name} not defined in dependencies") from ke + marker = Marker(package_info["marker"]) if "marker" in package_info else None + if marker and marker.evaluate() is False: + raise EnvironmentError( + f"Current environment does not meet requirements ({marker}) for package {name}" + ) + if not check_for_package(script.command): + sub_call(["poetry", "install", "--extras", name], cwd=get_project_root()) + try: + sub_call([script.command, *command]) + except CalledProcessError as cpe: + log(ERROR, str(cpe)) + sys_exit(cpe.returncode) + sys_exit(0) + + +def check_for_package(package_name: str) -> bool: + """Check if a package is installed.""" + return which(package_name) is not None + + +def get_nested( + dct: dict, keys: list, error: Literal["raise", "warn", None] = "raise" +) -> Any: + """Get a nested dictionary value. + + Parameters + ---------- + dct : dict + The dictionary to search + + keys : Iterable + The keys to search for + + error : Literal['raise', 'warn', None] + How to handle errors: + 'raise' : raise an error + 'warn' : log a warning and return None + None : return None without a warning + + Returns + ------- + Any + The value of the nested key or None + + Examples + -------- + >>> dct = {'a': {'b': {'c': 1}}} + >>> get_nested(dct, ['a', 'b', 'c']) + 1 + >>> get_nested(dct, ['a', 'b', 'd']) + KeyError: 'd' + >>> get_nested(dct, ['a', 'b', 'd'], error=None) + None + """ + key = keys.pop(0) + if key in dct: + if len(keys) == 0: + return dct[key] + return get_nested(dct[key], keys, error) + if error == "raise": + return dct[key] + if error == "warn": + log(WARNING, "Key %s not found in %s", key, dct) + return None + + +def get_wrapped(name: str) -> WrappedBare: + """Get the name of the script to run. + + Parameters + ---------- + name : str + The name of the package to run + + Returns + ------- + str + The name of the script to run + """ + if name not in WRAPPED: + scripts: Dict[str, ScriptInfo] = { + "gradients": { + "command": "ba_timeseries_gradients", + "helpstring": None, + "url": "https://cmi-dair.github.io/ba-timeseries-gradients/ba_timeseries_gradients.html", + } + } + if gradients_parser is not None: + scripts["gradients"]["helpstring"] = ( + gradients_parser() + .format_help() + .replace("usage: ba_timeseries_gradients", "cpac gradients") + ) + if name in scripts: + WRAPPED[name] = WrappedBare( + name, + scripts[name]["command"], + scripts[name]["helpstring"], + scripts[name]["url"], + ) + else: + raise KeyError(f"Package {name} not defined in scripts") + return WRAPPED[name] + + +__all__ = ["add_bare_wrapper", "call", "WRAPPED"] diff --git a/src/cpac/utils/utils.py b/src/cpac/utils/utils.py index cc54f8e3..98b61b03 100644 --- a/src/cpac/utils/utils.py +++ b/src/cpac/utils/utils.py @@ -2,6 +2,7 @@ from itertools import permutations import os +from pathlib import Path from typing import ClassVar, Iterator, Optional, Set, Union from warnings import warn @@ -10,6 +11,11 @@ from cpac import DIST_NAME +def get_project_root() -> Path: + """Get project root directory.""" + return Path(__file__).parents[3] + + class LocalsToBind: """Class to collect local directories to bind to containers."""