diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index dc349db0..336b5df9 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,5 +1,9 @@ # Change Log +## 0.12.0 + +- ✨ Add utils.load_pipeline() to load pipeline + ## 0.11.1 - Dismiss warning for fillna method for pandas 2.1 diff --git a/pipen/utils.py b/pipen/utils.py index 728f7942..17d08526 100644 --- a/pipen/utils.py +++ b/pipen/utils.py @@ -3,6 +3,8 @@ import re import sys +import importlib +import importlib.util import logging import textwrap import typing @@ -20,6 +22,7 @@ Iterable, List, Mapping, + Sequence, Tuple, Type, ) @@ -51,6 +54,7 @@ from .pipen import Pipen from .proc import Proc + from .procgroup import ProcGroup class RichHandler(_RichHandler): @@ -587,3 +591,115 @@ def is_valid_name(name: str) -> bool: True if valid, otherwise False """ return re.match(r"^[\w.-]+$", name) is not None + + +def _get_obj_from_spec(spec: str) -> Any: + """Get the object from a spec like `:name` or + `/path/to/script.py:name` + + Args: + spec: The spec + + Returns: + The object + + Raises: + AttributeError: If name cannot be found in the module + """ + modpath, sep, name = spec.rpartition(":") + if sep != ":": + raise ValueError( + f"Invalid specification: {spec}.\n" + "It must be in the format ':name' or \n" + "'/path/to/spec.py:name'" + ) + + path = Path(modpath) + if path.is_file(): + spec = importlib.util.spec_from_file_location(path.stem, modpath) + module = importlib.util.module_from_spec(spec) + spec.loader.exec_module(module) + else: + module = importlib.import_module(modpath) + + return getattr(module, name) + + +async def load_pipeline( + obj: str | Type[Proc] | Type[ProcGroup] | Type[Pipen], + cli_args: Sequence[str] = (), + **kwargs: Any, +) -> Pipen: + """Load a pipeline from a Pipen, Proc or ProcGroup object + + It does not only load the Pipen object or convert the Proc/ProcGroup + object to Pipen, but also build the process relationships. So that we + can access `pipeline.procs` and `requires/nexts` of each proc. + + To avoid running the pipeline and notify the plugins that this is just + for loading the pipeline, `sys.argv[0]` is set to `@pipen`. + + Args: + obj: The Pipen, Proc or ProcGroup object. It can also be a string in + the format of `part1:part2` to load the pipeline, where part1 is + a path to a python file or package directory, and part2 is the name + of the proc, procgroup or pipeline to load. + It should be able to be loaded by `getattr(module, part2)`, where + module is loaded from `part1`. + cli_args: The cli arguments, in case the pipeline or some plugins use + to parse the relationship of the processes. + kwargs: The kwargs to pass to the Pipen constructor + + Returns: + The loaded Pipen object + + Raises: + TypeError: If obj or loaded obj is not a Pipen, Proc or ProcGroup + object + """ + from .pipen import Pipen + from .proc import Proc + from .procgroup import ProcGroup + + if isinstance(obj, str): + obj = _get_obj_from_spec(obj) + if ( + not isinstance(obj, type) + or not issubclass(obj, (Pipen, Proc, ProcGroup)) + ): + raise TypeError( + f"Expected a Pipen, Proc or ProcGroup class, got {type(obj)}" + ) + + pipeline = obj + if isinstance(obj, type) and issubclass(obj, Proc): + kwargs.setdefault("name", f"{obj.name}Pipeline") + pipeline = Pipen(**kwargs).set_starts(obj) + + if isinstance(obj, type) and issubclass(obj, ProcGroup): + pipeline = obj().as_pipen(**kwargs) + + if isinstance(obj, type) and issubclass(obj, Pipen): + # Avoid "pipeline" to be used as pipeline name by varname + (pipeline, ) = (obj(**kwargs), ) + + if not isinstance(pipeline, Pipen): + raise TypeError( + f"Expected a Pipen, Proc or ProcGroup class, got {type(pipeline)}" + ) + + old_argv = sys.argv + sys.argv = ["@pipen"] + list(cli_args) + try: + # Initialize the pipeline so that the arguments definied by + # other plugins (i.e. pipen-args) to take in place. + pipeline.workdir = Path(pipeline.config.workdir).joinpath( + kwargs.get("name", pipeline.name) + ) + await pipeline._init() + pipeline.workdir.mkdir(parents=True, exist_ok=True) + pipeline.build_proc_relationships() + finally: + sys.argv = old_argv + + return pipeline diff --git a/pipen/version.py 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[[package]] name = "varname" @@ -1112,4 +1174,4 @@ uvloop = ">=0,<1" [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "272da97066f6d10a59a5aaeacd360d76022dbdcfe0ca287c99ea1efa717ec0c0" +content-hash = "c297258ee717dbcf6bf88c3099d2693f12cef4f1e3c316981a2735a897c47388" diff --git a/pyproject.toml b/pyproject.toml index ae93e758..08dc774e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api" [tool.poetry] name = "pipen" -version = "0.11.1" +version = "0.12.0" description = "A pipeline framework for python" authors = [ "pwwang ",] license = "MIT" @@ -35,18 +35,17 @@ varname = "^0.12" [tool.poetry.dev-dependencies] openpyxl = "^3" pytest = "^7" +pytest-asyncio = "^0.21" pytest-cov = "^4" pytest-xdist = "^3" # This also installs scipy and wcwidth -# datar = { version = "^0.15", extras = ["pandas"] } -datar-pandas = "^0.5" -datar = "^0.15" +datar = { version = "^0.15", extras = ["pandas"] } [tool.poetry.scripts] pipen = "pipen.cli:main" [tool.pytest.ini_options] -addopts = "-vv -n auto -p no:asyncio -p no:benchmark -W error::UserWarning --cov-config=.coveragerc --cov=pipen --cov-report xml:.coverage.xml --cov-report term-missing" +addopts = "-vv -n auto -p no:benchmark -W error::UserWarning --cov-config=.coveragerc --cov=pipen --cov-report xml:.coverage.xml --cov-report term-missing" # addopts = "-vv -n auto -p no:asyncio -W error::UserWarning" console_output_style = "progress" junit_family = "xunit1" diff --git a/tests/test_utils.py b/tests/test_utils.py index 77cec026..39693645 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,6 +1,6 @@ import pytest -from pathlib import Path import pipen +from pathlib import Path from pipen.utils import ( brief_list, desc_from_docstring, @@ -14,10 +14,16 @@ update_dict, mark, get_marked, + _get_obj_from_spec, + load_pipeline, ) +from pipen.proc import Proc +from pipen.procgroup import ProcGroup from pipen.exceptions import ConfigurationError from pipen.pluginmgr import plugin +HERE = Path(__file__).parent.resolve() + def test_get_logger(caplog): logger = get_logger("test", "info") @@ -126,3 +132,50 @@ class Z(Y): # Marks inherited, as Y/Z are not Proc nor ProcGroup assert get_marked(Z, "a", None) == 1 + + +def test_get_obj_from_spec(): + with pytest.raises(ValueError): + _get_obj_from_spec("a.b.c") + + obj = _get_obj_from_spec(f"{HERE}/helpers.py:SimpleProc") + assert obj.name == "SimpleProc" + + obj = _get_obj_from_spec(f"pipen:Pipen") + assert obj is pipen.Pipen + + +@pytest.mark.asyncio +async def test_load_pipeline(tmp_path): + with pytest.raises(TypeError): + await load_pipeline(f"{HERE}/helpers.py:create_dead_link") + with pytest.raises(TypeError): + await load_pipeline(ConfigurationError) + + # Proc + pipeline = await load_pipeline(f"{HERE}/helpers.py:SimpleProc") + assert pipeline.name == "SimpleProcPipeline" + + # ProcGroup + class PG(ProcGroup): + ... + + pg = PG() + + @pg.add_proc() + class P1(Proc): + pass + + pipeline = await load_pipeline(PG) + assert pipeline.name == "PG" + + # Pipen + obj = _get_obj_from_spec(f"{HERE}/helpers.py:pipen") + proc = _get_obj_from_spec(f"{HERE}/helpers.py:SimpleProc") + # Use the original function instead of fixture + p = obj.__wrapped__(tmp_path).__class__ + p.starts = [proc] + pipeline = await load_pipeline(p, name="LoadedPipeline") + assert pipeline.name == "LoadedPipeline" + assert pipeline.starts[0].name == "SimpleProc" + assert len(pipeline.procs) == 1