diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 49f35eb..a107bbf 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -89,26 +89,14 @@ uv run poe fix-and-check-all 1. Clone the repository recursively, ensure you are on the main branch, and that the working directory is clean. 2. Check out a new branch to prepare the library for release. -3. Bump the version of the library to the desired SemVer using [`uv run hatch version`](https://hatch.pypa.io/latest/version/#updating). - - `hatch version` supports updating to a specific version number. - For example, to update the project version to `0.2.0`: - ```console - uv run hatch version "0.2.0" - - ``` - `hatch version` also supports incrementing the major, minor, or patch segment. - For example, to bump the minor version segment: - ```console - uv run hatch version minor - ``` -5. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`. -6. Push the commit, open a PR, ensure tests pass, and seek reviews. -7. Squash merge the PR into the `main` branch. -8. Tag the new commit on the main branch with the bumped version number. +3. Bump the version of the library to the desired SemVer using [`uv version`](https://docs.astral.sh/uv/reference/cli/#uv-version). +4. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`. +5. Push the commit, open a PR, ensure tests pass, and seek reviews. +6. Squash merge the PR into the `main` branch. +7. Tag the new commit on the main branch with the bumped version number. > [!WARNING] -> The tag **must** be a valid SemVer version number and **must** match the version set by `uv run hatch version` in (3). The [publishing GitHub Action](.github/workflows/publish_syncup) is activated by a new tag on the `main` branch containing a valid SemVer version. +> The tag **must** be a valid SemVer version number and **must** match the version set by `uv version` in (3). The [publishing GitHub Action](.github/workflows/publish_syncup) is activated by a new tag on the `main` branch containing a valid SemVer version. GitHub Actions will take care of the remainder of the deployment and release process: diff --git a/LICENSE b/LICENSE index b438bd8..4831d7a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright © 2025 Fulcrum Genomics LLC +Copyright © 2025 Clint Valentine Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 8227f14..0d366bd 100644 --- a/README.md +++ b/README.md @@ -9,20 +9,30 @@ Synchronizers for lazy iterators. -## Recommended Installation - -Install the Python package and dependency management tool [`uv`](https://docs.astral.sh/uv/getting-started/installation/) using official documentation. - -Install the dependencies of the project with: - ```console -uv sync --locked +pip install syncup ``` -To check successful installation, run: - -```console -uv run syncup --help +## Example + +Iterate though a complete FASTX file and a filtered FASTX file, synchronizing on records present in both: + +```python +with ( + FastxFile(in_source) as source, + FastxFile(in_subseq) as subseq, +): + for count, (fq, fq_subseq) in enumerate( + sync( + iter1=source, + iter2=subseq, + key1=lambda rec: rec.name, + key2=lambda rec: rec.name, + cmp_func=lambda x, y: (x == y) - 1, # only advance iter1 when non-equal + ), + start=1, + ): + assert fq.name == fq_subseq.name, f"Names for record {count} should be equal!" ``` ## Development and Testing diff --git a/pyproject.toml b/pyproject.toml index d3a5ee3..a5215ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,20 +1,17 @@ [build-system] -requires = ["hatchling"] +requires = ["hatchling"] build-backend = "hatchling.build" [project] -name = "syncup" -version = "0.1.0" -description = "Synchronizers for lazy iterators." -readme = "README.md" -authors = [{ name="Fulcrum Genomics LLC", email="contact@fulcrumgenomics.com" }] -license = "MIT" -include = ["LICENSE"] +name = "syncup" +version = "0.1.0" +description = "Synchronizers for lazy iterators." +readme = "README.md" +authors = [{ name="Clint Valentine", email="valentine.clint@gmail.com" }] +license = "MIT" +include = ["LICENSE"] requires-python = ">=3.11" -dependencies = [ - "defopt~=6.4" -] -classifiers = [ +classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", @@ -33,9 +30,6 @@ classifiers = [ "repository" = "https://github.com/clintval/syncup" "Bug Tracker" = "https://github.com/clintval/syncup/issues" -[project.scripts] -syncup = "syncup.main:run" - [dependency-groups] dev = [ "ruff ==0.12.3", @@ -44,30 +38,26 @@ dev = [ "pytest-cov ~=6.2", "pytest-mock ~=3.14", "poethepoet ~=0.36", - "hatch ~=1.14", -] -ipython = [ - "ipython ~=9.2", ] [tool.poe.tasks] fix-format = "ruff format" -fix-lint = "ruff check --fix" +fix-lint = "ruff check --fix" fix-all.ignore_fail = "return_non_zero" -fix-all.sequence = [ +fix-all.sequence = [ "fix-format", "fix-lint" ] -check-lock = "uv lock --check" +check-lock = "uv lock --check" check-format = "ruff format --check --diff" -check-lint = "ruff check" -check-tests = "pytest" +check-lint = "ruff check" +check-tests = "pytest" check-typing = "mypy" check-all.ignore_fail = "return_non_zero" -check-all.sequence = [ +check-all.sequence = [ "check-lock", "check-format", "check-lint", @@ -76,7 +66,7 @@ check-all.sequence = [ ] fix-and-check-all.ignore_fail = "return_non_zero" -fix-and-check-all.sequence = [ +fix-and-check-all.sequence = [ "check-lock", "fix-format", "fix-lint", @@ -85,51 +75,47 @@ fix-and-check-all.sequence = [ ] [tool.mypy] -files = ["./"] -strict_optional = true -strict_equality = true -check_untyped_defs = true -disallow_incomplete_defs = true -disallow_untyped_calls = true +files = ["./"] +strict_optional = true +strict_equality = true +check_untyped_defs = true +disallow_incomplete_defs = true +disallow_untyped_calls = true disallow_untyped_decorators = true -disallow_untyped_defs = true -no_implicit_optional = true -warn_no_return = true -warn_redundant_casts = true -warn_return_any = true -warn_unreachable = true -warn_unused_configs = true -warn_unused_ignores = true -enable_error_code = [ +disallow_untyped_defs = true +no_implicit_optional = true +warn_no_return = true +warn_redundant_casts = true +warn_return_any = true +warn_unreachable = true +warn_unused_configs = true +warn_unused_ignores = true +enable_error_code = [ "ignore-without-code", "possibly-undefined", "exhaustive-match", ] -exclude = [ +exclude = [ "docs/", "site/", ] -[[tool.mypy.overrides]] -module = "defopt" -ignore_missing_imports = true - [tool.pytest.ini_options] minversion = "7.4" -addopts = [ +addopts = [ "--color=yes", "--import-mode=importlib", "--cov" ] [tool.ruff] -line-length = 100 +line-length = 100 target-version = "py311" -output-format = "full" -preview = true +output-format = "full" +preview = true [tool.ruff.lint] -select = [ +select = [ "A", # Builtin shadowing "ARG", # Unused arguments "C901", # McCabe complexity @@ -146,7 +132,7 @@ select = [ "W", # pycodestyle warnings "Q", # flake8-quotes ] -ignore = [ +ignore = [ "E203", "E701", "D212", # summary line should be located on the same line as opening quotes diff --git a/syncup/__init__.py b/syncup/__init__.py index e69de29..d90b0c0 100644 --- a/syncup/__init__.py +++ b/syncup/__init__.py @@ -0,0 +1,5 @@ +from ._syncup import Cmp as Cmp +from ._syncup import Comparable as Comparable +from ._syncup import sync as sync + +__all__ = ["sync", "Comparable", "Cmp"] diff --git a/syncup/_syncup.py b/syncup/_syncup.py new file mode 100644 index 0000000..8012b93 --- /dev/null +++ b/syncup/_syncup.py @@ -0,0 +1,60 @@ +from abc import abstractmethod +from typing import Callable +from typing import Iterator +from typing import Protocol +from typing import TypeVar + +T = TypeVar("T") +"""A type variable for generic items.""" + + +class Comparable(Protocol): + """A protocol for comparable objects.""" + + @abstractmethod + def __lt__(self: T, other: T) -> bool: + """Less than comparison.""" + + @abstractmethod + def __gt__(self: T, other: T) -> bool: + """Greater than comparison.""" + + +Cmp = TypeVar("Cmp", bound=Comparable) +"""A type variable for comparable types.""" + + +def sync( + iter1: Iterator[T], + iter2: Iterator[T], + key1: Callable[[T], Cmp], + key2: Callable[[T], Cmp], + cmp_func: Callable[[Cmp, Cmp], int] = lambda x, y: (x > y) - (x < y), +) -> Iterator[tuple[T, T]]: + """ + Sync two iterators based on a comparison function and key functions. + + Args: + iter1: The first iterator. + iter2: The second iterator. + key1: A function to extract the comparison key from items in iter1. + key2: A function to extract the comparison key from items in iter2. + cmp_func: A function to compare two keys, returning negative if the first is less than + the second, zero if they are equal, and positive if the first is greater than + the second. Defaults to the default equality operations. + + """ + try: + item1 = next(iter1) + item2 = next(iter2) + while True: + if (result := cmp_func(key1(item1), key2(item2))) == 0: + yield (item1, item2) + item1 = next(iter1) + item2 = next(iter2) + elif result < 0: + item1 = next(iter1) + else: + item2 = next(iter2) + except StopIteration: + return diff --git a/syncup/main.py b/syncup/main.py deleted file mode 100644 index 58295e6..0000000 --- a/syncup/main.py +++ /dev/null @@ -1,30 +0,0 @@ -import logging -import sys -from typing import Callable -from typing import List - -import defopt - -from syncup.tools.hello import hello - -_tools: List[Callable] = [hello] - - -def setup_logging(level: str = "INFO") -> None: - """Set up basic logging to print to the console.""" - logging.basicConfig( - level=level, - format="%(asctime)s %(name)s:%(funcName)s:%(lineno)s [%(levelname)s]: %(message)s", - ) - - -def run() -> None: - """Set up logging, then hand over to defopt for running command line tools.""" - setup_logging() - logger = logging.getLogger("syncup") - logger.info("Executing: " + " ".join(sys.argv)) - defopt.run( - funcs=_tools, - argv=sys.argv[1:], - ) - logger.info("Finished executing successfully.") diff --git a/syncup/tools/__init__.py b/syncup/tools/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/syncup/tools/hello.py b/syncup/tools/hello.py deleted file mode 100644 index 775129f..0000000 --- a/syncup/tools/hello.py +++ /dev/null @@ -1,11 +0,0 @@ -def hello( - *, - name: str = "World", -) -> None: - """ - Print a greeting. - - Args: - name: The person to greet. - """ - print(f"Hello, {name}!") diff --git a/tests/__init__.py b/tests/__init__.py index e69de29..be85b6e 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,6 @@ +def test_sync_empty_iterators() -> None: + """Test sync on empty iterators.""" + from syncup import sync + + result: list = list(sync(iter([]), iter([]), key1=lambda x: x, key2=lambda x: x)) + assert result == [] diff --git a/tests/test_main.py b/tests/test_main.py deleted file mode 100644 index 57fb006..0000000 --- a/tests/test_main.py +++ /dev/null @@ -1,22 +0,0 @@ -from inspect import isfunction -from typing import Callable - -import pytest -from defopt import signature - -from syncup import main - - -@pytest.mark.parametrize("tool", main._tools) -def test_tools_are_defined(tool: Callable) -> None: - """Test that all command line tools passed to defopt are defined functions.""" - assert isfunction(tool) - - -@pytest.mark.parametrize("tool", main._tools) -def test_tools_have_valid_docstrings(tool: Callable) -> None: - """Test that all command line tools have a valid defopt docstring.""" - try: - signature(tool) - except TypeError: - raise AssertionError(f"defopt could not parse docstring for {tool.__name__}") from None diff --git a/tests/test_syncup.py b/tests/test_syncup.py new file mode 100644 index 0000000..35b02e1 --- /dev/null +++ b/tests/test_syncup.py @@ -0,0 +1,61 @@ +from dataclasses import dataclass +from typing import Iterator + +import pytest + +from syncup import sync + + +@pytest.mark.parametrize( + "iter1,iter2", + [ + [iter([]), iter([])], + [iter([1, 2, 3]), iter([])], + [iter([]), iter([1, 2, 3])], + ], +) +def test_sync_empty_iterators(iter1: Iterator[int], iter2: Iterator[int]) -> None: + """Test sync on empty iterators.""" + result = sync(iter1, iter2, key1=lambda x: x, key2=lambda x: x) + assert list(result) == [] + + +@pytest.mark.parametrize( + "iter1,iter2,expected", + [ + [iter([1, 2, 3]), iter([1, 3]), [(1, 1), (3, 3)]], + [iter([1, 3]), iter([1, 2, 3]), [(1, 1), (3, 3)]], + ], +) +def test_sync_iterators_comparable( + iter1: Iterator[int], iter2: Iterator[int], expected: list[tuple[int, int]] +) -> None: + """Test sync on iterators with comparable elements.""" + result = sync(iter1, iter2, key1=lambda x: x, key2=lambda x: x) + assert list(result) == expected + + +@dataclass(eq=True, frozen=True) +class Wrapper: + """A custom class implementing the Comparable protocol for testing.""" + + value: int + + +def test_sync_on_custom_comparable() -> None: + """Test sync on iterators with custom comparable elements.""" + iter1 = iter([Wrapper(3), Wrapper(2), Wrapper(1)]) + iter2 = iter([Wrapper(3), Wrapper(1)]) + expected = [(Wrapper(3), Wrapper(3)), (Wrapper(1), Wrapper(1))] + + result = sync( + iter1=iter1, + iter2=iter2, + # Use the 'value' attribute for comparison + key1=lambda x: x.value, + key2=lambda x: x.value, + # Reverse the order of the comparison to test reverse sorted inputs + cmp_func=lambda x, y: (x < y) - 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