From df9b393c76dcfd7634454e5e88945ae200831613 Mon Sep 17 00:00:00 2001 From: simw Date: Tue, 4 Feb 2025 17:34:58 +0000 Subject: [PATCH 01/12] Add grouping and chaining operations --- .github/workflows/test.yml | 2 +- pyproject.toml | 2 +- src/pipedata/core/links.py | 9 ++++++--- src/pipedata/core/ops.py | 34 ++++++++++++++++++++++++++++++++ tests/core/test_chain.py | 40 ++++++++++++++++++++++++++++++++++++++ tests/ops/test_pipeline.py | 40 +++++++++++++++++++++++++++++++++++++- 6 files changed, 121 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 247bcff..185ce96 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -40,7 +40,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] steps: - uses: actions/checkout@v3 diff --git a/pyproject.toml b/pyproject.toml index 02be904..d0404de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,11 +22,11 @@ classifiers = [ "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: Software Development :: Libraries :: Python Modules", "Typing :: Typed", ] diff --git a/src/pipedata/core/links.py b/src/pipedata/core/links.py index 2fdf886..292e18a 100644 --- a/src/pipedata/core/links.py +++ b/src/pipedata/core/links.py @@ -1,3 +1,4 @@ +from dataclasses import dataclass from typing import ( Callable, Generic, @@ -23,7 +24,8 @@ def __iter__(self) -> Iterator[TStart]: def __next__(self) -> TStart: self._count += 1 try: - return next(self._iterator) + next_value = next(self._iterator) + return next_value except StopIteration as err: self._count -= 1 raise StopIteration from err @@ -45,9 +47,10 @@ def __init__( def __name__(self) -> str: # noqa: A003 return self._func.__name__ - def __call__(self, input_iterator: Iterator[TStart]) -> Iterator[TEnd]: + def __call__(self, input_iterator: Iterator[TStart]) -> CountingIterator[TEnd]: self._input = CountingIterator(input_iterator) - self._output = CountingIterator(self._func(self._input)) + result = self._func(self._input) + self._output = CountingIterator(result) return self._output def get_counts(self) -> Tuple[int, int]: diff --git a/src/pipedata/core/ops.py b/src/pipedata/core/ops.py index acdbd7c..0ac7360 100644 --- a/src/pipedata/core/ops.py +++ b/src/pipedata/core/ops.py @@ -46,3 +46,37 @@ def new_action(previous_step: Iterator[TEnd]) -> Iterator[TOther]: return (func(elements) for elements in _batched(previous_step, n)) super().__init__(new_action) + + +class chain_iterables(ChainLink[Iterator[TEnd], TEnd]): # noqa: N801 + def __init__(self) -> None: + def chain_iterables_(previous_step: Iterator[Iterator[TEnd]]) -> Iterator[TEnd]: + return itertools.chain.from_iterable(previous_step) + + super().__init__(chain_iterables_) + + +class grouper(ChainLink[TEnd, list[TEnd]]): # noqa: N801 + def __init__( + self, + *, + starter: Optional[Callable[[TEnd], bool]] = None, + ender: Optional[Callable[[TEnd], bool]] = None, + ) -> None: + def grouper_(previous_step: Iterator[TEnd]) -> Iterator[TOther]: + group: list[TEnd] = [] + for element in previous_step: + if starter is not None and starter(element) and len(group) > 0: + yield group + group = [element] + elif ender is not None and ender(element): + group.append(element) + yield group + group = [] + else: + group.append(element) + + if len(group) > 0: + yield group + + super().__init__(grouper_) diff --git a/tests/core/test_chain.py b/tests/core/test_chain.py index 052152d..3730cda 100644 --- a/tests/core/test_chain.py +++ b/tests/core/test_chain.py @@ -226,3 +226,43 @@ def add_values(values: Tuple[int, ...]) -> int: "outputs": 3, }, ] + + +def test_chain_iterables() -> None: + chain = Chain[int]().then(ops.chain_iterables()) + result = list(chain(iter([iter([0, 1]), iter([2, 3])]))) + assert result == [0, 1, 2, 3] + assert chain.get_counts() == [ + { + "name": "_identity", + "inputs": 2, + "outputs": 2, + }, + { + "name": "chain_iterables_", + "inputs": 2, + "outputs": 4, + }, + ] + + +def test_chain_grouper() -> None: + chain = ( + Chain[int]() + .then(ops.grouper(starter=lambda x: x == 1, ender=lambda x: x == 3)) + ) + inputs = [1, 2, 3, 4, 1, 2, 3, 4] + result = list(chain(iter(inputs))) + assert result == [[1, 2, 3], [4], [1, 2, 3], [4]] + assert chain.get_counts() == [ + { + "name": "_identity", + "inputs": 8, + "outputs": 8, + }, + { + "name": "grouper_", + "inputs": 8, + "outputs": 4, + }, + ] diff --git a/tests/ops/test_pipeline.py b/tests/ops/test_pipeline.py index 3c69a87..98d7c6e 100644 --- a/tests/ops/test_pipeline.py +++ b/tests/ops/test_pipeline.py @@ -5,7 +5,7 @@ import pyarrow.parquet as pq # type: ignore -from pipedata.core import Stream, ops +from pipedata.core import Chain, Stream, ops from pipedata.ops import json_records, parquet_writer, zipped_files @@ -52,3 +52,41 @@ def test_zipped_files() -> None: "a": [1, 3, 5, 7, 9, 11], "b": [2, 4, 6, 8, 10, 12], } + + +def test_zipped_file_contents() -> None: + contents = """ + + John + 30 + + + Smith + 40 + + """ + + with tempfile.TemporaryDirectory() as temp_dir: + zip_path = Path(temp_dir) / "test.zip" + + with zipfile.ZipFile(zip_path, "w") as zip_file: + zip_file.writestr("test.txt", contents) + zip_file.writestr("test2.txt", contents) + zip_file.writestr("test3.txt", contents) + + extract_xmls = ( + Chain() + .then(ops.grouper(starter=lambda line: line.strip().startswith(b" Date: Thu, 6 Feb 2025 15:47:27 +0000 Subject: [PATCH 02/12] Fix linting and tests --- src/pipedata/core/links.py | 1 - src/pipedata/core/ops.py | 2 +- tests/core/test_chain.py | 39 ++++++++++++++++++++++++++++++++------ tests/ops/test_pipeline.py | 11 ++++++----- 4 files changed, 40 insertions(+), 13 deletions(-) diff --git a/src/pipedata/core/links.py b/src/pipedata/core/links.py index 292e18a..1bf08e5 100644 --- a/src/pipedata/core/links.py +++ b/src/pipedata/core/links.py @@ -1,4 +1,3 @@ -from dataclasses import dataclass from typing import ( Callable, Generic, diff --git a/src/pipedata/core/ops.py b/src/pipedata/core/ops.py index 0ac7360..8b10418 100644 --- a/src/pipedata/core/ops.py +++ b/src/pipedata/core/ops.py @@ -63,7 +63,7 @@ def __init__( starter: Optional[Callable[[TEnd], bool]] = None, ender: Optional[Callable[[TEnd], bool]] = None, ) -> None: - def grouper_(previous_step: Iterator[TEnd]) -> Iterator[TOther]: + def grouper_(previous_step: Iterator[TEnd]) -> Iterator[list[TEnd]]: group: list[TEnd] = [] for element in previous_step: if starter is not None and starter(element) and len(group) > 0: diff --git a/tests/core/test_chain.py b/tests/core/test_chain.py index 3730cda..d4dcdf0 100644 --- a/tests/core/test_chain.py +++ b/tests/core/test_chain.py @@ -229,8 +229,10 @@ def add_values(values: Tuple[int, ...]) -> int: def test_chain_iterables() -> None: - chain = Chain[int]().then(ops.chain_iterables()) - result = list(chain(iter([iter([0, 1]), iter([2, 3])]))) + # TODO: make typing work with chain_iterables + chain = Chain[int]().then(ops.chain_iterables()) # type: ignore + inputs = iter([iter([0, 1]), iter([2, 3])]) + result = list(chain(inputs)) # type: ignore assert result == [0, 1, 2, 3] assert chain.get_counts() == [ { @@ -247,10 +249,13 @@ def test_chain_iterables() -> None: def test_chain_grouper() -> None: - chain = ( - Chain[int]() - .then(ops.grouper(starter=lambda x: x == 1, ender=lambda x: x == 3)) - ) + def is_one(val: int) -> bool: + return val == 1 + + def is_three(val: int) -> bool: + return val == 3 # noqa: PLR2004 + + chain = Chain[int]().then(ops.grouper(starter=is_one, ender=is_three)) inputs = [1, 2, 3, 4, 1, 2, 3, 4] result = list(chain(iter(inputs))) assert result == [[1, 2, 3], [4], [1, 2, 3], [4]] @@ -266,3 +271,25 @@ def test_chain_grouper() -> None: "outputs": 4, }, ] + + +def test_chain_grouper_no_end() -> None: + def is_four(val: int) -> bool: + return val == 4 # noqa: PLR2004 + + chain = Chain[int]().then(ops.grouper(ender=is_four)) + inputs = [1, 2, 3, 4, 1, 2, 3, 4] + result = list(chain(iter(inputs))) + assert result == [[1, 2, 3, 4], [1, 2, 3, 4]] + assert chain.get_counts() == [ + { + "name": "_identity", + "inputs": 8, + "outputs": 8, + }, + { + "name": "grouper_", + "inputs": 8, + "outputs": 2, + }, + ] diff --git a/tests/ops/test_pipeline.py b/tests/ops/test_pipeline.py index 98d7c6e..349ed2b 100644 --- a/tests/ops/test_pipeline.py +++ b/tests/ops/test_pipeline.py @@ -66,6 +66,7 @@ def test_zipped_file_contents() -> None: """ + # Note: can't do type checking with lambdas with tempfile.TemporaryDirectory() as temp_dir: zip_path = Path(temp_dir) / "test.zip" @@ -76,17 +77,17 @@ def test_zipped_file_contents() -> None: extract_xmls = ( Chain() - .then(ops.grouper(starter=lambda line: line.strip().startswith(b" Date: Thu, 6 Feb 2025 15:57:26 +0000 Subject: [PATCH 03/12] Pin poetry version in github test action --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 185ce96..0eccb28 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -50,7 +50,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Bootstrap poetry - run: curl -sSL https://install.python-poetry.org | python - -y + run: curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.4 python - -y - name: Configure poetry run: poetry config virtualenvs.in-project true From 79651e8998e6080d95a0aae3e8bbf66fee010ab0 Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:04:39 +0000 Subject: [PATCH 04/12] Update dependencies --- .github/workflows/publish.yml | 2 +- poetry.lock | 803 ++++++++++++++++++++-------------- pyproject.toml | 7 +- 3 files changed, 484 insertions(+), 328 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 4f1ea64..a81d8c3 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -27,7 +27,7 @@ jobs: - 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[tool.poetry.group.ops.dependencies] fsspec = [ @@ -47,10 +47,7 @@ pyarrow = [ ] # We don't have a direct numpy dependency, but pyarrow depends on numpy # and numpy has python version constraints with python 3.12 -numpy = [ - { version = "<1.25.0", python = "<3.9" }, - { version = ">1.25.0", python = ">=3.12" } -] +numpy = ">=2.0" [tool.poetry.group.lint.dependencies] black = "^23.9.1" From d3d8f5498fc66656a1e7e52d51d2d8298a65fa7c Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:15:11 +0000 Subject: [PATCH 07/12] Remove lower dependency testing --- Makefile | 3 --- scripts/test_dependency_versions.sh | 11 ----------- 2 files changed, 14 deletions(-) diff --git a/Makefile b/Makefile index 08ff935..bfe0bda 100644 --- a/Makefile +++ b/Makefile @@ -29,9 +29,6 @@ test: prepare .PHONY: test-python-versions test-python-versions: - poetry env use python3.8 - make test - poetry env use python3.9 make test diff --git a/scripts/test_dependency_versions.sh b/scripts/test_dependency_versions.sh index f59708c..30a6bd7 100755 --- a/scripts/test_dependency_versions.sh +++ b/scripts/test_dependency_versions.sh @@ -8,17 +8,6 @@ main() { PYTHON_MINOR_VERSION=$(poetry run python -c 'import sys; version=sys.version_info[:3]; print("{1}".format(*version))') echo "Python minor version: $PYTHON_MINOR_VERSION" - # The errors are mostly / all installation errors, - # about building from source. Could lower - # the requirements if able to build from source. - if (( $PYTHON_MINOR_VERSION < "11" )); then - poetry run pip install pyarrow==9.0.0 - poetry run python -m pytest - - poetry run pip install pyarrow==10.0.0 - poetry run python -m pytest - fi - if (( $PYTHON_MINOR_VERSION < "12" )); then poetry run pip install pyarrow==11.0.0 poetry run python -m pytest From cb58d062231365c037aa9c516142087055f2dc2b Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:17:34 +0000 Subject: [PATCH 08/12] Remove lower dependency testing --- poetry.lock | 2 +- pyproject.toml | 2 +- scripts/test_dependency_versions.sh | 6 ------ 3 files changed, 2 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index bfca5eb..f5a14f1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -640,4 +640,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "aec02b2a3ebc61cbb53f09dd12c2467914a1a7e9c9ad10286b0b7fe5c2171317" +content-hash = "6ddd17a13d7c6ce29d0c9452ed2b089946c51cac62c8a4bf5fe5b13ff953c3b6" diff --git a/pyproject.toml b/pyproject.toml index 6233eea..0aec96f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ fsspec = [ ] ijson = "^3.0.0" pyarrow = [ - { version = ">=11.0.0", python = "<3.13" }, + { version = ">=14.0.0", python = "<3.13" }, { version = ">=18.0.0", python = ">=3.13" }, ] # We don't have a direct numpy dependency, but pyarrow depends on numpy diff --git a/scripts/test_dependency_versions.sh b/scripts/test_dependency_versions.sh index 30a6bd7..d6751b3 100755 --- a/scripts/test_dependency_versions.sh +++ b/scripts/test_dependency_versions.sh @@ -9,12 +9,6 @@ main() { echo "Python minor version: $PYTHON_MINOR_VERSION" if (( $PYTHON_MINOR_VERSION < "12" )); then - poetry run pip install pyarrow==11.0.0 - poetry run python -m pytest - - poetry run pip install pyarrow==13.0.0 - poetry run python -m pytest - poetry run pip install fsspec==0.9.0 poetry run python -m pytest fi From 67a2036ff2c42699c40cf07b623bd562044b2b29 Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:21:01 +0000 Subject: [PATCH 09/12] Remove lower dependency testing --- poetry.lock | 2 +- pyproject.toml | 2 +- scripts/test_dependency_versions.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index f5a14f1..4791e2b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -640,4 +640,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "6ddd17a13d7c6ce29d0c9452ed2b089946c51cac62c8a4bf5fe5b13ff953c3b6" +content-hash = "909d33af2a7aa89ff33665e429eec6ea5bac3715bfaac58e6c06eef955c78517" diff --git a/pyproject.toml b/pyproject.toml index 0aec96f..a502574 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ fsspec = [ ] ijson = "^3.0.0" pyarrow = [ - { version = ">=14.0.0", python = "<3.13" }, + { version = ">=16.0.0", python = "<3.13" }, { version = ">=18.0.0", python = ">=3.13" }, ] # We don't have a direct numpy dependency, but pyarrow depends on numpy diff --git a/scripts/test_dependency_versions.sh b/scripts/test_dependency_versions.sh index d6751b3..592e577 100755 --- a/scripts/test_dependency_versions.sh +++ b/scripts/test_dependency_versions.sh @@ -13,7 +13,7 @@ main() { poetry run python -m pytest fi - poetry run pip install pyarrow==14.0.0 + poetry run pip install pyarrow==16.0.0 poetry run python -m pytest poetry run pip install ijson==3.0.0 From 75a7a7dd3b0af9124b601db691dd17f6cad64ce9 Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:25:47 +0000 Subject: [PATCH 10/12] Bump version to 0.4 --- pyproject.toml | 2 +- src/pipedata/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a502574..bc82d07 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "pipedata" -version = "0.3" +version = "0.4" description = "Framework for building pipelines for data processing" authors = ["Simon Wicks "] readme = "README.md" diff --git a/src/pipedata/__init__.py b/src/pipedata/__init__.py index d412d09..63a9b71 100644 --- a/src/pipedata/__init__.py +++ b/src/pipedata/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.3" +__version__ = "0.4" __all__ = [ "__version__", From e173b147bffdb3d1b635fd6694bd84501d3f9557 Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:31:40 +0000 Subject: [PATCH 11/12] Update dependency testing for python 3.13 --- scripts/test_dependency_versions.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/scripts/test_dependency_versions.sh b/scripts/test_dependency_versions.sh index 592e577..4e0741c 100755 --- a/scripts/test_dependency_versions.sh +++ b/scripts/test_dependency_versions.sh @@ -13,8 +13,10 @@ main() { poetry run python -m pytest fi - poetry run pip install pyarrow==16.0.0 - poetry run python -m pytest + if (( $PYTHON_MINOR_VERSION < "13" )); then + poetry run pip install pyarrow==16.0.0 + poetry run python -m pytest + fi poetry run pip install ijson==3.0.0 poetry run python -m pytest From eb712a36af2c859b724daf99c98fbee1a024e21e Mon Sep 17 00:00:00 2001 From: simw Date: Thu, 6 Feb 2025 16:36:08 +0000 Subject: [PATCH 12/12] Update dependency testing for python 3.13 --- poetry.lock | 56 +---------------------------- pyproject.toml | 8 +---- scripts/test_dependency_versions.sh | 5 --- 3 files changed, 2 insertions(+), 67 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4791e2b..d5dd8eb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -376,60 +376,6 @@ files = [ {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"}, ] -[[package]] -name = "numpy" -version = "2.0.2" -description = "Fundamental package for array computing in Python" -optional = false -python-versions = ">=3.9" -files = [ - 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if (( $PYTHON_MINOR_VERSION < "12" )); then - poetry run pip install fsspec==0.9.0 - poetry run python -m pytest - fi - if (( $PYTHON_MINOR_VERSION < "13" )); then poetry run pip install pyarrow==16.0.0 poetry run python -m pytest