From 2d5daa4368e8e1eb15e3c815135c0ed2a81f5b13 Mon Sep 17 00:00:00 2001 From: jdidion Date: Fri, 8 Sep 2023 13:37:49 -0700 Subject: [PATCH] 1. Drop support for python 3.6 and 3.7 * Update versions for most dependencies * Update python version matrix in CI workflow 2. Add cgranges as submodule * Add build script to compile cgranges * Update pyproject.toml to call build script, and include cgranges package * Tell mypy to ignore lines that reference cgranges * In CI workflow * Checkout with submodules * Install dev dependencies and build before install * Update poetry version 3. Misc * Put authors list in correct format, drop Nick, add myself * Replace references to `py.path` with `tmp_path` in unit tests --- .github/workflows/pythonpackage.yml | 10 +- .gitmodules | 3 + README.md | 6 +- build.py | 26 + cgranges | 1 + poetry.lock | 1326 ++++++++++++--------------- pybedlite/overlap_detector.py | 4 +- pybedlite/tests/test_pybedlite.py | 25 +- pyproject.toml | 49 +- 9 files changed, 643 insertions(+), 807 deletions(-) create mode 100644 .gitmodules create mode 100644 build.py create mode 160000 cgranges diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index b02eefe..705c7d5 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -2,16 +2,18 @@ name: Python package on: [push] env: - POETRY_VERSION: 1.1.15 + POETRY_VERSION: 1.6.1 jobs: testing: runs-on: ubuntu-20.04 strategy: matrix: - PYTHON_VERSION: ["3.6", "3.7", "3.8", "3.9"] + PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v2 + with: + submodules: 'true' - name: Set up Python ${{matrix.PYTHON_VERSION}} uses: actions/setup-python@v4 @@ -26,8 +28,6 @@ jobs: - name: Install poetry shell: bash run: | - # See: https://github.com/python-poetry/poetry/blob/46bf7fd3d1797b75ad9b07adc280039d93414e07/pyproject.toml#L78-L81 - python -m pip install --upgrade pip urllib3==1.25.10 pip install poetry==${{env.POETRY_VERSION}} - name: Configure poetry @@ -49,6 +49,8 @@ jobs: - name: Install deps shell: bash run: | + poetry install --only dev + poetry build poetry install --extras docs - name: Run pytest diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..0a7daea --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "cgranges"] + path = cgranges + url = https://github.com/lh3/cgranges diff --git a/README.md b/README.md index 8597700..801a5d8 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ required. [rtd-link]: http://pybedlite.readthedocs.org/en/stable -**Requires python 3.6+** +**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3) # Getting Setup for Development Work @@ -62,14 +62,14 @@ required. A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link]. E.g.: ```bash -conda create -n pybedlite python=3.6 poetry +conda create -n pybedlite python=3.8 poetry conda activate pybedlite poetry install ``` If the methods listed above do not work try the following: ```bash -mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.1.15" +mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1" mamba activate pybedlite poetry install ``` diff --git a/build.py b/build.py new file mode 100644 index 0000000..e352c3e --- /dev/null +++ b/build.py @@ -0,0 +1,26 @@ +from setuptools import Extension +from Cython.Build import build_ext + +ext_modules = [ + Extension( + "cgranges", + sources=["cgranges/python/cgranges.pyx", "cgranges/cgranges.c"], + depends=[ + "cgranges/cgranges.h", + "cgranges/khash.h", + "cgranges/python/cgranges.pyx" + ], + include_dirs=["cgranges"] + ) +] + +def build(setup_kwargs): + """ + This function is mandatory in order to build the extensions. + """ + setup_kwargs.update( + { + "ext_modules": ext_modules, + "cmdclass": {"build_ext": build_ext}, + } + ) \ No newline at end of file diff --git a/cgranges b/cgranges new file mode 160000 index 0000000..2fb5a2a --- /dev/null +++ b/cgranges @@ -0,0 +1 @@ +Subproject commit 2fb5a2a8b8876b5328308dcbab5ac54200807709 diff --git a/poetry.lock b/poetry.lock index 88fd220..b3c91a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,228 +1,384 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "main" optional = true -python-versions = "*" - -[[package]] -name = "appdirs" -version = "1.4.4" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "atomicwrites" -version = "1.4.0" -description = "Atomic file writes." 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= cr.cgranges() # type: ignore self._refname_to_indexed[refname] = False self._refname_to_intervals[refname] = [] diff --git a/pybedlite/tests/test_pybedlite.py b/pybedlite/tests/test_pybedlite.py index ac98f77..e9d46f1 100644 --- a/pybedlite/tests/test_pybedlite.py +++ b/pybedlite/tests/test_pybedlite.py @@ -2,7 +2,6 @@ import pytest from pathlib import Path -from py._path.local import LocalPath as TmpDir from typing import List import pybedlite as pybed from pybedlite.bed_writer import MAX_BED_FIELDS @@ -126,9 +125,8 @@ def compare_bed_records( 12, ], ) -def test_bed_parsing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]) -> None: - tmpdir_path = Path(tmpdir) - test_bed = tmpdir_path / "test.bed" +def test_bed_parsing(tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]) -> None: + test_bed = tmp_path / "test.bed" with BedWriter(test_bed, num_fields=bed_field_number) as test_out: test_out.write_all(bed_records, truncate=True, add_missing=True) @@ -157,10 +155,9 @@ def test_bed_parsing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[Be ], ) def test_preopened_bed_parsing( - tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord] + tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord] ) -> None: - tmpdir_path = Path(tmpdir) - test_bed = tmpdir_path / "test.bed" + test_bed = tmp_path / "test.bed" with BedWriter(test_bed, num_fields=bed_field_number) as test_out: test_out.write_all(bed_records, truncate=True, add_missing=True) @@ -190,10 +187,9 @@ def test_preopened_bed_parsing( 12, ], ) -def test_bed_writing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord]) -> None: - tmpdir_path = Path(tmpdir) - test_written_bed = tmpdir_path / "test_written.bed" - test_premade_bed = tmpdir_path / "test_premade.bed" +def test_bed_writing(tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord]) -> None: + test_written_bed = tmp_path / "test_written.bed" + test_premade_bed = tmp_path / "test_premade.bed" with BedWriter(test_written_bed, num_fields=bed_field_number) as test_out: test_out.write_all(bed_records, truncate=True, add_missing=True) @@ -228,11 +224,10 @@ def test_bed_writing(tmpdir: TmpDir, bed_field_number: int, bed_records: List[Be ], ) def test_preopened_bed_writing( - tmpdir: TmpDir, bed_field_number: int, bed_records: List[BedRecord] + tmp_path: Path, bed_field_number: int, bed_records: List[BedRecord] ) -> None: - tmpdir_path = Path(tmpdir) - test_written_bed = tmpdir_path / "test_written.bed" - test_premade_bed = tmpdir_path / "test_premade.bed" + test_written_bed = tmp_path / "test_written.bed" + test_premade_bed = tmp_path / "test_premade.bed" test_written_bed_fh = test_written_bed.open("w") diff --git a/pyproject.toml b/pyproject.toml index db861fc..89d3dfb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,12 @@ [tool.poetry] name = "pybedlite" -version = "0.0.4-dev" +version = "0.0.4-dev1" description = "Python classes for interfacing with bed intervals" -authors = ["Nils Homer", "Tim Fennell", "Nathan Roach"] +authors = [ + "Nils Homer ", + "Tim Fennell ", + "John Didion ", +] license = "MIT" readme = "README.md" homepage = "https://github.com/fulcrumgenomics/pybedlite" @@ -10,39 +14,38 @@ repository = "https://github.com/fulcrumgenomics/pybedlite" keywords = ["bioinformatics"] classifiers = [ "Development Status :: 3 - Alpha", - "Environment :: Console", + "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", + "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics", - "Topic :: Software Development :: Documentation", - "Topic :: Software Development :: Libraries :: Python Modules", -] -include = [ - "LICENSE", + "Topic :: Software Development :: Documentation", + "Topic :: Software Development :: Libraries :: Python Modules", ] +include = ["LICENSE"] +packages = [{ include = "pybedlite" }, { include = "cgranges" }] [tool.poetry.dependencies] -python = ">=3.6.0" -attrs = ">=19.3.0" -typing_extensions = { version = ">=3.7.4", python = "<3.8" } # Literal support -typing_inspect = { version = ">=0.3.1", python = "<3.8" } # inspecting types -sphinx = {version = "4.3.1", optional = true} -Cython = "^0.29.30" -cgranges = {git = "https://github.com/lh3/cgranges.git", rev = "v0.1"} +python = "^3.8.0" +attrs = "^23.0.0" +sphinx = { version = "^7.0.0", optional = true } [tool.poetry.dev-dependencies] -pytest = ">=5.4.2" -mypy = ">=0.770" -flake8 = ">=4.0.1" -black = ">=19.10b0" -pytest-cov = ">=2.8.1" +pytest = "^7.0.0" +mypy = "^1.5.0" +flake8 = "^5.0.0" +black = "^23.0.0" +pytest-cov = "^4.0.0" [tool.poetry.extras] docs = ["sphinx"] +[tool.poetry.build] +script = "build.py" +generate-setup-file = true + [build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api" +requires = ["poetry-core", "setuptools", "cython"] +build-backend = "poetry.core.masonry.api"