From 6b37ea9ed152efbe220d4231579c3a3949e4b5ef Mon Sep 17 00:00:00 2001 From: Dan Meliza Date: Thu, 2 Jan 2025 10:42:32 -0500 Subject: [PATCH] migrate to uv, update arf dependency --- .github/workflows/build_wheels.yml | 36 -- .github/workflows/python-package.yml | 32 +- arfx/__init__.py | 7 +- arfx/core.py | 9 +- arfx/lblio.py | 2 +- arfx/oephys.py | 6 +- arfx/pcmio.py | 2 +- arfx/select.py | 2 +- pyproject.toml | 106 ++++- setup.cfg | 65 --- uv.lock | 567 +++++++++++++++++++++++++++ 11 files changed, 696 insertions(+), 138 deletions(-) delete mode 100644 .github/workflows/build_wheels.yml delete mode 100644 setup.cfg create mode 100644 uv.lock diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml deleted file mode 100644 index 226483d..0000000 --- a/.github/workflows/build_wheels.yml +++ /dev/null @@ -1,36 +0,0 @@ -name: Build wheels - -on: [push, pull_request] - -jobs: - build: - name: Build source and wheels - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Build wheels - run: pipx run build - - uses: actions/upload-artifact@v4 - with: - path: ./dist/* - - upload_pypi: - needs: build - runs-on: ubuntu-latest - # upload to PyPI on every tag starting with 'v' - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') - # alternatively, to publish when a GitHub Release is created, use the following rule: - # if: github.event_name == 'release' && github.event.action == 'published' - steps: - - uses: actions/download-artifact@v4 - with: - # unpacks default artifact into dist/ - # if `name: artifact` is omitted, the action will create extra parent dir - name: artifact - path: dist - - - uses: pypa/gh-action-pypi-publish@v1.10.2 - with: - user: __token__ - password: ${{ secrets.pypi_password }} - #repository_url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 844bfe8..c329528 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,6 +1,3 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - name: Python tests on: [push, pull_request] @@ -12,22 +9,19 @@ jobs: matrix: os: [macos-13, macos-14, ubuntu-latest, windows-latest] # can't do pypy - no support for h5py - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] - exclude: - - os: macos-14 - python-version: "3.7" + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip setuptools wheel - pip install -e .[test] - - name: Test with pytest - run: | - pytest -v + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: uv sync --frozen + - name: Run tests + run: uv run pytest diff --git a/arfx/__init__.py b/arfx/__init__.py index 1d8f9b1..2bbc05c 100644 --- a/arfx/__init__.py +++ b/arfx/__init__.py @@ -5,5 +5,10 @@ operations involving single channel datasets, though it can also be used to copy entire entries between ARF files. """ +try: + from importlib.metadata import version -__version__ = "2.6.16" + __version__ = version("arfx") +except Exception: + # If package is not installed (e.g. during development) + __version__ = "unknown" diff --git a/arfx/core.py b/arfx/core.py index a7a62ca..f727b8e 100644 --- a/arfx/core.py +++ b/arfx/core.py @@ -573,6 +573,13 @@ def setup_log(log, debug=False): log.addHandler(ch) +def datatype_list(): + out = str(arf.DataTypes.__doc__) + for dtype in arf.DataTypes: + out += f"\n{dtype.name}:{dtype.value}" + return out + + def arfx(): p = argparse.ArgumentParser( description="copy data in and out of ARF files", @@ -584,7 +591,7 @@ def arfx(): "--help-datatypes", help="print available datatypes and exit", action="version", - version=arf.DataTypes._doc(), + version=datatype_list(), ) p.add_argument( "--help-formats", diff --git a/arfx/lblio.py b/arfx/lblio.py index 10c541f..005c57a 100644 --- a/arfx/lblio.py +++ b/arfx/lblio.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -*- mode: python -*- -"""Read and write lbl format files. +"""Read and write lbl format files. lbl is a format developed by the Margoliash lab. It's not a very good or flexible format, but it's what the venerable data inspection and labeling diff --git a/arfx/oephys.py b/arfx/oephys.py index ad61a3d..c9a0e46 100644 --- a/arfx/oephys.py +++ b/arfx/oephys.py @@ -330,7 +330,7 @@ def script(argv=None): name=rec_name, timestamp=timestamp, entry_creator="org.meliza.arfx/arfx-oephys " + core.__version__, - **rec.attrs + **rec.attrs, ) if args.attrs is not None: arf.set_attributes(entry, **args.attrs) @@ -371,7 +371,7 @@ def script(argv=None): datatype=args.datatype, offset=dset.offset, sampling_rate=dset.sampling_rate, - **info + **info, ) datasets.append((idx, tgt)) if len(datasets) == 0: @@ -398,7 +398,7 @@ def script(argv=None): datatype=arf.DataTypes.EVENT, sampling_rate=dset.sampling_rate, units=dset.units, - **dset.attrs + **dset.attrs, ) diff --git a/arfx/pcmio.py b/arfx/pcmio.py index dfdd4eb..85b34e4 100644 --- a/arfx/pcmio.py +++ b/arfx/pcmio.py @@ -40,7 +40,7 @@ def __init__( dtype="h", nchannels=1, byteorder="<", - **kwargs + **kwargs, ): from numpy import dtype as ndtype diff --git a/arfx/select.py b/arfx/select.py index 4169d96..c357e54 100644 --- a/arfx/select.py +++ b/arfx/select.py @@ -118,7 +118,7 @@ def main(argv=None): name, selected, offset=offset + src_dset_offset, - **src_dset_attrs + **src_dset_attrs, ) tgt_entry_index += 1 diff --git a/pyproject.toml b/pyproject.toml index 50de0ba..3131849 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,18 +1,104 @@ [build-system] -requires = ["setuptools", "wheel"] +requires = ["hatchling"] +build-backend = "hatchling.build" -build-backend = "setuptools.build_meta" +[project] +name = "arfx" +version = "2.7.0" +description = "Advanced Recording Format Tools" +readme = "README.rst" +requires-python = ">=3.8" +license = {text = "BSD 3-Clause License"} +authors = [ + {name = "C Daniel Meliza", email = "dan@meliza.org"}, +] +maintainers = [ + {name = "C Daniel Meliza", email = "dan@meliza.org"}, +] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Programming Language :: Python", + "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", + "Topic :: Scientific/Engineering", + "Operating System :: Unix", + "Operating System :: POSIX :: Linux", + "Operating System :: MacOS :: MacOS X", + "Operating System :: Microsoft :: Windows", + "Natural Language :: English" +] +dependencies = [ + "arf>=2.7.0", + "ewave>=1.0.7", + "tqdm", + "natsort", +] + +[project.urls] +Homepage = "https://github.com/melizalab/arfx" + +[project.scripts] +arfx = "arfx.core:arfx" +arfx-split = "arfx.splitter:main" +arfx-select = "arfx.select:main" +arfx-collect-sampled = "arfx.collect:collect_sampled_script" +arfx-oephys = "arfx.oephys:script" + +[project.entry-points."arfx.io"] +".pcm" = "arfx.pcmio:pcmfile" +".dat" = "arfx.pcmio:pcmfile" +".npy" = "arfx.npyio:npyfile" +".mda" = "arfx.mdaio:mdafile" +".wav" = "ewave:wavfile" + + +[dependency-groups] +dev = [ + "pytest>=8.3.3,<9", + "pytest-cov >= 4.1.0", + "ruff>=0.7.0" +] + +[tool.pytest.ini_options] +python_files = ["test_*.py", "*_test.py"] +addopts = "-v --cov=arfx --cov-report=term-missing" +testpaths = ["test"] + +[tool.black] +line-length = 88 +target-version = ["py38"] +include = '\.pyi?$' [tool.ruff] -target-version = "py37" +line-length = 88 +target-version = "py38" +extend-exclude = ["build", "attic"] [tool.ruff.lint] -extend-select = [ - "B", # flake8-bugbear - "I", # isort - "PGH", # pygrep-hooks - "RUF", # Ruff-specific - "NPY201", # numpy 2.0 migration +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # pyflakes + "I", # isort + "B", # flake8-bugbear ] -preview = true +ignore = ["E221", "E501", "E701"] + +[tool.ruff.lint.per-file-ignores] +"__init__.py" = ["F401"] + +[tool.mypy] +python_version = "3.8" +ignore_missing_imports = true +strict_optional = true +check_untyped_defs = true +[tool.hatch.build] +include = ["arfx/**"] +exclude = ["*test*"] +artifacts = ["README.rst"] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 22d74da..0000000 --- a/setup.cfg +++ /dev/null @@ -1,65 +0,0 @@ -[pep8] -ignore=E221,E501,E701 - -[metadata] -name = arfx -version = attr: arfx.__version__ -description = Advanced Recording Format Tools -long_description = file: README.rst -long_description_content_type = text/x-rst -license = BSD 3-Clause License -classifiers = - Development Status :: 5 - Production/Stable - Intended Audience :: Science/Research - License :: OSI Approved :: BSD License - Programming Language :: Python - 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 - Topic :: Scientific/Engineering - Operating System :: Unix - Operating System :: POSIX :: Linux - Operating System :: MacOS :: MacOS X - Operating System :: Microsoft :: Windows - Natural Language :: English -author = Dan Meliza -author_email = dan@meliza.org -maintainer = Dan Meliza -maintainer_email = dan@meliza.org -url = https://github.com/melizalab/arfx - -[options] -zip_safe = false -packages = arfx -python_requires = >= 3.8 -setup_requires = - setuptools >=58.1.0 -install_requires = - arf >=2.6.7 - ewave >=1.0.7 - tqdm - natsort -test_suite = tests - -[options.extras_require] -test = - pytest >= 7.0 - -[options.entry_points] -console_scripts = - arfx = arfx.core:arfx - arfx-split = arfx.splitter:main - arfx-select = arfx.select:main - arfx-collect-sampled = arfx.collect:collect_sampled_script - arfx-oephys = arfx.oephys:script -arfx.io = - .pcm = arfx.pcmio:pcmfile - .dat = arfx.pcmio:pcmfile - .npy = arfx.npyio:npyfile - .mda = arfx.mdaio:mdafile - .wav = ewave:wavfile - 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