migrate to uv, update arf dependency

.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        

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"

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",

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

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,
                         )
 
 

arfx/pcmio.py

@@ -40,7 +40,7 @@ def __init__(
         dtype="h",
         nchannels=1,
         byteorder="<",
-        **kwargs
+        **kwargs,
     ):
         from numpy import dtype as ndtype
 

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
 

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 = "[email protected]"},
+]
+maintainers = [
+    {name = "C Daniel Meliza", email = "[email protected]"},
+]
+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"]