next gen linting with ruff + only using pyproject.toml + pack/unpack …

…functions have option bitorder and parallel + mypy

.github/workflows/ci.yml

@@ -14,34 +14,34 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.8', '3.9']
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install it
       run: |
         python -m pip install -U pip setuptools wheel
-        python -m pip install -e .[tests]
-    - name: Lint with flake8
+        python -m pip install .[tests] -v
+    - name: Lint with Ruff
+      uses: chartboost/ruff-action@v1
+      with:
+        args: "check"
+    - name: Check types with mypy
       run: |
-        pip install flake8 wemake-python-styleguide
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --statistics
-    - name: Run pytest and Generate coverage report
+        mypy --strict ./sigpyproc/
+    - name: Test with pytest and Generate coverage report
       run: |
-        pip install pytest pytest-cov
         pytest --cov=./ --cov-report=xml
       continue-on-error: false
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         name: codecov-umbrella
         fail_ci_if_error: true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -69,6 +69,9 @@ docs/jupyter_execute/
 .dmypy.json
 dmypy.json
 
+# ruff
+.ruff_cache/
+
 # Mr Developer
 .mr.developer.cfg
 .project

pyproject.toml

@@ -1,35 +1,99 @@
 [build-system]
-requires = [
-    "setuptools>=47",
-    "wheel",
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sigpyproc"
+version = "1.1.0"
+description = "Python FRB/pulsar data toolbox"
+readme = "README.md"
+authors = [{ name = "Ewan Barr", email = "ewan.d.barr@gmail.com" }]
+maintainers = [{ name = "Pravir Kumar", email = "pravirka@gmail.com" }]
+requires-python = ">=3.8"
+classifiers = [
+    "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",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Astronomy",
+]
+dependencies = [
+    "numpy",
+    "numba",
+    "astropy",
+    "h5py",
+    "bottleneck",
+    "attrs",
+    "click",
+    "rich",
+    "bidict",
+    "typing_extensions",
 ]
 
-build-backend = "setuptools.build_meta"
+[project.urls]
+Repository = "https://github.com/FRBs/sigpyproc3"
 
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "pytest-cov",
+    "pytest-randomly",
+    "pytest-sugar",
+    "pytest-benchmark",
+    "mypy",
+]
+docs = ["sphinx", "sphinx-book-theme", "sphinx-click", "myst-nb"]
+develop = ["ruff"]
 
-[tool.black]
-line-length = 90
-target_version = ['py38', 'py39', 'py310']
+[project.scripts]
+spp_header = "sigpyproc.apps.spp_header:main"
+spp_decimate = "sigpyproc.apps.spp_decimate:main"
+spp_extract = "sigpyproc.apps.spp_extract:main"
+spp_clean = "sigpyproc.apps.spp_clean:main"
 
 
-[tool.pytest.ini_options]
-minversion = "6.0"
-testpaths = [
-    "tests",
-]
+[tool.ruff]
+include = ["pyproject.toml", "sigpyproc/**/*.py"]
+line-length = 88
+indent-width = 4
+target-version = "py39"
 
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = ["D1", "ANN1", "PLR2004"]
+
+[tool.ruff.lint.pylint]
+max-args = 10
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+
+[tool.pytest.ini_options]
+minversion = "8.0"
+testpaths = "tests"
 
 [tool.coverage.paths]
 source = ["./sigpyproc/"]
 
 [tool.coverage.run]
 omit = [
-    '*tests*',
-    '*docs*',
-    '*apps*',
-    '*setup.py',
-    '*__init__.py',
-    '*sigpyproc/core/kernels.py',
+    "tests/*",
+    "docs/*",
+    "apps/*",
+    "*__init__.py",
+    "sigpyproc/core/kernels.py",
 ]
 
 [tool.coverage.report]
@@ -38,7 +102,6 @@ show_missing = true
 ignore_errors = true
 exclude_lines = ['raise AssertionError', 'raise NotImplementedError']
 
-
 [tool.mypy]
 ignore_missing_imports = true
 plugins = ["numpy.typing.mypy_plugin"]

sigpyproc/apps/spp_clean.py

@@ -4,7 +4,7 @@
 
 
 @click.command(
-    context_settings=dict(help_option_names=["-h", "--help"], show_default=True)
+    context_settings={"help_option_names": ["-h", "--help"], "show_default": True},
 )
 @click.argument("filfile", type=click.Path(exists=True))
 @click.option(
@@ -15,24 +15,45 @@
     help="RFI cleaning method to use.",
 )
 @click.option(
-    "-t", "--threshold", type=float, default=3.0, help="Sigma threshold for RFI cleaning."
+    "-t",
+    "--threshold",
+    type=float,
+    default=3.0,
+    help="Sigma threshold for RFI cleaning.",
 )
 @click.option(
-    "-g", "--gulp", type=int, default=16384, help="Number of samples to read at once"
+    "-g",
+    "--gulp",
+    type=int,
+    default=16384,
+    help="Number of samples to read at once",
 )
 @click.option(
-    "-o", "--outfile", type=click.Path(exists=False), help="Output masked filterbank file"
+    "-o",
+    "--outfile",
+    type=click.Path(exists=False),
+    help="Output masked filterbank file",
 )
 @click.option(
-    "--save/--no-save", default=True, help="Save the mask information to a file"
+    "--save/--no-save",
+    default=True,
+    help="Save the mask information to a file",
 )
 def main(
-    filfile: str, method: str, threshold: float, outfile: str, gulp: int, save: bool
+    filfile: str,
+    method: str,
+    threshold: float,
+    outfile: str,
+    gulp: int,
+    save: bool,  # noqa: FBT001
 ) -> None:
     """Clean RFI from filterbank data."""
     fil = FilReader(filfile)
     _out_file, rfimask = fil.clean_rfi(
-        method=method, threshold=threshold, filename=outfile, gulp=gulp
+        method=method,
+        threshold=threshold,
+        filename=outfile,
+        gulp=gulp,
     )
     if save:
         rfimask.to_file()