Merge branch 'main' into pre-commit-ci-update-config

.pre-commit-config.yaml

@@ -27,39 +27,11 @@ repos:
  - id: requirements-txt-fixer
  - id: sort-simple-yaml
  - id: trailing-whitespace
- - repo: https://github.com/asottile/pyupgrade
- rev: v3.15.2
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.4.5
  hooks:
- - id: pyupgrade
- args: [--py38-plus]
- - repo: https://github.com/asottile/yesqa
- rev: v1.5.0
- hooks:
- - id: yesqa
- - repo: https://github.com/pycqa/isort
- rev: 5.13.2
- hooks:
- - id: isort
- args: [--profile, black, --float-to-top, --color]
- - repo: https://github.com/psf/black
- rev: 24.4.2
- hooks:
- - id: black
- - repo: https://github.com/PyCQA/autoflake
- rev: v2.3.1
- hooks:
- - id: autoflake
- - repo: https://github.com/PyCQA/flake8
- rev: 7.0.0
- hooks:
- - id: flake8
- additional_dependencies: [flake8-bugbear]
- args: ["--ignore=W503,B015,B028"]
- - repo: https://github.com/PyCQA/bandit
- rev: 1.7.8
- hooks:
- - id: bandit
- args: [--skip, "B101"]
+ - id: ruff
+ - id: ruff-format
  - repo: https://github.com/codespell-project/codespell
  rev: v2.3.0
  hooks:
@@ -82,17 +54,6 @@ repos:
  - id: nbqa-check-ast
  additional_dependencies: [pre-commit-hooks]
  args: [--nbqa-dont-skip-bad-cells]
- - id: nbqa-pyupgrade
- additional_dependencies: [pyupgrade==v3.15.0]
- args: [--py37-plus]
- - id: nbqa-isort
- additional_dependencies: [isort==5.13.2]
- args: [--profile=black, --float-to-top]
- - id: nbqa-black
- additional_dependencies: [black==24.1.1]
- - id: nbqa-pydocstyle
- additional_dependencies: [pydocstyle==6.3.0]
- args: ["--ignore=D100,D103"]
- - id: nbqa-flake8
- additional_dependencies: [flake8==7.0.0, flake8-bugbear]
- args: [--max-line-length=88, "--ignore=E203,E722,F821,W503,B001,B015"]
+ - id: nbqa-ruff
+ additional_dependencies: [ruff==v0.4.5]
+ args: ["--ignore=E722,F821,S110"]

CONTRIBUTING.md

@@ -7,7 +7,6 @@ Please follow these guidelines when contributing to this project.
 ## Developer Instructions
 
 ```bash
-pip install -r requirements.txt
 pip install -r requirements-dev.txt
 python setup.py develop
 
@@ -30,6 +29,12 @@ new code, and it can also be run at any time using the following command:
 pre-commit run --all
 ```
 
+or run on any files not yet committed to the repository using
+
+```bash
+pre-commit run --files <filename1> <filename2> ...
+```
+
 ### Running the tests
 
 (Requires `requirements-dev.txt` to be installed)

README.md

@@ -1,10 +1,11 @@
 # becquerel
 
-[![tests](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml/badge.svg?branch=)](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml)
-[![Coverage Status](https://coveralls.io/repos/github/lbl-anp/becquerel/badge.svg?branch=main)](https://coveralls.io/github/lbl-anp/becquerel?branch=main)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![PyPI version](https://img.shields.io/pypi/v/becquerel.svg)](https://pypi.org/project/becquerel)
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/becquerel.svg)](https://pypi.org/project/becquerel)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![PyPI license](https://img.shields.io/pypi/l/becquerel.svg)](https://pypi.python.org/project/becquerel)
+[![tests](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml/badge.svg?branch=)](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml)
+[![Coverage Status](https://coveralls.io/repos/github/lbl-anp/becquerel/badge.svg?branch=main)](https://coveralls.io/github/lbl-anp/becquerel?branch=main)
 
 Becquerel is a Python package for analyzing nuclear spectroscopic
 measurements. The core functionalities are reading and writing different
@@ -50,12 +51,13 @@ The dependencies `beautifulsoup4`, `lxml` and `html5lib` are necessary for
 [`pandas`][1].
 
 Developers require additional requirements which are listed in
-`requirements-dev.txt`. We use [`pytest`][2] for unit testing, [`black`][3] for
-code formatting and are converting to [`numpydoc`][4].
+`requirements-dev.txt`. We use [`pytest`][2] for unit testing, [`ruff`][3] for
+code formatting and linting, and are planning to eventually support
+[`numpydoc`][4] docstrings.
 
 [1]: https://pandas.pydata.org/pandas-docs/stable/install.html#dependencies
 [2]: https://docs.pytest.org/en/latest/
-[3]: https://black.readthedocs.io/en/stable/
+[3]: https://docs.astral.sh/ruff/
 [4]: https://numpydoc.readthedocs.io/en/latest/format.html
 
 ## Copyright Notice

becquerel/__init__.py

@@ -34,44 +34,44 @@
 warnings.simplefilter("default", DeprecationWarning)
 
 __all__ = [
- "__description__",
- "__url__",
- "__version__",
- "__license__",
- "__copyright__",
- "core",
- "utils",
- "fitting",
  "AutoCalibrator",
  "AutoCalibratorError",
- "LinearEnergyCal",
- "EnergyCalError",
  "BadInput",
  "Calibration",
  "CalibrationError",
  "CalibrationWarning",
+ "Element",
+ "EnergyCalError",
  "Fitter",
+ "GaussianPeakFilter",
+ "Isotope",
+ "IsotopeQuantity",
+ "LinearEnergyCal",
  "PeakFilter",
  "PeakFilterError",
- "GaussianPeakFilter",
  "PeakFinder",
  "PeakFinderError",
- "SpectrumPlotter",
  "PlottingError",
- "rebin",
  "RebinError",
  "RebinWarning",
  "Spectrum",
  "SpectrumError",
- "UncalibratedError",
+ "SpectrumPlotter",
  "SpectrumWarning",
+ "UncalibratedError",
  "UncertaintiesError",
+ "__copyright__",
+ "__description__",
+ "__license__",
+ "__url__",
+ "__version__",
+ "core",
+ "fitting",
+ "materials",
+ "nndc",
  "parsers",
+ "rebin",
  "tools",
- "nndc",
+ "utils",
  "xcom",
- "materials",
- "Element",
- "Isotope",
- "IsotopeQuantity",
 ]

becquerel/__metadata__.py

@@ -1,6 +1,5 @@
 """becquerel package metadata."""
 
-__name__ = "becquerel"
 __author__ = "The Becquerel Development Team"
 __maintainer__ = __author__
 __email__ = "[email protected]"

becquerel/core/autocal.py

@@ -141,7 +141,7 @@ def find_best_gain(
  snrs = np.array(snrs)
  n_req = len(required_energies)
  # make sure the required and optional sets do not overlap
- optional = sorted(list(set(optional) - set(required_energies)))
+ optional = sorted(set(optional) - set(required_energies))
  n_opt = len(optional)
  n_set = n_req + n_opt
  best_fom = None
@@ -187,9 +187,9 @@ def find_best_gain(
  "Valid calibration found:\n"
  f"FOM: {fom:15.9f}"
  f" gain: {gain:6.3f}"
- f" ergs: {str(comb_erg):50s}"
- f" de: {str(de):50s}"
- f" chans: {str(comb_chan):40s}"
+ f" ergs: {comb_erg!s:50s}"
+ f" de: {de!s:50s}"
+ f" chans: {comb_chan!s:40s}"
  )
  if best_fom is None:
  best_fom = fom + 1.0
@@ -204,15 +204,15 @@ def find_best_gain(
  "Best calibration so far:\n"
  f"FOM: {best_fom:15.9f}"
  f" gain: {best_gain:6.3f}"
- f" ergs: {str(best_ergs):50s}"
- f" de: {str(de):50s}"
- f" chans: {str(best_chans):40s}"
+ f" ergs: {best_ergs!s:50s}"
+ f" de: {de!s:50s}"
+ f" chans: {best_chans!s:40s}"
  )
  n_set -= 1
  if best_gain is None:
  return None
  else:
- print("found best gain: %f keV/channel" % best_gain)
+ print(f"found best gain: {best_gain:f} keV/channel")
  return {
  "gain": best_gain,
  "channels": best_chans,

becquerel/core/calibration.py

@@ -53,15 +53,15 @@ def _validate_domain_range(domain, rng):
  # must be length-2 iterables
  try:
  len(domain)
- except TypeError:
- raise CalibrationError(f"Domain must be length-2 iterable: {domain}")
+ except TypeError as exc:
+ raise CalibrationError(f"Domain must be length-2 iterable: {domain}") from exc
  domain = np.asarray(domain)
  if not (len(domain) == 2 and domain.ndim == 1):
  raise CalibrationError(f"Domain must be length-2 iterable: {domain}")
  try:
  len(rng)
- except TypeError:
- raise CalibrationError(f"Range must be length-2 iterable: {rng}")
+ except TypeError as exc:
+ raise CalibrationError(f"Range must be length-2 iterable: {rng}") from exc
  rng = np.asarray(rng)
  if not (len(rng) == 2 and rng.ndim == 1):
  raise CalibrationError(f"Range must contain two values: {rng}")
@@ -230,10 +230,10 @@ def _validate_expression(
  # apply black formatting for consistency and error checking
  try:
  expression = black.format_str(expression, mode=black.FileMode())
- except (black.InvalidInput, blib2to3.pgen2.tokenize.TokenError):
+ except (black.InvalidInput, blib2to3.pgen2.tokenize.TokenError) as exc:
  raise CalibrationError(
  f"Error while running black on expression:\n{expression}"
- )
+ ) from exc
 
  # make sure `ind_var` appears in the formula
  if ind_var not in ["x", "y"]:
@@ -252,10 +252,10 @@ def _validate_expression(
  # make sure each parameter appears at least once
  try:
  param_indices = _param_indices(expression)
- except ValueError:
+ except ValueError as exc:
  raise CalibrationError(
  f"Unable to extract indices to parameters:\n{expression}"
- )
+ ) from exc
  if len(param_indices) > 0:
  if param_indices.min() != 0:
  raise CalibrationError(
@@ -288,11 +288,11 @@ def _validate_expression(
  domain=domain,
  rng=rng,
  )
- except CalibrationError:
+ except CalibrationError as exc:
  raise CalibrationError(
  f"Cannot evaluate expression for float {ind_var} = {x_val}:\n"
  f"{expression}\n{safe_eval.symtable['x']}"
- )
+ ) from exc
  try:
  _eval_expression(
  expression,
@@ -303,11 +303,11 @@ def _validate_expression(
  domain=domain,
  rng=rng,
  )
- except CalibrationError:
+ except CalibrationError as exc:
  raise CalibrationError(
  f"Cannot evaluate expression for array {ind_var} = {x_arr}:\n"
  f"{expression}\n{safe_eval.symtable['x']}"
- )
+ ) from exc
 
  return expression.strip()
 
@@ -628,7 +628,7 @@ def __repr__(self):
  if len(self.attrs) > 0:
  for key in self.attrs:
  result += ", "
- result += f"{key}={repr(self.attrs[key])}"
+ result += f"{key}={self.attrs[key]!r}"
  result += ")"
  return result
 
@@ -907,7 +907,7 @@ def read(cls, name):
  -------
  calibration : becquerel.Calibration
  """
- dsets, attrs, skipped = io.h5.read_h5(name)
+ dsets, attrs, _ = io.h5.read_h5(name)
  if "params" not in dsets:
  raise CalibrationError('Expected dataset "params"')
  if "expression" not in dsets:
@@ -1237,7 +1237,7 @@ def plot(self, ax=None):
  has_points = self.points_x.size > 0
 
  if ax is None:
- fig, ax = plt.subplots(1 + has_points, 1, sharex=True)
+ _, ax = plt.subplots(1 + has_points, 1, sharex=True)
 
  if has_points:
  assert ax.shape == (2,)

becquerel/core/energycal.py

@@ -1,4 +1,4 @@
-""""Energy calibration classes"""
+"""Energy calibration classes"""
 
 import warnings
 from abc import ABCMeta, abstractmethod, abstractproperty
@@ -73,8 +73,8 @@ def from_points(cls, chlist, kevlist, include_origin=False):
 
  try:
  cond = len(chlist) != len(kevlist)
- except TypeError:
- raise BadInput("Inputs must be one dimensional iterables")
+ except TypeError as exc:
+ raise BadInput("Inputs must be one dimensional iterables") from exc
  if cond:
  raise BadInput("Channels and energies must be same length")
 
@@ -86,8 +86,8 @@ def from_points(cls, chlist, kevlist, include_origin=False):
  for ch, kev in zip(chlist, kevlist):
  try:
  cal.new_calpoint(ch, kev)
- except (ValueError, TypeError):
- raise BadInput("Inputs must be one dimensional iterables")
+ except (ValueError, TypeError) as exc:
+ raise BadInput("Inputs must be one dimensional iterables") from exc
  cal.update_fit()
  return cal
 
@@ -306,7 +306,7 @@ def plot(self, ax=None):
  has_points = self.channels.size > 0
 
  if ax is None:
- fig, ax = plt.subplots(1 + has_points, 1, sharex=True)
+ _, ax = plt.subplots(1 + has_points, 1, sharex=True)
 
  if has_points:
  assert ax.shape == (2,)
@@ -389,17 +389,21 @@ def slope(self):
 
  try:
  return self._coeffs["b"]
- except KeyError:
- raise EnergyCalError("Slope coefficient not yet supplied or calculated.")
+ except KeyError as exc:
+ raise EnergyCalError(
+ "Slope coefficient not yet supplied or calculated."
+ ) from exc
 
  @property
  def offset(self):
  """Return the offset coefficient value."""
 
  try:
  return self._coeffs["c"]
- except KeyError:
- raise EnergyCalError("Offset coefficient not yet supplied or calculated.")
+ except KeyError as exc:
+ raise EnergyCalError(
+ "Offset coefficient not yet supplied or calculated."
+ ) from exc
 
  def _ch2kev(self, ch):
  """Convert scalar OR np.array of channel(s) to energies.