Update pre-commit config, fix new issues

.pre-commit-config.yaml

@@ -1,17 +1,28 @@
 repos:
-  # https://pycqa.github.io/isort/docs/configuration/black_compatibility.html#integration-with-pre-commit
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the ref you want to point at
     hooks:
-      - id: isort
-        args: ["--profile", "black", "--filter-files"]
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+    - id: trailing-whitespace
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-merge-conflict
+    - id: end-of-file-fixer
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
     hooks:
-      - id: black-jupyter
-  # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html?highlight=other%20tools#flake8
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    - id: codespell
+      additional_dependencies:
+        - tomli
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.1
     hooks:
-      - id: flake8
-        args: [--max-line-length=88, "--extend-ignore=E203,E712"]
+      - id: ruff
+        args: [ --fix, --show-fixes ]
+      - id: ruff-format
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: "2024.01.24"
+    hooks:
+      - id: sp-repo-review

pyproject.toml

@@ -60,3 +60,67 @@ ctapipe_io_zfits = ["resources/*"]
 
 [tool.setuptools_scm]
 write_to = 'src/ctapipe_io_zfits/_version.py'
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+
+[tool.ruff.lint]
+extend-select = [
+    "I", # isort
+    "N", # pep8 naming
+    "D", # pydocstyle
+    "NPY", # numpy
+    "PT", # pytest
+    "UP", # pyupgrade
+    "COM", # flake8-commas
+    "ISC", # implicit string concat rules
+    "ICN", # import name conventions
+    "G", # logging
+    "B", # flake8-bugbear
+]
+ignore = [
+    "COM812", # incompatible with ruff format
+    "ISC001", # incompatible with ruff format
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+# no documentation linting for test files
+"**/tests/**" = ["D"]
+"**/tests_*.py" = ["D"]
+"docs/conf.py" = ["D"]
+"**/conftest.py" = ["D"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+
+[tool.repo-review]
+select = ["PY", "PP", "PC"]
+ignore = [
+    "PY007", # we do not use tox for now
+    "PC140", # mypy is not used
+    "PC170", # pygrep is not used
+    "PC180", # prettier is not used
+    "PC111", # blacken-docs is not used
+    "PC901", # no CI setup currently for updating pre-commit hooks
+]
+
+
+[tool.pytest.ini_options]
+minversion = "7"
+testpaths = ["src"]
+log_cli_level = "INFO"
+xfail_strict = true
+# print summary of failed tests, force errors if settings are misspelled
+addopts = ["-ra", "--strict-config", "--strict-markers"]
+filterwarnings = [
+    "error",
+]

src/ctapipe_io_zfits/__init__.py

@@ -1,6 +1,4 @@
-"""
-EventSource implementations for protozfits files
-"""
+"""EventSource implementations for protozfits files."""
 from .dl0 import ProtozfitsDL0EventSource, ProtozfitsDL0TelescopeEventSource
 from .version import __version__
 

src/ctapipe_io_zfits/_dev_version/__init__.py

@@ -6,4 +6,4 @@
 
     version = get_version(root="../..", relative_to=__file__)
 except Exception as e:
-    raise ImportError(f"setuptools_scm broken or not installed: {e}")
+    raise ImportError(f"setuptools_scm broken or not installed: {e}") from e

src/ctapipe_io_zfits/conftest.py

@@ -35,11 +35,16 @@
 
 
 def to_anyarray(array):
+    """Convert numpy to protobuf AnyArray."""
     type_ = DTYPE_TO_ANYARRAY_TYPE[array.dtype.type]
     return AnyArray(type=type_, data=array.tobytes())
 
 
 def evening_of_obs(time, tz):
+    """Get the evening an observation started.
+
+    Uses noon localtime in ``tz`` as a cutoff.
+    """
     dt = time.to_datetime(timezone.utc).astimezone(tz)
     if dt.hour < 12:
         return (dt - timedelta(days=1)).date()
@@ -49,6 +54,7 @@ def evening_of_obs(time, tz):
 
 @pytest.fixture(scope="session")
 def acada_base(tmp_path_factory):
+    """Base directory of acada data."""
     return tmp_path_factory.mktemp("acada_base_")
 
 

src/ctapipe_io_zfits/dl0.py

@@ -1,9 +1,6 @@
-"""
-DL0 Protozfits EventSource
-"""
+"""DL0 Protozfits EventSource."""
 import logging
 from contextlib import ExitStack
-from typing import Dict, Tuple
 
 import numpy as np
 from ctapipe.containers import (
@@ -47,7 +44,7 @@ def _is_compatible(input_url, extname, allowed_protos):
         try:
             hdul = stack.enter_context(fits.open(input_url))
         except Exception as e:
-            log.debug(f"Error trying to open input file as fits: {e}")
+            log.debug("Error trying to open input file as fits: %s", e)
             return False
 
         if extname not in hdul:
@@ -70,7 +67,7 @@ def _is_compatible(input_url, extname, allowed_protos):
         return False
 
     if proto_class not in allowed_protos:
-        log.debug(f"Unsupported PBFHEAD: {proto_class} not in {allowed_protos}")
+        log.debug("Unsupported PBFHEAD: %s not in %s", proto_class, allowed_protos)
         return False
 
     return True
@@ -150,7 +147,7 @@ class ProtozfitsDL0EventSource(EventSource):
 
     The ``input_url`` must be the subarray trigger file, the source
     will then look for the other data files according to the filename and
-    directory schema layed out in the draft of the ACADA - DPPS ICD.
+    directory schema laid out in the draft of the ACADA - DPPS ICD.
     """
 
     subarray_id = Integer(default_value=1).tag(config=True)
@@ -203,10 +200,11 @@ def _get_tel_events_directory(self, tel_id):
             / self._date_dirs
         )
 
-    @classmethod
-    def is_compatible(cls, input_url):
+    @staticmethod
+    def is_compatible(file_path):
+        """Return True if the given file can be read by this source."""
         return _is_compatible(
-            input_url,
+            file_path,
             extname="SubarrayEvents",
             allowed_protos={"DL0v1.Subarray.Event"},
         )
@@ -230,29 +228,30 @@ def _open_telescope_files(self):
             )
 
     def close(self):
+        """Close underlying files."""
         self._exit_stack.__exit__(None, None, None)
 
-    def __exit__(self, exc_type, exc_value, traceback):
+    def __exit__(self, exc_type, exc_value, traceback):  # noqa: D105
         self._exit_stack.__exit__(exc_type, exc_value, traceback)
 
     @property
-    def is_simulation(self) -> bool:
+    def is_simulation(self) -> bool:  # noqa: D102
         return False
 
     @property
-    def datalevels(self) -> Tuple[DataLevel]:
+    def datalevels(self) -> tuple[DataLevel]:  # noqa: D102
         return (DataLevel.DL0,)
 
     @property
-    def subarray(self) -> SubarrayDescription:
+    def subarray(self) -> SubarrayDescription:  # noqa: D102
         return self._subarray
 
     @property
-    def observation_blocks(self) -> Dict[int, ObservationBlockContainer]:
+    def observation_blocks(self) -> dict[int, ObservationBlockContainer]:  # noqa: D102
         return self._observation_blocks
 
     @property
-    def scheduling_blocks(self) -> Dict[int, SchedulingBlockContainer]:
+    def scheduling_blocks(self) -> dict[int, SchedulingBlockContainer]:  # noqa: D102
         return self._scheduling_blocks
 
     def _generator(self):
@@ -304,7 +303,7 @@ class ProtozfitsDL0TelescopeEventSource(EventSource):
     ignore_samples_end = Integer(default_value=0).tag(config=True)
 
     @classmethod
-    def is_compatible(cls, input_url):
+    def is_compatible(cls, input_url):  # noqa: D102
         return _is_compatible(
             input_url,
             extname="Events",
@@ -338,35 +337,30 @@ def __init__(self, input_url=None, **kwargs):
             self.sb_id: SchedulingBlockContainer(sb_id=np.uint64(self.sb_id))
         }
 
-    def close(self):
+    def close(self):  # noqa: D102
         self._exit_stack.__exit__(None, None, None)
 
-    def __exit__(self, exc_type, exc_value, traceback):
+    def __exit__(self, exc_type, exc_value, traceback):  # noqa: D105
         self._exit_stack.__exit__(exc_type, exc_value, traceback)
 
     @property
-    def is_simulation(self) -> bool:
-        """If data comes from simulations"""
+    def is_simulation(self) -> bool:  # noqa: D102
         return False
 
     @property
-    def datalevels(self) -> Tuple[DataLevel]:
-        """Provided data levels"""
+    def datalevels(self) -> tuple[DataLevel]:  # noqa: D102
         return (DataLevel.DL0,)
 
     @property
-    def subarray(self) -> SubarrayDescription:
-        """The subarray"""
+    def subarray(self) -> SubarrayDescription:  # noqa: D102
         return self._subarray
 
     @property
-    def observation_blocks(self) -> Dict[int, ObservationBlockContainer]:
-        """The observation blocks"""
+    def observation_blocks(self) -> dict[int, ObservationBlockContainer]:  # noqa: D102
         return self._observation_blocks
 
     @property
-    def scheduling_blocks(self) -> Dict[int, SchedulingBlockContainer]:
-        """The scheduling blocks"""
+    def scheduling_blocks(self) -> dict[int, SchedulingBlockContainer]:  # noqa: D102
         return self._scheduling_blocks
 
     def _fill_event(self, count, zfits_event) -> ArrayEventContainer:

src/ctapipe_io_zfits/instrument.py

@@ -1,7 +1,7 @@
+"""Definitionas of the instrument configuration."""
 import json
 from functools import cache
 from importlib.resources import as_file, files
-from typing import Tuple
 
 import astropy.units as u
 from astropy.coordinates import EarthLocation
@@ -57,21 +57,21 @@ def _load_array_elements():
 
 @cache
 def get_subarrays_by_id():
-    """Get a mapping of subarray_id to subarray definition"""
+    """Get a mapping of subarray_id to subarray definition."""
     data = _load_subarrays()
     return {subarray["id"]: subarray for subarray in data["subarrays"]}
 
 
 @cache
 def get_array_elements_by_id():
-    """Get a mapping of ae_id to array element definition"""
+    """Get a mapping of ae_id to array element definition."""
     data = _load_array_elements()
     return {ae["id"]: ae for ae in data["array_elements"]}
 
 
 @cache
-def get_array_element_ids(subarray_id: int) -> Tuple[int]:
-    """Get array element ids for a given subarray_id"""
+def get_array_element_ids(subarray_id: int) -> tuple[int]:
+    """Get array element ids for a given subarray_id."""
     subarray = get_subarrays_by_id().get(subarray_id)
     if subarray_id is None:
         raise ValueError(f"Unknown subarray_id: {subarray_id}")
@@ -80,10 +80,11 @@ def get_array_element_ids(subarray_id: int) -> Tuple[int]:
 
 
 def build_subarray_description(subarray_id):
+    """Create a SubarrayDescription from the subarray_id."""
     try:
         subarray = get_subarrays_by_id()[subarray_id]
     except KeyError:
-        raise ValueError(f"Unknown subarray_id: {subarray_id}")
+        raise ValueError(f"Unknown subarray_id: {subarray_id}") from None
 
     tel_ids = get_array_element_ids(subarray_id)
     array_elements = get_array_elements_by_id()