[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

strax/context.py

@@ -18,7 +18,6 @@
 import strax
 from strax import CutList
 
-
 export, __all__ = strax.exporter()
 __all__.extend(["RUN_DEFAULTS_KEY"])
 
@@ -1460,8 +1459,9 @@ def _add_saver(
         target_plugin: strax.Plugin,
         combining: bool = False,
     ):
-        """Adds savers to already existing savers. Checks if data_type can be stored in any storage
-        frontend.
+        """Adds savers to already existing savers.
+
+        Checks if data_type can be stored in any storage frontend.
 
         :param savers: Dictionary of already existing savers.
         :param d_to_save: String of the data_type to be saved.
@@ -1576,7 +1576,6 @@ def to_absolute_time_range(
         :param full_range: If True returns full time_range of the run.
 
         """
-
         selection = (
             (time_range is None)
             + (seconds_range is None)
@@ -1624,9 +1623,8 @@ def get_iter(
     ) -> ty.Iterator[strax.Chunk]:
         """Compute target for run_id and iterate over results.
 
-        Do NOT interrupt the iterator (i.e. break): it will keep running stuff
-        in background threads...
-        {get_docs}
+        Do NOT interrupt the iterator (i.e. break): it will keep running stuff in background
+        threads... {get_docs}
 
         """
         if hasattr(run_id, "decode"):
@@ -1837,9 +1835,9 @@ def make(
         combining=False,
         **kwargs,
     ) -> None:
-        """Compute target for run_id. Returns nothing (None).
+        """Compute target for run_id.
 
-        {get_docs}
+        Returns nothing (None).         {get_docs}
 
         """
         kwargs.setdefault("progress_bar", False)
@@ -2035,9 +2033,11 @@ def get_zarr(
         overwrite=True,
         **kwargs,
     ):
-        """Get persistent arrays using zarr. This is useful when loading large amounts of data that
-        cannot fit in memory zarr is very compatible with dask. Targets are loaded into separate
-        arrays and runs are merged. the data is added to any existing data in the storage location.
+        """Get persistent arrays using zarr.
+
+        This is useful when loading large amounts of data that cannot fit in memory zarr is very
+        compatible with dask. Targets are loaded into separate arrays and runs are merged. the data
+        is added to any existing data in the storage location.
 
         :param run_ids: (Iterable) run ids you wish to load.
         :param targets: (Iterable) targets to load.
@@ -2087,9 +2087,10 @@ def get_zarr(
         return group
 
     def key_for(self, run_id, target, chunk_number=None, combining=False):
-        """Get the DataKey for a given run and a given target plugin. The DataKey is inferred from
-        the plugin lineage. The lineage can come either from the _fixed_plugin_cache or computed on
-        the fly.
+        """Get the DataKey for a given run and a given target plugin.
+
+        The DataKey is inferred from the plugin lineage. The lineage can come either from the
+        _fixed_plugin_cache or computed on the fly.
 
         :param run_id: run id to get
         :param target: data type to get
@@ -2510,7 +2511,6 @@ def merge_per_chunk_storage(
         check_is_stored: bool = True,
     ):
         """Merge the per-chunked data from the per-chunked dependency into the target storage."""
-
         if check_is_stored and self.is_stored(run_id, target):
             raise ValueError(f"Data {target} for {run_id} already exists.")
 
@@ -2894,7 +2894,6 @@ def tree_levels(self):
         'class': 'Peaks', 'index': 0, 'order': 1}}
 
         """
-
         context_hash = self._context_hash()
         if self._fixed_level_cache is not None and context_hash in self._fixed_level_cache:
             return self._fixed_level_cache[context_hash]

strax/dtypes.py

@@ -1,8 +1,7 @@
 """Fundamental dtypes for use in strax.
 
-Note that if you change the dtype titles (comments), numba will crash if
-there is an existing numba cache. Clear __pycache__ and restart.
-TODO: file numba issue.
+Note that if you change the dtype titles (comments), numba will crash if there is an existing numba
+cache. Clear __pycache__ and restart. TODO: file numba issue.
 
 """
 
@@ -12,7 +11,6 @@
 import numba  # noqa: F401
 import strax
 
-
 __all__ = (
     "interval_dtype raw_record_dtype record_dtype hit_dtype peak_dtype "
     "DIGITAL_SUM_WAVEFORM_CHANNEL DEFAULT_RECORD_LENGTH "
@@ -134,8 +132,9 @@ def hitlet_dtype():
 
 
 def hitlet_with_data_dtype(n_samples=2):
-    """Hitlet dtype with data field. Required within the plugins to compute hitlet properties.
+    """Hitlet dtype with data field.
 
+    Required within the plugins to compute hitlet properties.
     :param n_samples: Buffer length of the data field. Make sure it can hold the longest hitlet.
 
     """
@@ -246,8 +245,9 @@ def peak_dtype(
 def copy_to_buffer(
     source: np.ndarray, buffer: np.ndarray, func_name: str, field_names: Optional[Tuple[str]] = None
 ):
-    """Copy the data from the source to the destination e.g. raw_records to records. To this end, we
-    dynamically create the njitted function with the name 'func_name' (should start with "_").
+    """Copy the data from the source to the destination e.g. raw_records to records.
+
+    To this end, we dynamically create the njitted function with the name 'func_name' (should start with "_").
 
     :param source: array of input
     :param buffer: array of buffer to fill with values from input

strax/plugins/plugin.py

@@ -408,8 +408,9 @@ def source_finished(self):
         raise RuntimeError("source_finished called on a regular plugin")
 
     def _fetch_chunk(self, d, iters, check_end_not_before=None):
-        """Add a chunk of the datatype d to the input buffer. Return True if this succeeded, False
-        if the source is exhausted.
+        """Add a chunk of the datatype d to the input buffer.
+
+        Return True if this succeeded, False if the source is exhausted.
 
         :param d: data type to fetch
         :param iters: iterators that produce data

strax/processing/general.py

@@ -123,8 +123,9 @@ class NoBreakFound(Exception):
 @export
 @numba.njit(nogil=True, cache=True)
 def _find_break_i(data, safe_break, not_before):
-    """Return first index of element right of the first gap larger than safe_break in data. Assumes
-    all x have the same length and are sorted!
+    """Return first index of element right of the first gap larger than safe_break in data.
+
+    Assumes all x have the same length and are sorted!
 
     :param tolerant: if no break found, yield an as good as possible break anyway.
 
@@ -211,8 +212,9 @@ def _fc_in(a_starts, b_starts, a_ends, b_ends, result):
 
 @export
 def split_by_containment(things, containers):
-    """Return list of thing-arrays contained in each container. Result is returned as a
-    numba.typed.List or list if containers are empty.
+    """Return list of thing-arrays contained in each container.
+
+    Result is returned as a numba.typed.List or list if containers are empty.
 
     Assumes everything is sorted, and containers are non-overlapping.
 

strax/processing/hitlets.py

@@ -23,11 +23,10 @@ def create_hitlets_from_hits(
     :param hits: Hits found in records.
     :param save_outside_hits: Tuple with left and right hit extension.
     :param channel_range: Detectors change range from channel map.
-    :param chunk_start: (optional) start time of a chunk. Ensures that
-        no hitlet is earlier than this timestamp.
-    :param chunk_end: (optional) end time of a chunk. Ensures that
-        no hitlet ends later than this timestamp.
-
+    :param chunk_start: (optional) start time of a chunk. Ensures that no hitlet is earlier than
+        this timestamp.
+    :param chunk_end: (optional) end time of a chunk. Ensures that no hitlet ends later than this
+        timestamp.
     :return: Hitlets with temporary fields (data, max_goodness_of_split...)
 
     """

strax/processing/peak_building.py

@@ -157,7 +157,6 @@ def store_downsampled_waveform(
         waveform in the peak.
 
     """
-
     n_samples = len(p["data"])
 
     p_length = p["length"]
@@ -255,9 +254,11 @@ def sum_waveform(
     store_data_start=False,
     select_peaks_indices=None,
 ):
-    """Compute sum waveforms for all peaks in peaks. Only builds summed waveform other regions in
-    which hits were found. This is required to avoid any bias due to zero-padding and baselining.
-    Will downsample sum waveforms if they do not fit in per-peak buffer.
+    """Compute sum waveforms for all peaks in peaks.
+
+    Only builds summed waveform other regions in which hits were found. This is required to avoid
+    any bias due to zero-padding and baselining. Will downsample sum waveforms if they do not fit in
+    per-peak buffer.
 
     :param peaks: Peaks for which the summed waveform should be build.
     :param hits: Hits which are inside peaks. Must be sorted according to record_i.
@@ -401,8 +402,9 @@ def sum_waveform(
 
 @numba.njit(cache=True, nogil=True)
 def _build_hit_waveform(hit, record, hit_waveform):
-    """Adds information for overlapping record and hit to hit_waveform. Updates hit_waveform
-    inplace. Result is still in ADC counts.
+    """Adds information for overlapping record and hit to hit_waveform.
+
+    Updates hit_waveform inplace. Result is still in ADC counts.
 
     :return: Boolean if record saturated within the hit.
 
@@ -477,8 +479,9 @@ def find_hit_integration_bounds(
     n_channels,
     allow_bounds_beyond_records=False,
 ):
-    """Update (lone) hits to include integration bounds. Please note that time and length of the
-    original hit are not changed!
+    """Update (lone) hits to include integration bounds.
+
+    Please note that time and length of the original hit are not changed!
 
     :param hits: Hits or lone hits which should be extended by integration bounds.
     :param excluded_intervals: Regions in which hits should not extend to. E.g. Peaks for lone hits.

strax/processing/peak_merging.py

@@ -36,7 +36,6 @@ def merge_peaks(
         constituent peaks, it being too time-consuming to revert to records/hits.
 
     """
-
     new_peaks, endtime = _merge_peaks(
         peaks,
         start_merge_at,

strax/processing/peak_properties.py

@@ -77,7 +77,6 @@ def compute_widths(peaks):
     :param peaks: single strax peak(let) or other data-bearing dtype
 
     """
-
     desired_widths = np.linspace(0, 1, len(peaks[0]["width"]))
     # 0% are width is 0 by definition, and it messes up the calculation below
     desired_widths = desired_widths[1:]
@@ -137,8 +136,8 @@ def compute_area_fraction_top(peaks, n_top_channels):
 
 @export
 def compute_properties(peaks, n_top_channels=0, select_peaks_indices=None):
-    """Compute properties: median_time, width, area_decile_from_midpoint,
-    center_time, and area_fraction_top for peaks.
+    """Compute properties: median_time, width, area_decile_from_midpoint, center_time, and
+    area_fraction_top for peaks.
 
     :param peaks: single strax peak(let) or other data-bearing dtype
     :param select_peaks_indices: array of integers informing which peaks to compute default to None

strax/processing/pulse_processing.py

@@ -20,8 +20,9 @@
 def baseline(
     records, baseline_samples=40, flip=True, allow_sloppy_chunking=False, fallback_baseline=16000
 ):
-    """Determine baseline as the average of the first baseline_samples of each pulse. Subtract the
-    pulse data from int(baseline), and store the baseline mean and rms.
+    """Determine baseline as the average of the first baseline_samples of each pulse.
+
+    Subtract the pulse data from int(baseline), and store the baseline mean and rms.
 
     :param baseline_samples: number of samples at start of pulse to average to determine the
         baseline.
@@ -165,8 +166,9 @@ def find_hits(
     min_amplitude: ty.Union[int, np.ndarray] = 15,
     min_height_over_noise: ty.Union[int, np.ndarray] = 0,
 ):
-    """Return hits (intervals >= threshold) found in records. Hits that straddle record boundaries
-    are split (perhaps we should fix this?)
+    """Return hits (intervals >= threshold) found in records.
+
+    Hits that straddle record boundaries are split (perhaps we should fix this?)
 
     NB: returned hits are NOT sorted yet!
 
@@ -316,8 +318,9 @@ def _waveforms_to_float(wv, bl):
 
 @export
 def filter_records(r, ir):
-    """Apply filter with impulse response ir over the records r. Assumes the filter origin is at the
-    impulse response maximum.
+    """Apply filter with impulse response ir over the records r.
+
+    Assumes the filter origin is at the impulse response maximum.
 
     :param ws: Waveform matrix, must be float
     :param ir: Impulse response, must have odd length. Will normalize.
@@ -338,8 +341,9 @@ def filter_records(r, ir):
 
 @export
 def filter_waveforms(ws, ir, prev_r, next_r):
-    """Convolve filter with impulse response ir over each row of ws. Assumes the filter origin is at
-    the impulse response maximum.
+    """Convolve filter with impulse response ir over each row of ws.
+
+    Assumes the filter origin is at the impulse response maximum.
 
     :param ws: Waveform matrix, must be float
     :param ir: Impulse response, must have odd length.

strax/run_selection.py

@@ -26,7 +26,6 @@ def list_available(self, target, runs=None, **kwargs) -> list:
     :param runs: Runs to check. If None, check all runs.
 
     """
-
     if len(kwargs):
         # noinspection PyMethodFirstArgAssignment
         self = self.new_context(**kwargs)
@@ -53,8 +52,10 @@ def list_available(self, target, runs=None, **kwargs) -> list:
 def keys_for_runs(
     self, target: str, run_ids: ty.Union[np.ndarray, list, tuple, str]
 ) -> ty.List[strax.DataKey]:
-    """Get the data-keys for a multitude of runs. If use_per_run_defaults is False which it
-    preferably is (#246), getting many keys should be fast as we only compute the lineage once.
+    """Get the data-keys for a multitude of runs.
+
+    If use_per_run_defaults is False which it preferably is (#246), getting many keys should be fast
+    as we only compute the lineage once.
 
     :param run_ids: Runs to get datakeys for
     :param target: datatype requested
@@ -467,8 +468,9 @@ def available_for_run(
     exclude_targets: ty.Union[None, list, tuple, str] = None,
     pattern_type: str = "fnmatch",
 ) -> pd.DataFrame:
-    """For a given single run, check all the targets if they are stored. Excludes the target if
-    never stored anyway.
+    """For a given single run, check all the targets if they are stored.
+
+    Excludes the target if never stored anyway.
 
     :param run_id: requested run
     :param include_targets: targets to include e.g. raw_records, raw_records* or *_nv. If multiple