fix linting issues and clean up

Note: pydocstyle complaints due to missing docstrings in overloaded magic
methods ignored as they should be fixed in the forseeable future (see
PyCQA/pydocstyle#525)

Author: ruestefa

src/atmcirclib/simulations.py

@@ -25,31 +25,32 @@
 
 # Third-party
 import numpy as np
+import numpy.typing as npt
 import pandas as pd
 
-# Generic type aliases
+# First-party
+from atmcirclib.typing import PathLike_T
 
-# Misc.
-RawPathT = Union[Path, str]
+# Generic type aliases
 
 # Time step notations
 DDHH = Tuple[int, int]
 DDHHMM = Tuple[int, int, int]
 YYYYMMDDHH = Tuple[int, int, int, int]
 
 # Raw time interval(s)
-RawIntervalT = Union[pd.Interval, Tuple[Union[DDHH, DDHHMM], Union[DDHH, DDHHMM]]]
-RawIntervalsT = Sequence[RawIntervalT]
-RawIntervalST = Union[RawIntervalT, RawIntervalsT]
+IntervalLike_T = Union[pd.Interval, Tuple[Union[DDHH, DDHHMM], Union[DDHH, DDHHMM]]]
+IntervalsLike_T = Sequence[IntervalLike_T]
+IntervalSLike_T = Union[IntervalLike_T, IntervalsLike_T]
 
 # Raw output stream type(s)
-RawOutputStreamTypeT = Union["OutputStreamType", str]
-RawOutputStreamTypesT = Sequence[RawOutputStreamTypeT]
-RawOutputStreamTypeST = Union[RawOutputStreamTypeT, RawOutputStreamTypesT]
+OutputStreamTypeLike_T = Union["OutputStreamType", str]
+OutputStreamTypesLike_T = Sequence[OutputStreamTypeLike_T]
+OutputStreamTypeSLike_T = Union[OutputStreamTypeLike_T, OutputStreamTypesLike_T]
 
 # Raw output streams dict
-RawOutputStreamsDictT = Dict[RawOutputStreamTypeST, RawIntervalST]
-RawOutputStreamsT = Union["OutputStreams", RawOutputStreamsDictT]
+OutputStreamsDictLike_T = Dict[OutputStreamTypeSLike_T, IntervalSLike_T]
+OutputStreamsLike_T = Union["OutputStreams", OutputStreamsDictLike_T]
 
 
 class NamedObj(Protocol):
@@ -104,6 +105,7 @@ def __getitem__(
             return obj
 
     def __repr__(self) -> str:
+        """Return string representation."""
         return f"{type(self).__name__}([\n " + "\n ".join(map(str, self)) + "\n])"
 
 
@@ -185,6 +187,7 @@ class OutputStream:
     intervals: list[pd.Interval]
 
     def __post_init__(self) -> None:
+        """Finalize initialization."""
         self._run: Optional[SimulationRun] = None
         self.check_intervals()
 
@@ -304,8 +307,8 @@ def check_intervals(self, steps: Optional[pd.DatetimeIndex] = None) -> None:
     @classmethod
     def create(
         cls,
-        stream_type: RawOutputStreamTypeT,
-        intervals: RawIntervalST,
+        stream_type: OutputStreamTypeLike_T,
+        intervals: IntervalSLike_T,
         *,
         output_stream_types: Optional[OutputStreamTypes] = None,
         start: Optional[pd.Timestamp] = None,
@@ -371,6 +374,17 @@ def get_all_steps(self) -> pd.DatetimeIndex:
             stream.check_intervals(all_steps)
         return all_steps
 
+    def count_per_step(self) -> tuple[npt.NDArray[np.int_], pd.DatetimeIndex]:
+        """Count the number of streams overing each step."""
+        steps = self.get_all_steps()
+        counts = np.zeros(steps.size, np.int32)
+        for stream in self:
+            for interval in stream.intervals:
+                i0 = steps.get_loc(interval.left)
+                i1 = steps.get_loc(interval.right)
+                counts[i0 : i1 + 1] += 1
+        return counts, steps
+
     def set_run(self, run: SimulationRun) -> None:
         """Associate all output streams with a simulation run."""
         for stream in self:
@@ -379,7 +393,7 @@ def set_run(self, run: SimulationRun) -> None:
     @classmethod
     def create(
         cls,
-        output: RawOutputStreamsT,
+        output: OutputStreamsLike_T,
         *,
         output_stream_types: Optional[OutputStreamTypes] = None,
         start: Optional[pd.Timestamp] = None,
@@ -388,9 +402,9 @@ def create(
         if isinstance(output, OutputStreams):
             return copy(output)
         streams = cls()
-        stream_type_s: RawOutputStreamTypeST
-        stream_type: RawOutputStreamTypeT
-        interval_s: RawIntervalST
+        stream_type_s: OutputStreamTypeSLike_T
+        stream_type: OutputStreamTypeLike_T
+        interval_s: IntervalSLike_T
         for stream_type_s, interval_s in output.items():
             if isinstance(stream_type_s, str) or not isinstance(
                 stream_type_s, Collection
@@ -444,61 +458,14 @@ def __init__(
         self,
         *,
         start: Union[pd.Timestamp, YYYYMMDDHH],
-        path: Optional[RawPathT] = None,
-        rel_path: Optional[RawPathT] = None,
-        output: Optional[RawOutputStreamsT] = None,
+        path: Optional[PathLike_T] = None,
+        rel_path: Optional[PathLike_T] = None,
+        output: Optional[OutputStreamsLike_T] = None,
         end_rel: Optional[Union[pd.Timedelta, DDHH, DDHHMM]] = None,
         end_type: Optional[Union[SimulationRunEndType, str]] = None,
         simulation_run_end_types: Optional[SimulationRunEndTypes] = None,
     ) -> None:
         """Create an instance of ``SimulationRun``."""
-
-        def init_end_rel(
-            raw_end_rel: Optional[Union[pd.Timedelta, DDHH, DDHHMM]],
-            output: OutputStreams,
-            start: pd.Timestamp,
-        ) -> pd.Timedelta:
-            """Initialize ``end_rel``."""
-            if raw_end_rel is None:
-                if not output:
-                    raw_end_rel = pd.Timedelta(0)
-                else:
-                    last_output = max(
-                        interval.right
-                        for stream in output
-                        for interval in stream.intervals
-                    )
-                    raw_end_rel = last_output - start
-            return init_timedelta(raw_end_rel)
-
-        def init_end_type(
-            raw_end_type: Optional[Union[SimulationRunEndType, str]]
-        ) -> SimulationRunEndType:
-            """Initialize ``end_type``."""
-            if isinstance(raw_end_type, SimulationRunEndType):
-                return raw_end_type
-            if simulation_run_end_types is None:
-                raise ValueError(
-                    "must pass simulation_run_end_types if end_type is not of type"
-                    " SimulationRunEndType"
-                )
-            return simulation_run_end_types[raw_end_type or "success"]
-
-        def init_label(paths: Collection[Optional[Path]]) -> str:
-            label = ""
-            for path in paths:
-                if path is not None:
-                    if not label:
-                        label = path.name
-                    elif label != path.name:
-                        raise ValueError(
-                            f"inconsistent labels: {label} != {path.name}; paths: "
-                            + ", ".join(map(str, paths))
-                        )
-            if not label:
-                raise ValueError(f"could not derive label from paths: {paths}")
-            return label
-
         self.abs_path: Optional[Path] = None if path is None else Path(path)
         self.rel_path: Optional[Path] = None if rel_path is None else Path(rel_path)
         self.start: pd.Timestamp = init_timestamp(start)
@@ -508,11 +475,15 @@ def init_label(paths: Collection[Optional[Path]]) -> str:
             path = self.abs_path or self.rel_path
             raise Exception(f"error creating output streams for run at {path}") from e
         self.output: OutputStreams = streams
-        self.end_rel: pd.Timedelta = init_end_rel(end_rel, self.output, self.start)
-        self.end_type: SimulationRunEndType = init_end_type(end_type)
+        self.end_rel: pd.Timedelta = self._init_end_rel(
+            end_rel, self.output, self.start
+        )
+        self.end_type: SimulationRunEndType = self._init_end_type(
+            end_type, simulation_run_end_types
+        )
 
         self.output.set_run(self)
-        self.label: str = init_label([self.abs_path, self.rel_path])
+        self.label: str = self._init_label([self.abs_path, self.rel_path])
         self.end: pd.Timestamp = self.start + self.end_rel
         self.write_start: pd.Timestamp = min(
             [interval.left for stream in self.output for interval in stream.intervals]
@@ -554,7 +525,9 @@ def get_full_path(self) -> Path:
             )
         return path
 
-        def init_path(path: Optional[RawPathT], rel_path: Optional[RawPathT]) -> Path:
+        def init_path(
+            path: Optional[PathLike_T], rel_path: Optional[PathLike_T]
+        ) -> Path:
             if path is None and rel_path is None:
                 raise ValueError("path and rel_path are both None")
             elif rel_path is not None:
@@ -569,16 +542,65 @@ def exists(self) -> bool:
         return self.get_full_path().exists()
 
     def __repr__(self) -> str:
+        """Return a string representation."""
         path = self.get_full_path()
         return f"{type(self).__name__}('{path}', {self.start})"
 
+    @staticmethod
+    def _init_end_rel(
+        raw_end_rel: Optional[Union[pd.Timedelta, DDHH, DDHHMM]],
+        output: OutputStreams,
+        start: pd.Timestamp,
+    ) -> pd.Timedelta:
+        """Initialize ``end_rel``."""
+        if raw_end_rel is None:
+            if not output:
+                raw_end_rel = pd.Timedelta(0)
+            else:
+                last_output = max(
+                    interval.right for stream in output for interval in stream.intervals
+                )
+                raw_end_rel = last_output - start
+        return init_timedelta(raw_end_rel)
+
+    @staticmethod
+    def _init_end_type(
+        raw_end_type: Optional[Union[SimulationRunEndType, str]],
+        simulation_run_end_types: Optional[SimulationRunEndTypes],
+    ) -> SimulationRunEndType:
+        """Initialize ``end_type``."""
+        if isinstance(raw_end_type, SimulationRunEndType):
+            return raw_end_type
+        if simulation_run_end_types is None:
+            raise ValueError(
+                "must pass simulation_run_end_types if end_type is not of type"
+                " SimulationRunEndType"
+            )
+        return simulation_run_end_types[raw_end_type or "success"]
+
+    @staticmethod
+    def _init_label(paths: Collection[Optional[Path]]) -> str:
+        label = ""
+        for path in paths:
+            if path is not None:
+                if not label:
+                    label = path.name
+                elif label != path.name:
+                    raise ValueError(
+                        f"inconsistent labels: {label} != {path.name}; paths: "
+                        + ", ".join(map(str, paths))
+                    )
+        if not label:
+            raise ValueError(f"could not derive label from paths: {paths}")
+        return label
+
 
 class Simulation:
     """A simulation comprised of one or more simulation runs."""
 
     def __init__(
         self,
-        path: RawPathT,
+        path: PathLike_T,
         runs: Optional[Sequence[SimulationRun]] = None,
     ) -> None:
         """Create an instance of ``Simulation``."""
@@ -632,16 +654,10 @@ def find_redundant_output(
             if stream_type.removed_files:
                 continue
             try:
-                steps = streams.get_all_steps()
+                counts, steps = streams.count_per_step()
             except EmptyOutputStreamError:
                 continue
-            coverage = np.zeros(steps.size)
-            for stream in streams:
-                for interval in stream.intervals:
-                    i0 = steps.get_loc(interval.left)
-                    i1 = steps.get_loc(interval.right)
-                    coverage[i0 : i1 + 1] += 1
-            idcs = np.where(steps[coverage > 1])[0]
+            idcs = np.where(steps[counts > 1])[0]
             if idcs.size == 0:
                 continue
             multi_steps[stream_type] = {}
@@ -657,6 +673,7 @@ def find_redundant_output(
         return multi_steps
 
     def __repr__(self) -> str:
+        """Return a string representation."""
         return f"{type(self).__name__}([" + ", ".join(map(str, self.get_runs())) + "])"
 
 
@@ -734,6 +751,7 @@ def collect_redundant_output_files(self) -> list[list[Path]]:
         return paths_sims
 
     def __repr__(self) -> str:
+        """Return a string representation."""
         return f"{type(self).__name__}([\n " + "\n ".join(map(str, self)) + "\n])"
 
     @classmethod
@@ -790,7 +808,7 @@ def init_timedelta(val: Union[pd.Timedelta, DDHH, DDHHMM]) -> pd.Timedelta:
 
 
 def init_interval(
-    val: RawIntervalT,
+    val: IntervalLike_T,
     start: Optional[pd.Timestamp] = None,
 ) -> pd.Interval:
     """Initialize a time interval object."""