Fix updating the flexure component

.pre-commit-config.yaml

@@ -22,11 +22,14 @@ repos:
     types_or: [python, pyi, jupyter]
     additional_dependencies: [".[jupyter]"]
 
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
+- repo: https://github.com/pycqa/flake8
+  rev: 4.0.1
   hooks:
-  - id: flake8
-    # additional_dependencies: [flake8-bugbear]
+    - id: flake8
+      additional_dependencies:
+        - flake8-bugbear
+        - flake8-comprehensions
+        - flake8-simplify
 
 - repo: https://gitlab.com/iamlikeme/nbhooks
   rev: 1.0.0

news/71.feature

@@ -0,0 +1,4 @@
+
+Changed the :class:`~sequence.sediment_flexure.SedimentFlexure` component so
+that it is no longer dependent on the ordering of components. It has been
+simplified so that it now takes sediment loading as its only input field.

requirements.txt

@@ -8,3 +8,4 @@ pyyaml
 rich-click
 scipy
 tomlkit
+tqdm

sequence/cli.py

@@ -4,6 +4,7 @@
 import os
 import pathlib
 import re
+from contextlib import suppress
 from io import StringIO
 from os import PathLike
 from typing import Any, Iterable, Iterator, Optional, Union
@@ -91,11 +92,13 @@ def as_csv(data: ArrayLike, header: str = "") -> str:
     contents = {
         "sequence.yaml": yaml.dump(params, default_flow_style=False),
         "sequence.toml": toml.dumps(
-            dict(
-                sequence=dict(
-                    _time=0.0, processes=SequenceModel.ALL_PROCESSES, **params
-                )
-            )
+            {
+                "sequence": {
+                    "_time": 0.0,
+                    "processes": SequenceModel.ALL_PROCESSES,
+                    **params,
+                }
+            }
         ),
         "bathymetry.csv": as_csv(
             [[0.0, 20.0], [100000.0, -80.0]], header="X [m], Elevation [m]"
@@ -122,7 +125,7 @@ def as_csv(data: ArrayLike, header: str = "") -> str:
     return contents[str(infile)]
 
 
-def _time_from_filename(name: Union[str, PathLike[str]]) -> Union[int, None]:
+def _time_from_filename(name: Union[str, PathLike[str]]) -> Optional[int]:
     """Parse a time stamp from a file name.
 
     Parameters
@@ -299,14 +302,11 @@ def run(ctx: Any, with_citations: bool, dry_run: bool) -> None:
             disable=True if silent else None,
         )
 
-        try:
-            with progressbar as bar:
-                while 1:
-                    model.run_one_step()
-                    model.set_params(params.update(1))
-                    bar.update(1)
-        except StopIteration:
-            pass
+        with suppress(StopIteration), progressbar as bar:
+            while 1:
+                model.run_one_step()
+                model.set_params(params.update(1))
+                bar.update(1)
 
         if verbose and not silent:
             total = sum(model.timer.values())
@@ -394,7 +394,7 @@ def plot(ctx: Any, set: str) -> None:
         config.update(
             TimeVaryingConfig.from_file(folder / "sequence.toml")
             .as_dict()
-            .get("plot", dict())
+            .get("plot", {})
         )
 
     config.update(**_load_params_from_strings(set))
@@ -403,8 +403,8 @@ def plot(ctx: Any, set: str) -> None:
         logger.info(
             os.linesep.join(
                 [
-                    "Reading configuration\n",
-                    toml.dumps(dict(sequence=dict(plot=config))),
+                    "Reading configuration",
+                    toml.dumps({"sequence": {"plot": config}}),
                 ]
             )
         )
@@ -471,7 +471,7 @@ def _walk_dict(indict: Union[dict, Any], prev: Optional[list] = None) -> Iterato
         for key, value in indict.items():
             if isinstance(value, dict):
                 yield from _walk_dict(value, [key] + prev)
-            elif isinstance(value, list) or isinstance(value, tuple):
+            elif isinstance(value, (list, tuple)):
                 yield prev + [key, value]
             else:
                 yield prev + [key, value]

sequence/input_reader.py

@@ -183,7 +183,7 @@ def dump(self, fmt: str = "toml") -> str:
             doc["_time"] = time
 
         if fmt == "toml":
-            return toml.dumps(dict(sequence=docs))
+            return toml.dumps({"sequence": docs})
         elif fmt == "yaml":
             return yaml.dump(docs, default_flow_style=False)
         else:
@@ -276,9 +276,9 @@ def load_toml(stream: TextIO) -> list[tuple[float, dict]]:
             The configurations and their associated times.
         """
 
-        def _tomlkit_to_popo(d: dict) -> Any:
+        def _tomlkit_to_popo(d: Any) -> Any:
             try:
-                result = getattr(d, "value")
+                result = d.value
             except AttributeError:
                 result = d
 
@@ -446,7 +446,7 @@ def _walk_dict(
         for key, value in indict.items():
             if isinstance(value, dict):
                 yield from _walk_dict(value, prev_dicts + [key])
-            elif isinstance(value, list) or isinstance(value, tuple):
+            elif isinstance(value, (list, tuple)):
                 yield tuple(prev_dicts + [key]), value
             else:
                 yield tuple(prev_dicts + [key]), value

sequence/netcdf.py

@@ -204,7 +204,7 @@ def to_netcdf(
     at: Optional[Union[str, Sequence[str]]] = None,
     ids: Optional[Union[dict[str, Iterable[int]], int, Iterable[int], slice]] = None,
     names: Optional[
-        Union[dict[str, Union[Iterable[str], None]], str, Iterable[str]]
+        Union[dict[str, Optional[Iterable[str]]], str, Iterable[str]]
     ] = None,
     with_layers: bool = True,
 ) -> None:

sequence/plot.py

@@ -253,7 +253,7 @@ def plot_file(filename: Union[str, PathLike], **kwds: Any) -> None:
     )
 
 
-def _get_layers_to_plot(start: int, stop: int, num: int = -1) -> Union[slice, None]:
+def _get_layers_to_plot(start: int, stop: int, num: int = -1) -> Optional[slice]:
     if num == 0:
         return None
     elif num < 0 or num > stop - start + 1:
@@ -292,8 +292,8 @@ def _outline_layer(
     x: NDArray,
     y_of_bottom_layer: NDArray,
     y_of_top_layer: NDArray,
-    bottom_limits: Optional[tuple[Union[float, None], Union[float, None]]] = None,
-    top_limits: Optional[tuple[Union[float, None], Union[float, None]]] = None,
+    bottom_limits: Optional[tuple[Optional[float], Optional[float]]] = None,
+    top_limits: Optional[tuple[Optional[float], Optional[float]]] = None,
 ) -> tuple[NDArray, NDArray]:
     if bottom_limits is None:
         bottom_limits = (None, None)