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

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docs/benchmark.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "22e7a0b1",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Benchmark\n",
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "826ee07a",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e4c0580c",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "08b632e7",
+   "id": "3",
    "metadata": {},
    "source": [
     "You can checkout a specific commit by going to the link\n",
@@ -64,7 +64,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fdde9f88",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bf5ab1db",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -85,7 +85,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fc860bce",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "78fd5db3",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "de1c5c0d",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e0166d6",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "84aa49a3",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "raw",
-   "id": "0b9ec071",
+   "id": "11",
    "metadata": {},
    "source": [
     "\"\"\"\n",
@@ -177,7 +177,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9025f6f9",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -218,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "00a9e504",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": []

docs/convergence_spatial.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "1a923a9c",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Spatial convergence test"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7aeb3b0a",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -30,7 +30,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7e7a0a72",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,7 +49,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a74905c1",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0831698c",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ec625211",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "57803fec",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -126,7 +126,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "561fc32d",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -197,7 +197,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6ada5ff9",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": []

docs/convergence_temporal.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "6d9e2805",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Temporal convergence test"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d7a5935",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -30,7 +30,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ea6686e3",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,7 +49,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "912103ff",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "810bc713",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ba4f1586",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2768b0b0",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [

src/simcardems/geometry.py

@@ -147,13 +147,11 @@ def validate(self):
 
     @staticmethod
     @abc.abstractmethod
-    def default_markers() -> Dict[str, Tuple[int, int]]:
-        ...
+    def default_markers() -> Dict[str, Tuple[int, int]]: ...
 
     @staticmethod
     @abc.abstractmethod
-    def default_parameters() -> Dict[str, Any]:
-        ...
+    def default_parameters() -> Dict[str, Any]: ...
 
     @staticmethod
     def default_stimulus_domain(mesh: dolfin.Mesh) -> StimulusDomain:
@@ -231,16 +229,13 @@ def _default_microstructure(
         self,
         mesh: dolfin.Mesh,
         ffun: dolfin.MeshFunction,
-    ) -> pulse.Microstructure:
-        ...
+    ) -> pulse.Microstructure: ...
 
     @abc.abstractmethod
-    def _default_ffun(self, mesh: dolfin.Mesh) -> dolfin.MeshFunction:
-        ...
+    def _default_ffun(self, mesh: dolfin.Mesh) -> dolfin.MeshFunction: ...
 
     @abc.abstractmethod
-    def _default_mesh(self) -> dolfin.Mesh:
-        ...
+    def _default_mesh(self) -> dolfin.Mesh: ...
 
     @property
     def facet_normal(self) -> dolfin.FacetNormal:

src/simcardems/models/cell_model.py

@@ -11,5 +11,4 @@ class BaseCellModel(CardiacCellModel, ABC):
     def update_disease_parameters(
         params: Dict[str, float],
         disease_state: str = "healthy",
-    ) -> None:
-        ...
+    ) -> None: ...

src/simcardems/models/explicit_ORdmm_Land/cell_model.py

@@ -2,6 +2,7 @@
 
 The module was autogenerated from a gotran ode file
 """
+
 from collections import OrderedDict
 from typing import Dict
 

src/simcardems/models/fully_coupled_ORdmm_Land/cell_model.py

@@ -1,6 +1,7 @@
 """This module contains a ORdmm_Land_em_coupling cardiac cell model
 The module was autogenerated from a gotran ode file
 """
+
 from __future__ import division
 
 from collections import OrderedDict

src/simcardems/models/fully_coupled_Tor_Land/cell_model.py

@@ -2,6 +2,7 @@
 
 The module was modified from a file that was autogenerated from a gotran ode file
 """
+
 from __future__ import division
 
 from collections import OrderedDict

src/simcardems/models/pureEP_ORdmm_Land/cell_model.py

@@ -2,6 +2,7 @@
 
 The module was autogenerated from a gotran ode file
 """
+
 from collections import OrderedDict
 from typing import Dict
 

src/simcardems/value_extractor.py

@@ -78,8 +78,7 @@ def __init__(self, mesh):
 
     @staticmethod
     @abc.abstractmethod
-    def nodes() -> typing.Sequence[str]:
-        ...
+    def nodes() -> typing.Sequence[str]: ...
 
 
 class LVBoundary(Boundary):

tests/smoke.py

@@ -1,4 +1,5 @@
 """Same as simple demo, but only 20 ms"""
+
 from pathlib import Path
 
 import simcardems