Proper Release alongside paper

.github/workflows/pre_commit.yml

@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - main
+      - dev
 
 jobs:
   pre-commit:

.github/workflows/run_tests.yml

@@ -0,0 +1,34 @@
+name: Run tests
+
+on:
+  pull_request:
+
+jobs:
+  run-test:
+    strategy:
+      matrix:
+        python-version: [ "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-latest ]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r ./tests/requirements.txt
+
+      - name: Checks with pre-commit
+        uses: pre-commit/[email protected]
+
+      - name: Test with pytest
+        run: |
+          python -m pip install .
+          python -m pytest tests/

docs/api/stepper/difficulty/convection.md → docs/api/stepper/generic/difficulty/difficulty_convection.md

@@ -1,6 +1,6 @@
 # Convection
 
-::: exponax.normalized.DifficultyConvectionStepper
+::: exponax.stepper.generic.DifficultyConvectionStepper
     options:
         members:
             - __init__

docs/api/stepper/difficulty/gradient_norm.md → docs/api/stepper/generic/difficulty/difficulty_gradient_norm.md

@@ -1,6 +1,6 @@
 # Gradient Norm
 
-::: exponax.normalized.DifficultyGradientNormStepper  
+::: exponax.stepper.generic.DifficultyGradientNormStepper  
     options:
         members:
             - __init__

docs/api/stepper/difficulty/linear.md → docs/api/stepper/generic/difficulty/difficulty_linear.md

@@ -1,6 +1,6 @@
 # Linear
 
-::: exponax.normalized.DifficultyLinearStepper  
+::: exponax.stepper.generic.DifficultyLinearStepper  
     options:
         members:
             - __init__

docs/api/stepper/difficulty/nonlinear.md → docs/api/stepper/generic/difficulty/difficulty_nonlinear.md

@@ -1,6 +1,6 @@
 # Nonlinear
 
-::: exponax.normalized.DifficultyGeneralNonlinearStepper
+::: exponax.stepper.generic.DifficultyNonlinearStepper
     options:
         members:
             - __init__

docs/api/stepper/difficulty/polynomial.md → docs/api/stepper/generic/difficulty/difficulty_polynomial.md

@@ -1,6 +1,6 @@
 # Polynomial
 
-::: exponax.normalized.DifficultyPolynomialStepper  
+::: exponax.stepper.generic.DifficultyPolynomialStepper  
     options:
         members:
             - __init__

docs/api/stepper/normalized/convection.md → docs/api/stepper/generic/normalized/normalized_convection.md

@@ -1,6 +1,6 @@
 # Convection
 
-::: exponax.normalized.NormalizedConvectionStepper  
+::: exponax.stepper.generic.NormalizedConvectionStepper  
     options:
         members:
             - __init__

docs/api/stepper/normalized/gradient_norm.md → docs/api/stepper/generic/normalized/normalized_gradient_norm.md

@@ -1,6 +1,6 @@
 # Gradient NormA
 
-::: exponax.normalized.NormalizedGradientNormStepper  
+::: exponax.stepper.generic.NormalizedGradientNormStepper  
     options:
         members:
             - __init__

docs/api/stepper/normalized/linear.md → docs/api/stepper/generic/normalized/normalized_linear.md

@@ -1,5 +1,5 @@
 
-::: exponax.normalized.NormalizedLinearStepper
+::: exponax.stepper.generic.NormalizedLinearStepper
     options:
         members:
             - __init__

docs/api/stepper/normalized/nonlinear.md → docs/api/stepper/generic/normalized/normalized_nonlinear.md

@@ -1,6 +1,6 @@
 # Nonlinear
 
-::: exponax.normalized.NormalizedGeneralNonlinearStepper  
+::: exponax.stepper.generic.NormalizedNonlinearStepper  
     options:
         members:
             - __init__

docs/api/stepper/normalized/polynomial.md → docs/api/stepper/generic/normalized/normalized_polynomial.md

@@ -1,6 +1,6 @@
 # Polynomial
 
-::: exponax.normalized.NormalizedPolynomialStepper  
+::: exponax.stepper.generic.NormalizedPolynomialStepper  
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_convection.md → docs/api/stepper/generic/physical/general_convection.md

@@ -1,6 +1,6 @@
 # General Convection Stepper
 
-::: exponax.stepper.GeneralConvectionStepper
+::: exponax.stepper.generic.GeneralConvectionStepper
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_gradient_norm.md → docs/api/stepper/generic/physical/general_gradient_norm.md

@@ -1,6 +1,6 @@
 # General Gradient Norm Stepper
 
-::: exponax.stepper.GeneralGradientNormStepper
+::: exponax.stepper.generic.GeneralGradientNormStepper
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_linear.md → docs/api/stepper/generic/physical/general_linear.md

@@ -1,6 +1,6 @@
 # General Linear Stepper
 
-::: exponax.stepper.GeneralLinearStepper
+::: exponax.stepper.generic.GeneralLinearStepper
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_nonlinear.md → docs/api/stepper/generic/physical/general_nonlinear.md

@@ -1,6 +1,6 @@
 # General Nonlinear Stepper
 
-::: exponax.stepper.GeneralNonlinearStepper
+::: exponax.stepper.generic.GeneralNonlinearStepper
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_polynomial.md → docs/api/stepper/generic/physical/general_polynomial.md

@@ -1,6 +1,6 @@
 # General Polynomial Stepper
 
-::: exponax.stepper.GeneralPolynomialStepper
+::: exponax.stepper.generic.GeneralPolynomialStepper
     options:
         members:
             - __init__

docs/api/stepper/physical/general/general_vorticity_convection.md → docs/api/stepper/generic/physical/general_vorticity_convection.md

@@ -1,6 +1,6 @@
 # General Vorticity Convection Stepper
 
-::: exponax.stepper.GeneralVorticityConvectionStepper
+::: exponax.stepper.generic.GeneralVorticityConvectionStepper
     options:
         members:
             - __init__

docs/api/stepper/overview.md

@@ -0,0 +1,23 @@
+# Overview
+
+`Exponax` comes with many pre-built dynamics. They are all based on the idea of
+solving semi-linear PDEs
+
+$$
+\partial_t u = \mathcal{L} u + \mathcal{N}(u)
+$$
+
+where $\mathcal{L}$ is a linear operator and $\mathcal{N}$ is a non-linear
+differential operator.
+
+TODO: add classification of dynamics based on:
+
+- linear or nonlinear or reaction-diffusion
+- specific (i.e. concrete equations like advection, Burgers etc.) or generic
+  based on providing a collection of linear and nonlinear coefficients
+- if generic: whether it uses a physical, normalized or difficulty-based
+  interface
+- in higher dimensions: whether it behaves isotropic or anisotropic (with
+  different coefficients per direction)
+
+Then the resulting behavior can also be classified into ...

docs/api/stepper/physical/reaction_diffusion/allen_cahn.md → docs/api/stepper/reaction/allen_cahn.md

@@ -1,6 +1,6 @@
 # Allen-Cahn
 
-::: exponax.reaction.AllenCahn
+::: exponax.stepper.reaction.AllenCahn
     options:
         members:
             - __init__

docs/api/stepper/physical/reaction_diffusion/cahn_hilliard.md → docs/api/stepper/reaction/cahn_hilliard.md

@@ -1,6 +1,6 @@
 # Cahn-Hilliad
 
-::: exponax.reaction.CahnHilliard
+::: exponax.stepper.reaction.CahnHilliard
     options:
         members:
             - __init__

docs/api/stepper/physical/reaction_diffusion/fisher_kpp.md → docs/api/stepper/reaction/fisher_kpp.md

@@ -1,6 +1,6 @@
 # Fisher-KPP
 
-::: exponax.reaction.FisherKPP
+::: exponax.stepper.reaction.FisherKPP
     options:
         members:
             - __init__

docs/api/stepper/physical/reaction_diffusion/gray_scott.md → docs/api/stepper/reaction/gray_scott.md

@@ -1,6 +1,6 @@
 # Gray-Scott
 
-::: exponax.reaction.GrayScott
+::: exponax.stepper.reaction.GrayScott
     options:
         members:
             - __init__