astoeriko · edvinskis · Jun 15, 2026 · Jun 18, 2026 · Jun 24, 2026 · Jun 24, 2026
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -40,7 +40,7 @@ jobs:
           pytest tests/ -v --tb=short \
             --cov=src/reactix \
             --cov-report=term-missing \
-            --cov-report=
+            --cov-report=xml:reports/coverage/coverage.xml
 
       - name: Add coverage to job summary
         run: |
@@ -50,11 +50,7 @@ jobs:
           coverage report --show-missing >> $GITHUB_STEP_SUMMARY
           echo '```' >> $GITHUB_STEP_SUMMARY
 
-      # If uploading the coverage report to Codecov:
-      # uncomment the following lines and make sure you have a Codecov token set in your repository secrets.
-      # More information: https://docs.codecov.com/docs/quick-start
-      #
-      # - name: Upload coverage reports to Codecov with GitHub Action
-      #   uses: codecov/codecov-action@v5
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.md b/README.md
@@ -1,4 +1,12 @@
-# Reactix – Simulating 1-D reactive transport with differentiable models in JAX
+![](https://raw.githubusercontent.com/astoeriko/reactix/refs/heads/develop/img/logo.svg)
+# Simulating 1-D reactive transport with differentiable models in JAX
+
+[![PyPI](https://img.shields.io/pypi/v/reactix)](https://pypi.org/project/reactix/)
+[![Python](https://img.shields.io/pypi/pyversions/reactix)](https://pypi.org/project/reactix/)
+[![PyTest](https://github.com/astoeriko/reactix/actions/workflows/pytest.yml/badge.svg)](https://github.com/astoeriko/reactix/actions/workflows/pytest.yml)
+[![codecov](https://codecov.io/gh/astoeriko/reactix/branch/develop/graph/badge.svg)](https://codecov.io/gh/astoeriko/reactix)
+[![License](https://img.shields.io/github/license/astoeriko/reactix)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-latest-blue)](https://astoeriko.github.io/reactix/)
 
 Reactix is a Python package for simulating reactive transport of chemical species suitable for one-dimensional systems with **advection, dispersion and kinetic reactions**.
 
@@ -55,8 +63,7 @@ reactix-env\Scripts\activate      # Windows
 
 Activate the environment before installing the package.
 
-> [!NOTE]  
-> If you don't have `uv` installed, you can get it with:
+> **Note:** If you don't have `uv` installed, you can get it with:
 
 ```bash
 # Linux/macOS

diff --git a/diagrams/class-diagram.png b/diagrams/class-diagram.png
diff --git a/diagrams/class-diagram.svg b/diagrams/class-diagram.svg
diff --git a/diagrams/model-workflow.png b/diagrams/model-workflow.png
diff --git a/diagrams/model-workflow.svg b/diagrams/model-workflow.svg
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/docs/_quarto.yml b/docs/_quarto.yml
@@ -15,6 +15,7 @@ website:
   back-to-top-navigation: true
 
   navbar:
+    logo: img/logo_without_text.svg
     left:
       - href: index.qmd
         text: Home
@@ -42,17 +43,17 @@ website:
             - index.qmd
             - installation.qmd
             - quickstart.qmd
-        
+
         - text: "---"
         - section: Examples
           contents:
             - examples/index.qmd
             - examples/transport-model.qmd
-        
-        - text: "---"   
+
+        - text: "---"
         - href: api/index.qmd
           text: API reference
-       
+
         - text: "---"
         - section: Development
           contents:
@@ -69,13 +70,18 @@ quartodoc:
   title: "API reference"
   sections:
     - title: Transport
-      desc: Core 1D reactive transport system objects and solver helpers.
+      desc: Spatial discretization, advection/dispersion schemes, and boundary conditions.
       contents:
-        - System
         - Cells
         - Advection
         - Dispersion
         - FixedConcentrationBoundary
+
+    - title: Systems
+      desc: Reactive transport and system containers, and solver helpers.
+      contents:
+        - TransportSystem
+        - MixedSystem
         - make_solver
         - user_system_parameters
 

diff --git a/docs/api/Advection.qmd b/docs/api/Advection.qmd
@@ -106,7 +106,7 @@ Compute the advection rate for mobile species.
 |--------|-----------------|---------------------------------|------------|
 | time   | jax.Array       | Current simulation time.        | _required_ |
 | state  | AbstractSpecies | Current species concentrations. | _required_ |
-| system | System          | The reactive transport system.  | _required_ |
+| system | TransportSystem | The reactive transport system.  | _required_ |
 
 #### Returns {.doc-section .doc-section-returns}
 

diff --git a/docs/api/Dispersion.qmd b/docs/api/Dispersion.qmd
@@ -62,10 +62,10 @@ Compute dispersion coefficients for each species.
 
 #### Parameters {.doc-section .doc-section-parameters}
 
-| Name   | Type      | Description                    | Default    |
-|--------|-----------|--------------------------------|------------|
-| time   | jax.Array | Current simulation time.       | _required_ |
-| system | System    | The reactive transport system. | _required_ |
+| Name   | Type            | Description                    | Default    |
+|--------|-----------------|--------------------------------|------------|
+| time   | jax.Array       | Current simulation time.       | _required_ |
+| system | TransportSystem | The reactive transport system. | _required_ |
 
 #### Returns {.doc-section .doc-section-returns}
 
@@ -87,7 +87,7 @@ Compute the dispersion contribution to the species rate of change.
 |--------|-----------------|---------------------------------|------------|
 | time   | jax.Array       | Current simulation time.        | _required_ |
 | state  | AbstractSpecies | Current species concentrations. | _required_ |
-| system | System          | The reactive transport system.  | _required_ |
+| system | TransportSystem | The reactive transport system.  | _required_ |
 
 #### Returns {.doc-section .doc-section-returns}
 

diff --git a/docs/api/FixedConcentrationBoundary.qmd b/docs/api/FixedConcentrationBoundary.qmd
@@ -18,12 +18,12 @@ unphysical behavior.
 
 ## Parameters {.doc-section .doc-section-parameters}
 
-| Name                | Type                                          | Description                                                                                 | Default                             |
-|---------------------|-----------------------------------------------|---------------------------------------------------------------------------------------------|-------------------------------------|
-| fixed_concentration | float or Callable\[\[jax.Array\], jax.Array\] | The fixed concentration value, either constant or time-dependent.                           | _required_                          |
-| is_active           | Callable\[\[jax.Array, System\], jax.Array\]  | Function determining if the boundary condition is active. Inherited from BoundaryCondition. | `lambda t, system: jnp.array(True)` |
-| species_selector    | Callable                                      | Function to select which species this applies to. Inherited from BoundaryCondition.         | _required_                          |
-| boundary            | Literal\[\'left\', \'right\'\]                | Which boundary this applies to. Inherited from BoundaryCondition.                           | _required_                          |
+| Name                | Type                                                  | Description                                                                                 | Default                             |
+|---------------------|-------------------------------------------------------|---------------------------------------------------------------------------------------------|-------------------------------------|
+| fixed_concentration | float or Callable\[\[jax.Array\], jax.Array\]         | The fixed concentration value, either constant or time-dependent.                           | _required_                          |
+| is_active           | Callable\[\[jax.Array, TransportSystem\], jax.Array\] | Function determining if the boundary condition is active. Inherited from BoundaryCondition. | `lambda t, system: jnp.array(True)` |
+| species_selector    | Callable                                              | Function to select which species this applies to. Inherited from BoundaryCondition.         | _required_                          |
+| boundary            | Literal\[\'left\', \'right\'\]                        | Which boundary this applies to. Inherited from BoundaryCondition.                           | _required_                          |
 
 ## Notes {.doc-section .doc-section-notes}
 
@@ -46,11 +46,11 @@ Compute the advective and dispersive flux at the boundary.
 
 #### Parameters {.doc-section .doc-section-parameters}
 
-| Name                | Type      | Description                         | Default    |
-|---------------------|-----------|-------------------------------------|------------|
-| time                | jax.Array | Current simulation time.            | _required_ |
-| system              | System    | The reactive transport system.      | _required_ |
-| boundary_cell_state | jax.Array | Concentration in the boundary cell. | _required_ |
+| Name                | Type            | Description                         | Default    |
+|---------------------|-----------------|-------------------------------------|------------|
+| time                | jax.Array       | Current simulation time.            | _required_ |
+| system              | TransportSystem | The reactive transport system.      | _required_ |
+| boundary_cell_state | jax.Array       | Concentration in the boundary cell. | _required_ |
 
 #### Returns {.doc-section .doc-section-returns}
 

diff --git a/docs/api/MixedSystem.qmd b/docs/api/MixedSystem.qmd
@@ -0,0 +1,88 @@
+# MixedSystem { #reactix.MixedSystem }
+
+```python
+MixedSystem(
+    reactions=list(),
+    discharge,
+    inflow_concentration,
+    volume,
+    parameters=None,
+)
+```
+
+Represents a mixed (batch) reactor system without spatial transport.
+
+This class models a well-mixed reactor where species concentrations are
+uniform throughout the volume. It supports kinetic reactions, inflow/outflow,
+and user-defined parameters.
+
+## Parameters {.doc-section .doc-section-parameters}
+
+| Name                 | Type                                              | Description                                                                                        | Default    |
+|----------------------|---------------------------------------------------|----------------------------------------------------------------------------------------------------|------------|
+| reactions            | list\[KineticReaction\]                           | List of kinetic reactions. Default is empty list.                                                  | `list()`   |
+| discharge            | Callable\[\[jax.Array\], jax.Array\] or jax.Array | Function that computes discharge (volumetric flow rate) given time, or a constant discharge value. | _required_ |
+| inflow_concentration | AbstractSpecies                                   | Concentration of species in the inflow.                                                            | _required_ |
+| volume               | jax.Array                                         | Volume of the mixed reactor.                                                                       | _required_ |
+| parameters           | Any                                               | Additional system parameters. Default is None.                                                     | `None`     |
+
+## Methods
+
+| Name | Description |
+| --- | --- |
+| [build](#reactix.MixedSystem.build) | Build a configured mixed reactor system. |
+| [compute_inflow_outflow](#reactix.MixedSystem.compute_inflow_outflow) | Compute the inflow/outflow contribution to the rate of change of concentrations. |
+
+### build { #reactix.MixedSystem.build }
+
+```python
+MixedSystem.build(
+    reactions=None,
+    discharge,
+    inflow_concentration,
+    volume,
+    parameters=None,
+)
+```
+
+Build a configured mixed reactor system.
+
+This convenience constructor validates input shapes and
+normalizes scalar inputs before creating a MixedSystem instance.
+
+#### Parameters {.doc-section .doc-section-parameters}
+
+| Name                 | Type                                              | Description                                    | Default    |
+|----------------------|---------------------------------------------------|------------------------------------------------|------------|
+| reactions            | list\[KineticReaction\] or None                   | List of kinetic reactions. Default is None.    | `None`     |
+| discharge            | Callable\[\[jax.Array\], jax.Array\] or jax.Array | Discharge function or scalar discharge value.  | _required_ |
+| inflow_concentration | AbstractSpecies                                   | Concentration of species in the inflow.        | _required_ |
+| volume               | jax.Array                                         | Volume of the mixed reactor.                   | _required_ |
+| parameters           | Any or None                                       | Additional system parameters. Default is None. | `None`     |
+
+#### Returns {.doc-section .doc-section-returns}
+
+| Name   | Type        | Description                      |
+|--------|-------------|----------------------------------|
+|        | MixedSystem | Configured mixed reactor system. |
+
+### compute_inflow_outflow { #reactix.MixedSystem.compute_inflow_outflow }
+
+```python
+MixedSystem.compute_inflow_outflow(time, state)
+```
+
+Compute the inflow/outflow contribution to the rate of change of concentrations.
+
+#### Parameters {.doc-section .doc-section-parameters}
+
+| Name   | Type            | Description                     | Default    |
+|--------|-----------------|---------------------------------|------------|
+| time   | jax.Array       | Current simulation time.        | _required_ |
+| state  | AbstractSpecies | Current species concentrations. | _required_ |
+
+#### Returns {.doc-section .doc-section-returns}
+
+| Name   | Type            | Description                                   |
+|--------|-----------------|-----------------------------------------------|
+|        | AbstractSpecies | Rate of change due to inflow/outflow (dc/dt). |
diff --git a/docs/api/System.qmd → docs/api/TransportSystem.qmd b/docs/api/System.qmd → docs/api/TransportSystem.qmd
@@ -1,7 +1,7 @@
-# System { #reactix.System }
+# TransportSystem { #reactix.TransportSystem }
 
 ```python
-System(
+TransportSystem(
     porosity,
     discharge,
     cells,
@@ -38,13 +38,13 @@ species mobility, reactions, and boundary conditions.
 
 | Name | Description |
 | --- | --- |
-| [build](#reactix.System.build) | Build a configured reactive transport system. |
-| [cell_velocity](#reactix.System.cell_velocity) | Compute the pore-water velocity in each cell. |
+| [build](#reactix.TransportSystem.build) | Build a configured reactive transport system. |
+| [cell_velocity](#reactix.TransportSystem.cell_velocity) | Compute the pore-water velocity in each cell. |
 
-### build { #reactix.System.build }
+### build { #reactix.TransportSystem.build }
 
 ```python
-System.build(
+TransportSystem.build(
     cells,
     advection,
     dispersion,
@@ -60,7 +60,7 @@ System.build(
 Build a configured reactive transport system.
 
 This convenience constructor validates input shapes and
-normalizes scalar inputs before creating a System instance.
+normalizes scalar inputs before creating a TransportSystem instance.
 
 #### Parameters {.doc-section .doc-section-parameters}
 
@@ -71,27 +71,27 @@ normalizes scalar inputs before creating a System instance.
 | dispersion        | Dispersion                                        | Dispersion scheme parameters.                                                                                       | _required_ |
 | bcs               | list\[BoundaryCondition\] or None                 | List of boundary conditions. Default is None.                                                                       | `None`     |
 | species_is_mobile | AbstractSpecies                                   | Species mobility information.                                                                                       | _required_ |
-| reactions         | list\[BoundaryCondition\] or None                 | List of kinetic reactions. Default is None.                                                                         | `None`     |
+| reactions         | list\[KineticReaction\] or None                   | List of kinetic reactions. Default is None.                                                                         | `None`     |
 | discharge         | Callable\[\[jax.Array\], jax.Array\] or jax.Array | Discharge function or scalar discharge value.                                                                       | _required_ |
 | porosity          | jax.Array                                         | Porosity of the medium, either scalar or per cell.                                                                  | _required_ |
 | parameters        | Any or None                                       | Additional system parameters. Default is None. Must be created with @user_system_parameters for spatial operations. | `None`     |
 
 #### Returns {.doc-section .doc-section-returns}
 
-| Name   | Type   | Description                           |
-|--------|--------|---------------------------------------|
-|        | System | Configured reactive transport system. |
+| Name   | Type            | Description                           |
+|--------|-----------------|---------------------------------------|
+|        | TransportSystem | Configured reactive transport system. |
 
 #### Raises {.doc-section .doc-section-raises}
 
 | Name   | Type       | Description                                                                                         |
 |--------|------------|-----------------------------------------------------------------------------------------------------|
 |        | ValueError | If porosity has an invalid shape or a boundary condition is incompatible with the selected species. |
 
-### cell_velocity { #reactix.System.cell_velocity }
+### cell_velocity { #reactix.TransportSystem.cell_velocity }
 
 ```python
-System.cell_velocity(t)
+TransportSystem.cell_velocity(t)
 ```
 
 Compute the pore-water velocity in each cell.

diff --git a/docs/api/_sidebar.yml b/docs/api/_sidebar.yml
@@ -3,14 +3,17 @@ website:
   - contents:
     - api/index.qmd
     - contents:
-      - api/System.qmd
       - api/Cells.qmd
       - api/Advection.qmd
       - api/Dispersion.qmd
       - api/FixedConcentrationBoundary.qmd
+      section: Transport
+    - contents:
+      - api/TransportSystem.qmd
+      - api/MixedSystem.qmd
       - api/make_solver.qmd
       - api/user_system_parameters.qmd
-      section: Transport
+      section: Systems
     - contents:
       - api/declare_species.qmd
       section: Species

diff --git a/docs/api/index.qmd b/docs/api/index.qmd
@@ -2,16 +2,24 @@
 
 ## Transport
 
-Core 1D reactive transport system objects and solver helpers.
+Spatial discretization, advection/dispersion schemes, and boundary conditions.
 
 | | |
 | --- | --- |
-| [System](System.qmd#reactix.System) | Represents a 1D reactive transport system. |
 | [Cells](Cells.qmd#reactix.Cells) | Represents the spatial discretization of a 1D domain into cells. |
 | [Advection](Advection.qmd#reactix.Advection) | Handles advection terms in the 1D transport equation using TVD schemes. |
 | [Dispersion](Dispersion.qmd#reactix.Dispersion) | Handles dispersion and diffusion terms in the transport equation. |
 | [FixedConcentrationBoundary](FixedConcentrationBoundary.qmd#reactix.FixedConcentrationBoundary) | Boundary condition with fixed concentration at the domain boundary. |
-| [make_solver](make_solver.qmd#reactix.make_solver) | Create a JIT-compiled solver function for reactive transport simulations. |
+
+## Systems
+
+Reactive transport and system containers, and solver helpers.
+
+| | |
+| --- | --- |
+| [TransportSystem](TransportSystem.qmd#reactix.TransportSystem) | Represents a 1D reactive transport system. |
+| [MixedSystem](MixedSystem.qmd#reactix.MixedSystem) | Represents a mixed (batch) reactor system without spatial transport. |
+| [make_solver](make_solver.qmd#reactix.make_solver) | Create a JIT-compiled solver function for reactix simulations. |
 | [user_system_parameters](user_system_parameters.qmd#reactix.user_system_parameters) | Decorate system parameter classes with spatial awareness. |
 
 ## Species