Prepare release

CITATION.cff

@@ -19,6 +19,11 @@ authors:
     email: f.nattino@esciencecenter.nl
     affiliation: Netherlands eScience Center
     orcid: 'https://orcid.org/0000-0003-3286-0139'
+  - given-names: Simone
+    family-names: Ciarella
+    email: s.ciarella@esciencecenter.nl
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0002-9247-139X'
   - given-names: Michiel
     family-names: Kallenberg
     email: michiel.kallenberg@wur.nl
@@ -35,7 +40,7 @@ authors:
     affiliation: Wageningen University & Research
     orcid: 'https://orcid.org/0000-0002-5517-6404'
 date-released: 2025-10-29
-version: "0.2.0"
+version: "0.3.0"
 repository-code: "https://github.com/WUR-AI/diffwofost"
 keywords:
   - "wofost"

docs/api_reference.md

@@ -6,15 +6,16 @@ hide:
 
 ## **Crop modules**
 
-::: diffwofost.physical_models.crop.leaf_dynamics.WOFOST_Leaf_Dynamics
-
-::: diffwofost.physical_models.crop.root_dynamics.WOFOST_Root_Dynamics
-
 ::: diffwofost.physical_models.crop.phenology.DVS_Phenology
 
+::: diffwofost.physical_models.crop.partitioning.DVS_Partitioning
+
 ::: diffwofost.physical_models.crop.assimilation.WOFOST72_Assimilation
 
-::: diffwofost.physical_models.crop.partitioning.DVS_Partitioning
+::: diffwofost.physical_models.crop.leaf_dynamics.WOFOST_Leaf_Dynamics
+
+::: diffwofost.physical_models.crop.root_dynamics.WOFOST_Root_Dynamics
+
 
 ## **Utility (under development)**
 

docs/examples.md

@@ -8,10 +8,13 @@ We provide an example notebook showing optimization of models' parameters with
 
 | Model | Open the notebook | Access the source | View the notebook |
 |---|----|------------|---------------|
-| Leaf and Root dynamics| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][leaf_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][leaf_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization.ipynb) |
 | Phenology | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][pheno_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][pheno_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization_phenology.ipynb) |
+| Root dynamics| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][root_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][root_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization_root_dynamics.ipynb) |
+| Leaf dynamics| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][leaf_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][leaf_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization_leaf_dynamics.ipynb) |
+
 
 !!! note
+
     When calculating gradients, it is important to ensure that the predicted
     physical parameters are within realistic bounds regarding the crop and
     environmental conditions.
@@ -22,7 +25,47 @@ We provide an example notebook showing optimization of models' parameters with
     output w.r.t the parameter will be close to zero, which may not provide
     useful information for optimization.
 
-[leaf_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb
-[leaf_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb
+
+## Computing configuration
+
+The object `ComputeConfig` provides a central configuration for PyTorch device
+and dtype settings across all simulation objects in diffWOFOST. Instead of
+setting device and dtype individually for each class, use this central
+configuration to apply settings globally.
+
+**Default Behavior:**
+
+- **Device**: Automatically defaults to 'cuda' if available, otherwise 'cpu'
+- **Dtype**: Defaults to torch.float64
+
+**Basic Usage:**
+
+```python
+from diffwofost.physical_models.config import ComputeConfig
+import torch
+# Set device to CPU
+ComputeConfig.set_device('cpu')
+
+# Or use a torch.device object
+ComputeConfig.set_device(torch.device('cuda'))
+
+# Set dtype to float32
+ComputeConfig.set_dtype(torch.float32)
+
+# Get current settings
+device = ComputeConfig.get_device()  # Returns: torch.device('cpu')
+dtype = ComputeConfig.get_dtype()    # Returns: torch.float32
+```
+
+**More info:**
+
+See the [ComputeConfig API
+reference](./api_reference.md#diffwofost.physical_models.config.ComputeConfig)
+for more details.
+
+[leaf_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_leaf_dynamics.ipynb
+[leaf_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_leaf_dynamics.ipynb
+[root_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_root_dynamics.ipynb
+[root_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_root_dynamics.ipynb
 [pheno_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_phenology.ipynb
 [pheno_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_phenology.ipynb

docs/index.md

@@ -106,6 +106,5 @@ The package is structured as follows:
 ```
 
 !!! note
-    At the moment only two modules of `leaf_dynamics` and `root_dynamics` are
-    differentiable w.r.t two parameters of `SPAN` and `TDWI`. But the package is under
-    continuous development. So make sure that you install the latest version.
+    At the moment the package is under continuous development. So make sure that
+    you install the latest version.

docs/notebooks/optimization_leaf_dynamics.ipynb

@@ -79,6 +79,18 @@
     "from diffwofost.physical_models.utils import get_test_data"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9c2ca761-22b0-4707-9f55-619f62617d12",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# --- run on CPU ------\n",
+    "from diffwofost.physical_models.config import ComputeConfig\n",
+    "ComputeConfig.set_device('cpu')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

docs/notebooks/optimization_phenology.ipynb

@@ -73,6 +73,18 @@
     "from diffwofost.physical_models.utils import get_test_data"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8a06565c-139a-4039-92d5-bcfd7bcf8344",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# --- run on CPU ------\n",
+    "from diffwofost.physical_models.config import ComputeConfig\n",
+    "ComputeConfig.set_device('cpu')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

docs/notebooks/optimization_root_dynamics.ipynb

@@ -88,6 +88,18 @@
     "from diffwofost.physical_models.utils import get_test_data"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10c6361e-ad31-455f-aed1-b7a282cb793c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# --- run on CPU ------\n",
+    "from diffwofost.physical_models.config import ComputeConfig\n",
+    "ComputeConfig.set_device('cpu')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,

docs/run_model.md

@@ -14,13 +14,21 @@ In a nutshell, we can run a model, for example, `leaf_dynamics` using diffWOFOST
 
 ```python
 from diffwofost.physical_models.utils import EngineTestHelper
+from diffwofost.physical_models.config import Configuration
+from diffwofost.physical_models.crop.leaf_dynamics import WOFOST_Leaf_Dynamics
+
+# create config
+leaf_dynamics_config = Configuration(
+    CROP=WOFOST_Leaf_Dynamics,
+    OUTPUT_VARS=["LAI", "TWLV"],
+)
 
 # create the model
 model = EngineTestHelper(
     crop_parameters_provider,  # this provides the crop parameters
     weather_data_provider,
     agromanagement_provider,
-    leaf_dynamics_config_file,  # this where the differentiable model is specified
+    leaf_dynamics_config,  # this where the differentiable model is specified
     external_states,  # any external states if needed
 )
 

pyproject.toml

@@ -34,7 +34,7 @@ license = {file = "LICENSE"}
 name = "diffwofost"
 readme = {file = "README.md", content-type = "text/markdown"}
 requires-python = ">=3.11"
-version = "0.2.0"
+version = "0.3.0"
 
 [project.optional-dependencies]
 dev = [
@@ -131,7 +131,7 @@ force-single-line = true
 no-lines-before = ["future","standard-library","third-party","first-party","local-folder"]
 
 [tool.bumpversion]
-current_version = "0.2.0"
+current_version = "0.3.0"
 
 [[tool.bumpversion.files]]
 filename = "src/diffwofost/__init__.py"
@@ -141,6 +141,3 @@ filename = "pyproject.toml"
 
 [[tool.bumpversion.files]]
 filename = "CITATION.cff"
-
-[[tool.bumpversion.files]]
-filename = "docs/conf.py"

src/diffwofost/__init__.py

@@ -2,19 +2,23 @@
 
 import logging
 from diffwofost.physical_models import utils
+from diffwofost.physical_models.crop import assimilation
 from diffwofost.physical_models.crop import leaf_dynamics
+from diffwofost.physical_models.crop import partitioning
 from diffwofost.physical_models.crop import phenology
 from diffwofost.physical_models.crop import root_dynamics
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = ""
 __email__ = ""
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 
 __all__ = [
     "leaf_dynamics",
     "root_dynamics",
     "phenology",
+    "assimilation",
+    "partitioning",
     "utils",
 ]