merge base branch

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.11", "3.12"]
+        python-version: ["3.9", "3.11", "3.12", "3.13"]
         os: [ubuntu-latest, windows-latest, macos-13]
     runs-on: ${{ matrix.os }}
     steps:
@@ -23,7 +23,7 @@ jobs:
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.8.3
+          poetry-version: 1.8.4
       - name: Cache Poetry virtualenv
         uses: actions/cache@v4
         id: cache
@@ -49,7 +49,7 @@ jobs:
         run: poetry run pytest --cov . --cov-report xml:coverage-reports/coverage-hydrolib-core.xml --junitxml=xunit-reports/xunit-result-hydrolib-core.xml
 
       - name: Autoformat code if the check fails
-        if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.12) }}
+        if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.13) }}
         run: |
           poetry run isort .
           poetry run black .

.github/workflows/docs.yml

@@ -12,12 +12,12 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.8.3
+          poetry-version: 1.8.4
       - name: Cache Poetry virtualenv
         uses: actions/cache@v4
         id: cache

.github/workflows/docs_release.yml

@@ -13,12 +13,12 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.8.3
+          poetry-version: 1.8.4
       - name: Cache Poetry virtualenv
         uses: actions/cache@v4
         id: cache

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.12]
+        python-version: [3.13]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     steps:
@@ -29,7 +29,7 @@ jobs:
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.8.3
+          poetry-version: 1.8.4
 
       - name: Cache Poetry virtualenv
         uses: actions/cache@v4

.github/workflows/release.yml

@@ -36,12 +36,12 @@ jobs:
       - name: Set up python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.8.3
+          poetry-version: 1.8.4
 
       - name: Cache Poetry virtualenv
         uses: actions/cache@v4

docs/changelog.md

@@ -1,3 +1,14 @@
+## 0.8.1 (2025-02-04)
+
+### Feat
+
+- Support Fortran scientific notation in .tim files (e.g., 1d0) (#720)
+- Corrected comment for layerType (#697)
+
+### Fix
+
+- failing docs (#728)
+
 ## 0.8.0 (2024-07-09)
 
 ### Feat

docs/guides/contributing.md

@@ -62,38 +62,27 @@ To prepare for releasing, please make sure you have a clean checkout of the late
  * Go to the root level your hydrolib-core checkout location
  * Open your command line in this location
  * Perform the following commands:
-	 * If commitizen is not installed yet:
+	 * Ensure that you are using the poetry environment (this contains commitizen), optionally run this command in a fresh environment:
 	 ```
-	 pip install commitizen
+	 poetry install
 	 ```
-	 * Prepare the Changelog before bumping the release version:
+	 * Update the Changelog before bumping the release version (use the version tag instead of the raw version number (so without "v" in our case)):
 	 ```
 	 cz changelog --unreleased-version="0.3.1" --incremental
 	 ```
-	 In the above command, use the version tag instead of the raw version number (so without "v" in our case).
-	 If you don't know the version tag yet, you can do a dry-run of the next step, for example via:
-	 ```
-	 cz bump --dry-run --increment PATCH
-	 ```
-	 * In the updated `docs/changelog.md`, manually add links to GitHub PR numbers (or issue numbers) at the end of each line, if appropriate.
-         It is recommended to use the macros `{{gh_pr(123)}}`, resp. `{{gh_issue(345)}}` to get automatic hyperlinks (where 123 and 345 are GitHub's PR and issue numbers, respectively).
 	 * Use MAJOR, MINOR or PATCH to increment the version
 	 ```
 	 cz bump --increment {MAJOR,MINOR,PATCH}
 	 ```
-	 * Or let commitizen detect the increment automatically
-	 ```
-	 cz bump
-	 ```
 	 * Push the tags and changes to git
 	 ```
 	 git push --tags
 	 git push
 	 ```
-	 * Build the wheels and publish the package to PyPi
+	 * Build the wheels and publish the package to PyPi (get an API token in your PyPI account)
 	 ```
 	 poetry build
-	 poetry publish
+	 poetry publish --username __token__ --password [PYPI_API_TOKEN]
 	 ```
 	 You will need a PyPI account and permissions for this publish step. Ask a maintainer for help if you need this.
 * Go to the hydrolib-core GitHub page.

hydrolib/core/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.8.1"

hydrolib/core/dflowfm/bc/models.py

@@ -950,7 +950,7 @@ class ForcingModel(INIModel):
 
     The `ForcingModel` class is the top-level model that aggregates metadata
     and multiple `[Forcing]` blocks. It provides functionality for parsing,
-    serializing, and managing data within a boundary conditions (.bc) file.
+    serializing, and managing data within a .bc file.
 
     Attributes:
         general (ForcingGeneral):
@@ -969,12 +969,6 @@ class ForcingModel(INIModel):
         serializer_config (DataBlockINIBasedSerializerConfig, optional):
             Serialization settings. Default to a predefined configuration.
 
-    Returns:
-        None
-
-    Raises:
-        ValueError: If invalid data is provided during initialization or parsing.
-
     See Also:
         ForcingBase: Represents individual forcing blocks within the file.
         ForcingGeneral: Metadata model for the `[General]` section.

hydrolib/core/dflowfm/ext/__init__.py

@@ -1,9 +1,10 @@
-from .models import Boundary, ExtGeneral, ExtModel, Lateral, Meteo
+from .models import Boundary, ExtGeneral, ExtModel, Lateral, Meteo, SourceSink
 
 __all__ = [
     "Boundary",
     "Lateral",
     "Meteo",
     "ExtGeneral",
     "ExtModel",
+    "SourceSink",
 ]

hydrolib/core/dflowfm/ext/models.py

@@ -51,7 +51,7 @@ class Boundary(INIBasedModel):
     locationfile: DiskOnlyFileModel = Field(
         default_factory=lambda: DiskOnlyFileModel(None), alias="locationFile"
     )
-    forcingfile: ForcingModel = Field(alias="forcingFile")
+    forcingfile: Union[ForcingModel, List[ForcingModel]] = Field(alias="forcingFile")
     bndwidth1d: Optional[float] = Field(alias="bndWidth1D")
     bndbldepth: Optional[float] = Field(alias="bndBlDepth")
 
@@ -212,7 +212,9 @@ class SourceSink(INIBasedModel):
     zsink: Optional[Union[float, List[float]]] = Field(alias="zSink")
     area: Optional[float] = Field(alias="Area")
 
-    bc_forcing: ForcingModel = Field(alias="bcForcing")
+    discharge: ForcingData = Field(alias="discharge")
+    salinitydelta: Optional[ForcingData] = Field(alias="salinityDelta")
+    temperaturedelta: Optional[ForcingData] = Field(alias="temperatureDelta")
 
     @classmethod
     def _exclude_from_validation(cls, input_data: Optional[dict] = None) -> Set:
@@ -380,7 +382,7 @@ def is_intermediate_link(self) -> bool:
 
 
 class ExtGeneral(INIGeneral):
-    """The external forcing file's `[General]` section with file meta data."""
+    """The external forcing file's `[General]` section with file meta-data."""
 
     _header: Literal["General"] = "General"
     fileversion: str = Field("2.01", alias="fileVersion")
@@ -397,19 +399,19 @@ class ExtModel(INIModel):
         general (ExtGeneral): `[General]` block with file metadata.
         boundary (List[Boundary]): List of `[Boundary]` blocks for all boundary conditions.
         lateral (List[Lateral]): List of `[Lateral]` blocks for all lateral discharges.
-        source_sink (List[SourceSink]): List of `[SourceSink]` blocks for all source/sink terms.
+        sourcesink (List[SourceSink]): List of `[SourceSink]` blocks for all source/sink terms.
         meteo (List[Meteo]): List of `[Meteo]` blocks for all meteorological forcings.
     """
 
     general: ExtGeneral = ExtGeneral()
     boundary: List[Boundary] = Field(default_factory=list)
     lateral: List[Lateral] = Field(default_factory=list)
-    source_sink: List[SourceSink] = Field(default_factory=list)
+    sourcesink: List[SourceSink] = Field(default_factory=list)
     meteo: List[Meteo] = Field(default_factory=list)
     serializer_config: INISerializerConfig = INISerializerConfig(
         section_indent=0, property_indent=0
     )
-    _split_to_list = make_list_validator("boundary", "lateral", "meteo")
+    _split_to_list = make_list_validator("boundary", "lateral", "meteo", "sourcesink")
 
     @classmethod
     def _ext(cls) -> str:

hydrolib/core/dflowfm/ini/models.py

@@ -324,12 +324,12 @@ def validate(cls: Type["INIBasedModel"], value: Any) -> "INIBasedModel":
         return super().validate(value)
 
     @classmethod
-    def _exclude_from_validation(cls, input_data: Optional = None) -> Set:
+    def _exclude_from_validation(cls, input_data: Optional[dict] = None) -> Set:
         """
         Fields that should not be checked when validating existing fields as they will be dynamically added.
 
         Args:
-            input_data (Optional): Input data to process.
+            input_data (Optional[dict]): Input data to process.
 
         Returns:
             Set: Set of field names to exclude from validation.

hydrolib/core/dflowfm/tim/models.py

@@ -8,6 +8,7 @@
 from hydrolib.core.basemodel import BaseModel, ModelSaveSettings, ParsableFileModel
 from hydrolib.core.dflowfm.tim.parser import TimParser
 from hydrolib.core.dflowfm.tim.serializer import TimSerializer, TimSerializerConfig
+from hydrolib.core.utils import FortranUtils
 
 
 class TimRecord(BaseModel):
@@ -176,6 +177,26 @@ def _get_serializer(
     def _get_parser(cls) -> Callable[[Path], Dict]:
         return TimParser.parse
 
+    @validator("timeseries", pre=True, check_fields=True, allow_reuse=True)
+    def replace_fortran_scientific_notation_for_floats(cls, value, field):
+        for record in value:
+            if isinstance(record, dict):
+                record["time"] = FortranUtils.replace_fortran_scientific_notation(
+                    record["time"]
+                )
+                record["data"] = FortranUtils.replace_fortran_scientific_notation(
+                    record["data"]
+                )
+            elif isinstance(record, TimRecord):
+                record.time = FortranUtils.replace_fortran_scientific_notation(
+                    record.time
+                )
+                record.data = FortranUtils.replace_fortran_scientific_notation(
+                    record.data
+                )
+
+        return value
+
     @validator("timeseries")
     @classmethod
     def _validate_timeseries_values(cls, v: List[TimRecord]) -> List[TimRecord]:
@@ -367,7 +388,7 @@ def get_units(self):
                 >>> tim_model = TimModel(filepath="tests/data/input/source-sink/tim-5-columns.tim")
                 >>> tim_model.quantities_names = ["discharge", "waterlevel", "temperature", "salinity", "initialtracer"]
                 >>> print(tim_model.get_units())
-                ['m3/s', 'm', 'C', 'ppt', '-']
+                ['m3/s', 'm', 'degC', '1e-3', '-']
 
                 ```
         """
@@ -390,14 +411,14 @@ def map_to_units(quantities_names: List[str]) -> List[str]:
             >>> from hydrolib.core.dflowfm.tim.models import TimModel
             >>> quantities_names = ["discharge", "waterlevel", "salinity", "temperature"]
             >>> TimModel.map_to_units(quantities_names)
-            ['m3/s', 'm', 'ppt', 'C']
+            ['m3/s', 'm', '1e-3', 'degC']
         """
         # Define the mapping of keywords to units
         unit_mapping = {
             "discharge": "m3/s",
             "waterlevel": "m",
-            "salinity": "ppt",
-            "temperature": "C",
+            "salinity": "1e-3",
+            "temperature": "degC",
         }
 
         # Generate the list of units based on the mapping
@@ -408,7 +429,7 @@ def map_to_units(quantities_names: List[str]) -> List[str]:
                     units.append(unit)
                     break
             else:
-                # Append "Unknown" if no keywords match
+                # Append "-" if no keywords match
                 units.append("-")
 
         return units

hydrolib/core/utils.py

@@ -6,6 +6,8 @@
 from pathlib import Path
 from typing import Any, Callable, List, Optional
 
+from pydantic import validator
+from pydantic.v1.fields import ModelField
 from strenum import StrEnum
 
 
@@ -332,3 +334,23 @@ def _calculate_md5_checksum(filepath: Path) -> str:
             for chunk in iter(lambda: file.read(4096), b""):
                 md5_hash.update(chunk)
         return md5_hash.hexdigest()
+
+
+class FortranUtils:
+    """Utility class for Fortran specific conventions."""
+
+    _scientific_exp_d_notation_regex = re.compile(
+        r"([\d.]+)([dD])([+-]?\d{1,3})"
+    )  # matches a float: 1d9, 1D-3, 1.D+4, etc.
+
+    @staticmethod
+    def replace_fortran_scientific_notation(value):
+        """Replace Fortran scientific notation ("D" in exponent) with standard
+        scientific notation ("e" in exponent).
+        """
+        if isinstance(value, str):
+            return FortranUtils._scientific_exp_d_notation_regex.sub(r"\1e\3", value)
+        elif isinstance(value, list):
+            return list(map(FortranUtils.replace_fortran_scientific_notation, value))
+
+        return value