added t-route unit tests

doc/docker/dockerfile_notebook.md

@@ -0,0 +1,38 @@
+# Dockerfile.Notebook
+
+This document describes the Docker setup for running JupyterLab with mounted volumes for development and analysis.
+
+## Container Overview
+
+The container provides a JupyterLab environment with:
+- Python environment for data analysis
+- Web interface accessible via port 8000
+
+This container is a great way to run examples and integrated tests
+
+## Docker Configuration
+
+### Dockerfile
+The Dockerfile sets up:
+- Base Python environment
+- JupyterLab installation
+- Volume mount points for data and code
+- Port 8000 exposed for web interface
+- Working directory configuration
+
+### Getting Started
+
+Build:
+```bash
+docker build -t troute-notebook -f docker/Dockerfile.notebook .
+```
+
+Run:
+```bash
+docker run -p 8000:8000 troute-notebook
+```
+
+Then, take the URL from the output and put that into your browser. An example one is below:
+```
+http://127.0.0.1:8000/lab?token=<token>
+```

docker/Dockerfile.notebook

@@ -0,0 +1,29 @@
+FROM rockylinux:9.2 as rocky-base
+RUN yum install -y epel-release 
+RUN yum install -y netcdf netcdf-fortran netcdf-fortran-devel netcdf-openmpi
+
+RUN yum install -y git cmake python python-devel pip 
+
+WORKDIR "/t-route/"
+
+COPY . /t-route/
+
+RUN ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/openmpi-x86_64/netcdf.mod
+
+ENV VIRTUAL_ENV=/opt/venv
+RUN python3 -m venv $VIRTUAL_ENV
+
+# Equivalent to source /opt/venv/bin/activate
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+RUN python -m pip install .
+RUN python -m pip install .[jupyter]
+RUN python -m pip install .[test]
+
+RUN ./compiler.sh no-e
+
+EXPOSE 8000
+
+# increase max open files soft limit
+RUN ulimit -n 10000
+CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8000", "--no-browser", "--allow-root"]

pyproject.toml

@@ -0,0 +1,28 @@
+[project]
+name = "troute_project"
+authors = [
+    {name = "DongHa Kim", email = "dongha.kim@noaa.gov"},
+    {name = "Sean Horvath", email = "sean.horvath@noaa.gov"},
+    {name = "Amin Torabi", email = "amin.torabi@noaa.gov"},
+    {name = "Zach Jurgen", email = "jurgen.zach@noaa.gov"},
+    {name = "Austin Raney", email = "austin.raney@noaa.gov"},
+]
+dynamic = ["version", "dependencies"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+
+[project.optional-dependencies]
+test = [
+    "pytest==8.3.2",
+    "bmipy==2.0.0",
+]
+
+jupyter = [
+    "contextily==1.6.0",
+    "matplotlib>=3.7.0,<3.8.0",  # More stable version range
+    "ipykernel>=6.29.0,<7.0.0",
+    "jupyterlab>=3.6.7,<4.0.0",
+    "xarray>=2024.1.1",
+    "matplotlib-inline>=0.1.6"  # Add explicit version
+]

src/troute-config/test/__init__.py

@@ -0,0 +1,31 @@
+import os
+
+from contextlib import contextmanager
+from pathlib import Path
+
+
+@contextmanager
+def temporarily_change_dir(path: Path):
+    """Temporarily changes the current working directory
+
+    This context manager changes the current working directory to the specified path,
+    yields control back to the caller, and then changes back to the original directory
+    when exiting the context
+
+    Parameters
+    ----------
+    path : Path
+        The path to temporarily change the current working directory to
+
+    Yields
+    ------
+    None
+    """
+    original_cwd = Path.cwd()
+    if original_cwd != path:
+        os.chdir(path)
+    try:
+        yield
+    finally:
+        if original_cwd != path:
+            os.chdir(original_cwd)

src/troute-config/test/conftest.py

@@ -0,0 +1,40 @@
+from pathlib import Path
+from typing import Any, Dict, List, Tuple
+
+import pytest
+import yaml
+from _pytest.fixtures import FixtureRequest
+
+
+def find_config_files() -> List[Path]:
+    """Finds all `.yaml` configuration files within specified directories
+
+    Returns
+    -------
+    List[Path]
+        A list of Path objects pointing to each valid configuration
+    """
+    test_dir = Path(__file__).parents[3] / "test"  # Searching for the t-route/test dir
+    target_dirs = ["LowerColorado_TX", "LowerColorado_TX_v4", "LowerColorado_TX_HYFeatures_v22", "unit_test_hyfeature"]
+    files = []
+    for dir_name in target_dirs:
+        files.extend(list((test_dir / dir_name).glob("*.yaml")))
+    return files
+
+
+@pytest.fixture(params=find_config_files())
+def config_data(request: FixtureRequest) -> Tuple[Path, Dict[str, Any]]:
+    """A fixture for loading yaml files into python dictionary mappings
+
+    Parameters
+    ----------
+    request : FixtureRequest
+        The pytest request object, containing the current parameter value
+
+    Returns
+    -------
+    Tuple[Path, Dict[str, Any]]
+        A tuple containing the path to the YAML file and the loaded data as a dictionary
+    """
+    data = yaml.load(request.param.read_text(), Loader=yaml.Loader)
+    return request.param, data

src/troute-config/test/test_config.py

@@ -1,21 +1,98 @@
-import pytest
-
-import yaml
 from pathlib import Path
-from typing import List
+from test import temporarily_change_dir
+from typing import Any, Dict, Tuple
 
+import pytest
+from pydantic import ValidationError
 from troute.config import Config
 
-TEST_DIR = Path(__file__).parent
-ROOT_TEST_DIR = TEST_DIR / "../../../test"
 
+def test_config_validation(config_data: Tuple[Path, Dict[str, Any]]) -> None:
+    """Validates all config files contained within the `test/` folder
+
+    Parameters
+    ----------
+    config_data : Tuple[Path, Dict[str, Any]]
+        A tuple containing the path to the config file and the parsed config data
+        - The first element is a Path object pointing to the config file
+        - The second element is a dictionary containing the parsed config yaml file data.
+
+    Raises
+    ------
+    pytest.fail
+        If a ValidationError occurs during Config creation, this function will
+        call pytest.fail with a detailed error message showing the config file that fails
+
+    Notes
+    -----
+    This test function uses the `temporarily_change_dir` context manager to
+    change the working directory before attempting to create the Config object
+    """
+    path, data = config_data
+    with temporarily_change_dir(path.parent):
+        try:
+            Config(**data)
+        except ValidationError as e:
+            error_details = "\n".join(
+                f"{' -> '.join(map(str, err['loc']))}: {err['msg']}"
+                for err in e.errors()
+            )
+            pytest.fail(f"Validation failed for {path}:\n{error_details}")
+
+
+def test_strict_config_validation(config_data: Tuple[Path, Dict[str, Any]]) -> None:
+    """Validates all config files contained within the `test/` folder via strict handling
+
+    Parameters
+    ----------
+    config_data : Tuple[Path, Dict[str, Any]]
+        A tuple containing the path to the config file and the parsed config data
+        - The first element is a Path object pointing to the config file
+        - The second element is a dictionary containing the parsed config yaml file data.
+
+    Raises
+    ------
+    pytest.fail
+        If a ValidationError occurs during Config creation, this function will
+        call pytest.fail with a detailed error message showing the config file that fails
 
-def config_files() -> List[Path]:
-    files = list(ROOT_TEST_DIR.glob("*/*.yaml"))
-    return files
+    Notes
+    -----
+    - This test function uses the `temporarily_change_dir` context manager to
+    change the working directory before attempting to create the Config object
+    - If this code runs into a "value_error.path.not_exists" error, this is either because:
+      1. there is a relative path in the config
+      2. the file doesn't exist
+      Thus, we will make the relative path absolute and retry the validation. If that fails, we
+      know the file does not existt
+    """
+    path, data = config_data
+    parent_path = path.parent
+    try:
+        with temporarily_change_dir(path.parent):
+            Config.with_strict_mode(**data)
+    except ValidationError as e:
+        for error in e.errors():
+            if error["type"] == "value_error.path.not_exists":
+                keys = error["loc"]
+                invalid_path = error["ctx"]["path"]
+                corrected_path = Path(parent_path, invalid_path).__str__()
 
+                # Ensuring the code path exists before changing relative path to absolute
+                if Path(corrected_path).exists():
+                    current = data
+                    for key in keys[:-1]:
+                        current = current.setdefault(key, {})
+                    current[keys[-1]] = corrected_path
+                else:
+                    pytest.fail(f"Path does not exist: {corrected_path}")
 
-@pytest.mark.parametrize("file", config_files())
-def test_naive_deserialization(file: Path):
-    data = yaml.load(file.read_text(), Loader=yaml.Loader)
-    Config(**data)
+        try:
+            with temporarily_change_dir(path.parent):
+                Config.with_strict_mode(**data)
+        except ValidationError as e:
+            error_details = "\n".join(
+                f"{' -> '.join(map(str, err['loc']))}: {err['msg']}"
+                for err in e.errors()
+            )
+            pytest.fail(f"Validation failed for {path}:\n{error_details}")

src/troute-config/test/test_types.py

@@ -2,7 +2,6 @@
 
 import pytest
 from pydantic import BaseModel, ValidationError
-
 from troute.config._utils import use_strict
 from troute.config.types import DirectoryPath, FilePath
 

src/troute-network/test/__init__.py

@@ -0,0 +1,31 @@
+import os
+
+from contextlib import contextmanager
+from pathlib import Path
+
+
+@contextmanager
+def temporarily_change_dir(path: Path):
+    """Temporarily changes the current working directory
+
+    This context manager changes the current working directory to the specified path,
+    yields control back to the caller, and then changes back to the original directory
+    when exiting the context
+
+    Parameters
+    ----------
+    path : Path
+        The path to temporarily change the current working directory to
+
+    Yields
+    ------
+    None
+    """
+    original_cwd = Path.cwd()
+    if original_cwd != path:
+        os.chdir(path)
+    try:
+        yield
+    finally:
+        if original_cwd != path:
+            os.chdir(original_cwd)