Davide/remove hres eccb

.conda/env_dev.yml

@@ -0,0 +1,16 @@
+channels:
+  - accessnri
+  - conda-forge
+  - coecms
+  - nodefaults
+
+dependencies:
+  - mule
+  - numpy <= 1.23.4 # https://stackoverflow.com/a/75148219/21024780
+  - scitools-iris
+  - xarray
+  - versioneer
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - hypothesis

.gitignore

@@ -1,6 +1,5 @@
 test_data/
 .coverage
-*.sh
 __pycache__/
 *.py[cod]
 .ruff_cache/

README.md

@@ -1,5 +1,48 @@
-[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
-
 # replace_landsurface
 
-This repository contains Python scripts for use by Regional Nesting Suites to replace specific land surface fields in static input data.
+## About
+
+`replace_landsurface` is a `Python` utility to be used within ACCESS-NRI versions of the Regional Nesting Suites to replace specific land surface initial/boundary conditions.
+
+
+## Development/Testing instructions
+For development/testing, it is recommended to install `replace_landsurface` as a development package within a `micromamba`/`conda` testing environment.
+
+### Clone replace_landsurface GitHub repo
+```
+git clone [email protected]:ACCESS-NRI/replace_landsurface.git
+```
+
+### Create a micromamba/conda testing environment
+> [!TIP]  
+> In the following instructions `micromamba` can be replaced with `conda`.
+
+```
+cd replace_landsurface
+micromamba env create -n replace_landsurface_dev --file .conda/env_dev.yml
+micromamba activate replace_landsurface_dev
+```
+
+### Install replace_landsurface as a development package
+```
+pip install --no-deps --no-build-isolation -e .
+```
+
+### Running the tests
+
+The test suite currently includes only integration tests.
+
+To manually run the tests, from the `replace_landsurface` directory, you can:
+
+1. Activate your [micromamba/conda testing environment](#create-a-micromamba-conda-testing-environment)
+2. Run the following command:
+   ```
+   pytest -n 4
+   ```
+
+> [!TIP]
+> The `-n 4` option is a [pytest-xdist](https://pytest-xdist.readthedocs.io/en/stable/) option to run the tests in parallel across 4 different workers.
+
+> [!IMPORTANT]
+> Integration tests are designed to be run on `Gadi`.
+> If you run tests on a local machine, the integration tests will be skipped.

pyproject.toml

@@ -26,8 +26,7 @@ dependencies = [
 Repository = "https://github.com/ACCESS-NRI/replace_landsurface"
 
 [project.scripts]
-hres_eccb = "replace_landsurface.hres_eccb:main"
-hres_ic = "replace_landsurface.hres_ic:main"
+replace_landsurface = "replace_landsurface.replace_landsurface:main"
 
 [build-system]
 build-backend = "setuptools.build_meta"

src/replace_landsurface/hres_ic.py → src/replace_landsurface/replace_landsurface.py

@@ -6,8 +6,7 @@
 # Created by: Chermelle Engel <[email protected]>
 
 """
-Replace the land/surface fields in the astart file with higher-resolution
-era5-land or BARRA2-R data (if requested).
+Replace the land-surface fields in the astart file with higher-resolution data
 """
 
 import argparse
@@ -25,16 +24,17 @@
 def main():
 
     """
-    The main function that creates a worker pool and generates single GRIB files 
-    for requested date/times in parallel.
+    Calls the command line argument parser and process the arguments using the right function.
 
     Parameters
     ----------
-    None.  The arguments are given via the command-line
+    None
+    The arguments are given via the command-line
 
     Returns
     -------
-    None.  The astart file is updated and overwritten
+    None
+    An output file is written
     """ 
 
     # Parse the command-line arguments

tests/integration/test_integration.py

@@ -0,0 +1,146 @@
+import contextlib
+import filecmp
+import os
+import shutil
+import socket
+from unittest.mock import patch
+import pytest
+
+# If not on Gadi, skip the tests because the test data is not available
+GADI_HOSTNAME = "gadi.nci.org.au"
+hostname = socket.gethostname()
+# Marker to skip tests if not on Gadi
+skip_marker = pytest.mark.skipif(
+    not hostname.endswith(GADI_HOSTNAME),
+    reason=f"Skipping integration tests because they cannot be executed on {hostname}.\n"
+    "Integration tests are specifically designed to run on Gadi (gadi.nci.org.au).",
+)
+# Marker to suppress warnings
+warning_marker = pytest.mark.filterwarnings("ignore::Warning")
+# Apply the markers to all tests in this file
+pytestmark = [skip_marker, warning_marker]
+
+############################################
+## === Integration tests setup === ##
+############################################
+TEST_DATA_DIR = "/g/data/vk83/testing/data/replace_landsurface/integration_tests"
+INPUT_DIR = os.path.join(TEST_DATA_DIR, "input_data")
+OUTPUT_DIR = os.path.join(TEST_DATA_DIR, "expected_outputs")
+DRIVING_DATA_DIR = os.path.join(TEST_DATA_DIR, "driving_data")
+# Set the ROSE_DATA environment variable to the driving data directory
+os.environ["ROSE_DATA"] = str(DRIVING_DATA_DIR)
+from replace_landsurface import replace_landsurface  # importing here because we need to set the ROSE_DATA env variable before importing # noqa
+
+
+############################################
+## === Integration tests === ##
+############################################
+def get_test_args(num, start, _type):
+    test_dir = f"test_{num}"
+    hres_ic = (
+        os.path.join(INPUT_DIR, test_dir, "hres_ic")
+        if _type == "astart"
+        else "NOT_USED"
+    )
+    return [
+        "script_name",
+        "--file",
+        os.path.join(INPUT_DIR, test_dir, "file" + ".tmp"),
+        "--mask",
+        os.path.join(INPUT_DIR, test_dir, "mask"),
+        "--start",
+        start,
+        "--type",
+        _type,
+        "--hres_ic",
+        hres_ic,
+    ]
+
+
+def get_error_msg(num, output, expected_output):
+    return f"Test {num}: Test output '{output}' does not match the expected output '{expected_output}'!"
+
+
+@pytest.fixture
+def mock_sys_argv():
+    @contextlib.contextmanager
+    def _mock_sys_argv(num, start, _type):
+        with patch("sys.argv", get_test_args(num, start, _type)):
+            yield mock_sys_argv
+
+    return _mock_sys_argv
+
+
+@pytest.fixture(scope="module")
+def working_dir(tmp_path_factory):
+    return tmp_path_factory.mktemp("replace_landsurface_integration_tests")
+
+
+@pytest.fixture()
+def get_output_path(working_dir):
+    def _get_output_path(num):
+        return os.path.join(working_dir, f"output_{num}")
+
+    return _get_output_path
+
+
+@pytest.fixture()
+def get_expected_output_path():
+    def _get_expected_output_path(num):
+        return os.path.join(OUTPUT_DIR, f"output_{num}")
+
+    return _get_expected_output_path
+
+@pytest.fixture(scope="module")
+def original_shutil_move():
+    return shutil.move
+
+
+@pytest.fixture()
+def new_shutil_move(original_shutil_move, get_output_path):
+    def _new_shutil_move(num):
+        def _wrapper(src, dst, **kwargs):
+            output_path = get_output_path(num)
+            return original_shutil_move(src=src, dst=output_path, **kwargs)
+
+        return _wrapper
+
+    return _new_shutil_move
+
+
+@pytest.mark.parametrize(
+    "num, start, _type",
+    [
+        (1, "202202260000", "era5land"),
+        (2, "202008090000", "barra"),
+        (3, "202112310000", "astart"),
+        (4, "202305040000", "era5land"),
+    ],
+    ids=[
+        "replace_landsurface_era5land",
+        "replace_landsurface_barra",
+        "replace_landsurface_astart",
+        "replace_landsurface_era5land_2",
+    ],
+)
+def test_replace_landsurface(
+    new_shutil_move,
+    get_output_path,
+    get_expected_output_path,
+    mock_sys_argv,
+    num,
+    start,
+    _type,
+):
+    """
+    Test the replace_landsurface entry point
+    """
+    with mock_sys_argv(num, start, _type):
+        with patch("shutil.move", side_effect=new_shutil_move(num)):
+            replace_landsurface.main()
+    output = get_output_path(num)
+    expected_output = get_expected_output_path(num)
+    # Compare the output file with the expected output
+    assert filecmp.cmp(output, expected_output), get_error_msg(
+        num, output, expected_output
+    )