Remove --mask argument + restructure

.conda/env_dev.yml

@@ -0,0 +1,17 @@
+channels:
+  - accessnri
+  - conda-forge
+  - coecms
+  - nodefaults
+
+dependencies:
+  - mule
+  - numpy <= 1.23.4 # https://stackoverflow.com/a/75148219/21024780
+  - scitools-iris
+  - xarray
+  - versioneer
+  - ipykernel
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - hypothesis

.gitignore

@@ -1,9 +1,10 @@
 test_data/
 .coverage
-*.sh
 __pycache__/
 *.py[cod]
 .ruff_cache/
 .mypy_cache/
 .pytest_cache/
-.vscode/
+.vscode/
+build/
+*.egg-info/

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 git@github.com: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

@@ -6,16 +6,13 @@
 # Created by: Chermelle Engel <Chermelle.Engel@anu.edu.au>
 
 """
-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
 import shutil
 from pathlib import Path
 
-import pandas
-
 from replace_landsurface import (
     replace_landsurface_with_BARRA2R_IC,
     replace_landsurface_with_ERA5land_IC,
@@ -25,43 +22,37 @@
 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
     parser = argparse.ArgumentParser()
-    parser.add_argument('--mask', required=True, type=Path)
     parser.add_argument('--file', required=True, type=Path)
-    parser.add_argument('--start', required=True, type=pandas.to_datetime)
+    parser.add_argument('--start', required=True, type=str, help="A date in the format 'YYYYmmddHHMM'.")
     parser.add_argument('--type', default="era5land")
     parser.add_argument('--hres_ic', type=Path)
     args = parser.parse_args()
-    print(args)
-
-    # Convert the date/time to a formatted string
-    t = args.start.strftime("%Y%m%dT%H%MZ")
-    print(args.mask, args.file, t)
 
     # If necessary replace ERA5 land/surface fields with higher-resolution options
     if "era5land" in args.type:
-        replace_landsurface_with_ERA5land_IC.swap_land_era5land(args.mask, args.file, t)
+        replace_landsurface_with_ERA5land_IC.swap_land_era5land(args.file, args.start)
         shutil.move(args.file.as_posix(), args.file.as_posix().replace('.tmp', ''))
     elif "barra" in args.type:
-        replace_landsurface_with_BARRA2R_IC.swap_land_barra(args.mask, args.file, t)
+        replace_landsurface_with_BARRA2R_IC.swap_land_barra(args.file, args.start)
         shutil.move(args.file.as_posix(), args.file.as_posix().replace('.tmp', ''))
     elif "astart" in args.type:
-        replace_landsurface_with_FF_IC.swap_land_ff(args.mask, args.file, args.hres_ic,t)
+        replace_landsurface_with_FF_IC.swap_land_ff(args.file, args.hres_ic)
         shutil.move(args.file.as_posix(), args.file.as_posix().replace('.tmp', ''))
-
     else:
         print("No need to swap out IC")