Add tests with pytest and add github CI action.

.github/workflows/CI.yml

@@ -0,0 +1,25 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[test]
+      - name: Test with pytest
+        run: |
+          pytest metoppy/tests --cov=metoppy --cov-report=xml

README.md

@@ -35,10 +35,11 @@ The following dependencies are only required for building/editing/testing the so
 | Dependency | Version | License | Home URL |
 |------|---------|---------|--------------|
 | pytest | 8.4.1  | MIT License (MIT) | https://docs.pytest.org/en/latest |
+| pytest-cov | 7.0 | MIT License (MIT) | https://pytest-cov.readthedocs.io/en/latest |
 | pytest-html | 4.1.1 | MIT License (MIT)   | https://github.com/pytest-dev/pytest-html  |
 | pytest-mock | 3.14.1  | MIT License (MIT) | https://github.com/pytest-dev/pytest-mock |
-| coverage | 7.10.5  | Apache Software License (Apache License Version 2.0) | https://github.com/nedbat/coveragepy |
 | pre-commit | 4.3.0  | MIT License (MIT) | https://github.com/pre-commit/pre-commit  |
+| numpy | 2.3.4 | BSD License (BSD) | https://numpy.org/ |
 
 ## Example
 
@@ -144,12 +145,12 @@ print(metop_reader.shape(longitude_slice))
 
 </details>
 
-6. Covert julia array to numpy (requires that numpy is also installed)
+6. View the julia array as numpy (requires that numpy is also installed)
 
 ```python
 import numpy as np
-# Covert the julia array as numpy
-longitude_slice_np = np.array(longitude_slice) # "copy = None" can be used to reduce memory
+# View the julia array as a numpy array
+longitude_slice_np = np.array(longitude_slice, copy = None)
 print(longitude_slice_np)
 ```
 <details>
@@ -193,13 +194,13 @@ docker run -v ./:/usr/local/bin/metoppy -it python:3.12 /bin/bash
 
 3. Move to the repository and install the package for testing
 ```
-cd /usr/local/bin/metoppy && pip install -e .
+cd /usr/local/bin/metoppy && pip install -e .[test]
 ```
 
 4. Modify the local code and test in the container.
 
 ```
-python3 metoppy/tests/test_get_test_data_artifact.py
+pytest metoppy/tests
 ```
 
-5. When you are happy, push code to your fork and open a MR (Gitlab) or PR (Github)
+5. When you are happy, push code to your fork and open a PR (Github)

metoppy/tests/test_basic_interface.py

@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+#
+# Package Name: metoppy
+# Author: Simon Kok Lupemba, Francesco Murdaca
+# License: MIT License
+# Copyright (c) 2025 EUMETSAT
+
+# This package is licensed under the MIT License.
+# See the LICENSE file for more details.
+
+"""Test file."""
+
+import pytest
+from pathlib import Path
+from metoppy.metopreader import MetopReader
+
+
+@pytest.fixture(scope="module")
+def metop_reader():
+    """
+    Initialize the MetopReader once for the entire module
+    """
+    reader = MetopReader()
+    return reader  # Make it available to tests
+
+
+@pytest.fixture
+def test_file(request, metop_reader):
+    """
+    Fixture to get test file
+    """
+    product_type = request.param  # get parameter from the test
+
+    reduced_data_folder = Path(metop_reader.get_test_data_artifact())
+    reduced_data_files = [f for f in reduced_data_folder.iterdir() if f.is_file()]
+    test_file_name = next((f for f in reduced_data_files if f.name.startswith(product_type)), None)
+    test_file_path = reduced_data_folder / test_file_name
+
+    return test_file_path
+
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZO"], indirect=True)
+def test_get_keys(metop_reader, test_file):
+    """
+    Simple test for metop_reader.get_key
+    """
+    # arrange
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # act
+    keys = metop_reader.get_keys(ds)
+
+    # assert
+    assert "latitude" in keys
+    assert "record_start_time" in keys
+    assert "sigma0_trip" in keys
+    assert "utc_line_nodes" in keys
+    assert "latitude_full" not in keys
+
+    # clean 
+    metop_reader.close_dataset(ds)
+
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZO"], indirect=True)
+def test_close_dataset(metop_reader, test_file):
+    """
+    Test for metop_reader.test_close_dataset. It should not be 
+    possible to read from a closed dataset
+    """
+    # arrange
+    import juliacall
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # act
+    metop_reader.close_dataset(ds)
+
+    # assert
+    with pytest.raises(juliacall.JuliaError):
+        ds['longitude'][0,0]
+
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZO"], indirect=True)
+def test_shape(metop_reader, test_file):
+    """
+    Simple test for metop_reader.shape.
+    """
+    # arrange
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # act
+    latitude = ds['latitude']
+    longitude_slice = ds['longitude'][10:14,0:2]
+
+    shape_latitude = metop_reader.shape(latitude)
+    shape_longitude_slice = metop_reader.shape(longitude_slice)
+
+    # assert
+    assert shape_latitude == (42,10)
+    assert shape_longitude_slice == (4,2)
+
+    # clean 
+    metop_reader.close_dataset(ds)
+
+
+@pytest.mark.parametrize("test_file", ["IASI_xxx"], indirect=True)
+def test_read_single_value(metop_reader, test_file):
+    """
+    Test reading scalar value and assert that the value is correct. 
+    The test also checks that Julia datetimes are converted to Python datetime.datetime
+    """
+    # arrange
+    import datetime
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # act
+    CO2_radiance = ds["gs1cspect"][91, 0, 0, 0]
+    start_time = ds["record_start_time"][0]
+
+    # assert
+    assert CO2_radiance == pytest.approx(0.0006165, abs=2e-5) 
+    assert isinstance(CO2_radiance, float)
+
+    assert start_time.year == 2024
+    assert start_time.month == 9
+    assert start_time.day == 25
+    assert isinstance(start_time, datetime.datetime)
+
+    # clean 
+    metop_reader.close_dataset(ds)
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZR"], indirect=True)
+def test_read_array(metop_reader, test_file):
+    """
+    Test reading varible as an array and conveting it to numpy.
+    This test uses default parameter which results in less performant
+    dynamic types.
+    """
+    # arrange
+    import numpy as np
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # act
+    latitude_julia = metop_reader.as_array(ds['latitude'])
+    longitude_julia = metop_reader.as_array(ds['longitude'])
+    longitude_slice_julia = ds['longitude'][10:14,0:2]
+    latitude = np.array(latitude_julia, copy = None)
+    longitude = np.array(longitude_julia, copy = None)
+    longitude_slice = np.array(longitude_slice_julia, copy = None)
+
+    # assert
+    assert np.all((0 < longitude)&(longitude < 360))
+    assert np.all((-90 < latitude)&(latitude < 90))
+    assert np.all((0 < longitude_slice)&(longitude_slice < 360))
+    assert longitude_slice.shape == (4,2)
+
+    # clean 
+    metop_reader.close_dataset(ds)
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZR"], indirect=True)
+def test_type_stable_array(metop_reader, test_file):
+    """
+    Test reading varible as an array and conveting it to numpy the performant way.
+    This also check that the numpy data type is set correctly. 
+    "maskingvalue = float("nan")" is used to generate arrays with concrete data type.
+    """
+    # arrange
+    import numpy as np
+    ds = metop_reader.open_dataset(file_path=str(test_file), maskingvalue = float("nan"))
+
+    # act
+    latitude = np.array(metop_reader.as_array(ds['latitude']), copy = None)
+    longitude = np.array(metop_reader.as_array(ds['longitude']), copy = None)
+
+    # assert
+    assert latitude.dtype == np.dtype('float64')
+    assert longitude.dtype == np.dtype('float64')
+    assert np.all((0 < longitude)&(longitude < 360))
+    assert np.all((-90 < latitude)&(latitude < 90))
+
+    # clean 
+    metop_reader.close_dataset(ds)
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZF", "ASCA_SZO","ASCA_SZR", "MHSx_xxx", "HIRS_xxx", "AMSA_xxx", "IASI_SND", "IASI_xxx"], indirect=True)
+def test_different_file_types(metop_reader, test_file):
+    """
+    Test that different types of test files can be opened.
+    """
+    # act
+    ds = metop_reader.open_dataset(file_path=str(test_file))
+
+    # assert
+    assert ds is not None
+    assert "record_start_time" in metop_reader.get_keys(ds)
+
+    # clean 
+    metop_reader.close_dataset(ds)

pyproject.toml

@@ -37,10 +37,11 @@ Organization = "https://github.com/eumetsat"
 [project.optional-dependencies]
 test = [
     "pytest==8.4.1",
+    "pytest-cov==7.0",
     "pytest-html==4.1.1",
     "pytest-mock==3.14.1",
-    "coverage==7.10.5",
     "pre-commit==4.3.0",
+    "numpy==2.3.4",
 ]
 
 [build-system]