From fb8e9fee344beec95f74bffacd5ea8bbb9e0c99f Mon Sep 17 00:00:00 2001
From: Alex Nimmo Smith <alex@nimmosmith.co.uk>
Date: Thu, 18 Jun 2026 15:53:43 +0100
Subject: [PATCH] Add tests for pyopia.cli generate-config and modify-config

First pass at #142. Confirms typer's CliRunner works cleanly under
pytest in this environment, and that the TensorFlow/pytest
incompatibility noted in the issue (filed 2023) no longer applies
with current TF/Keras versions.

Scoped to the simple, side-effect-light commands for now
(generate-config for each instrument, modify-config). Heavier
commands (process, init-project, process-realtime) that exercise
full pipeline runs and downloads are left for a follow-up, following
the example-data patterns already used in test_pipeline.py.
---
 pyopia/__init__.py       |  2 +-
 pyopia/tests/test_cli.py | 95 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 96 insertions(+), 1 deletion(-)
 create mode 100644 pyopia/tests/test_cli.py

diff --git a/pyopia/__init__.py b/pyopia/__init__.py
index c4ed6cf..b15cdcb 100644
--- a/pyopia/__init__.py
+++ b/pyopia/__init__.py
@@ -1 +1 @@
-__version__ = "2.16.6"
+__version__ = "2.16.7"
diff --git a/pyopia/tests/test_cli.py b/pyopia/tests/test_cli.py
new file mode 100644
index 0000000..cbd528b
--- /dev/null
+++ b/pyopia/tests/test_cli.py
@@ -0,0 +1,95 @@
+'''
+Tests for the pyopia.cli command line interface, using typer's CliRunner.
+'''
+
+import os
+import tempfile
+
+import toml
+from typer.testing import CliRunner
+
+from pyopia.cli import app
+
+runner = CliRunner()
+
+
+def test_generate_config_silcam():
+    with tempfile.TemporaryDirectory() as tempdir:
+        result = _invoke_in(tempdir, [
+            'generate-config', 'silcam', 'images/*.silc', 'model.keras', 'proc', 'test'
+        ])
+
+        assert result.exit_code == 0
+        config_path = os.path.join(tempdir, 'silcam-config.toml')
+        assert os.path.isfile(config_path)
+
+        toml_settings = toml.load(config_path)
+        assert toml_settings['general']['raw_files'] == 'images/*.silc'
+        assert toml_settings['steps']['classifier']['model_path'] == 'model.keras'
+
+
+def test_generate_config_holo():
+    with tempfile.TemporaryDirectory() as tempdir:
+        result = _invoke_in(tempdir, [
+            'generate-config', 'holo', 'images/*.pgm', 'model.keras', 'proc', 'test'
+        ])
+
+        assert result.exit_code == 0
+        config_path = os.path.join(tempdir, 'holo-config.toml')
+        assert os.path.isfile(config_path)
+
+        toml_settings = toml.load(config_path)
+        assert toml_settings['general']['raw_files'] == 'images/*.pgm'
+        assert toml_settings['steps']['initial']['pipeline_class'] == 'pyopia.instrument.holo.Initial'
+
+
+def test_generate_config_uvp():
+    with tempfile.TemporaryDirectory() as tempdir:
+        result = _invoke_in(tempdir, [
+            'generate-config', 'uvp', 'images/*.png', 'model.keras', 'proc', 'test'
+        ])
+
+        assert result.exit_code == 0
+        config_path = os.path.join(tempdir, 'uvp-config.toml')
+        assert os.path.isfile(config_path)
+
+        toml_settings = toml.load(config_path)
+        assert toml_settings['general']['raw_files'] == 'images/*.png'
+
+
+def test_modify_config():
+    with tempfile.TemporaryDirectory() as tempdir:
+        generate_result = _invoke_in(tempdir, [
+            'generate-config', 'silcam', 'images/*.silc', 'model.keras', 'proc', 'test'
+        ])
+        assert generate_result.exit_code == 0
+
+        modify_result = _invoke_in(tempdir, [
+            'modify-config', 'silcam-config.toml', 'modified-config.toml',
+            '--raw-files', 'other_images/*.silc',
+            '--pixel-size', '12.5',
+            '--step-name', 'segmentation',
+            '--modify-arg', 'threshold',
+            '--modify-value', '0.85',
+        ])
+        assert modify_result.exit_code == 0
+
+        modified_path = os.path.join(tempdir, 'modified-config.toml')
+        assert os.path.isfile(modified_path)
+
+        toml_settings = toml.load(modified_path)
+        assert toml_settings['general']['raw_files'] == 'other_images/*.silc'
+        assert toml_settings['general']['pixel_size'] == 12.5
+        assert toml_settings['steps']['segmentation']['threshold'] == 0.85
+
+
+def _invoke_in(tempdir, args):
+    '''Invoke the CLI app with the working directory set to tempdir, restoring
+    the original working directory afterwards.
+    '''
+    original_cwd = os.getcwd()
+    os.chdir(tempdir)
+    try:
+        return runner.invoke(app, args)
+    finally:
+        os.chdir(original_cwd)