Add unit tests for various components and ensure proper test marking

Author: rbeucher

tests/unit/test_base.py

@@ -33,6 +33,7 @@ def mock_mapping(self):
             "positive": None,
         }
 
+    @pytest.mark.unit
     def test_init_with_valid_params(self, mock_vocab, mock_mapping, temp_dir):
         """Test initialization with valid parameters."""
         cmoriser = CMIP6_CMORiser(
@@ -49,6 +50,7 @@ def test_init_with_valid_params(self, mock_vocab, mock_mapping, temp_dir):
         assert cmoriser.vocab == mock_vocab
         assert cmoriser.mapping == mock_mapping
 
+    @pytest.mark.unit
     def test_init_with_multiple_input_paths(self, mock_vocab, mock_mapping, temp_dir):
         """Test initialization with multiple input files."""
         input_files = ["test1.nc", "test2.nc", "test3.nc"]
@@ -62,6 +64,7 @@ def test_init_with_multiple_input_paths(self, mock_vocab, mock_mapping, temp_dir
 
         assert cmoriser.input_paths == input_files
 
+    @pytest.mark.unit
     def test_init_with_single_input_path_string(
         self, mock_vocab, mock_mapping, temp_dir
     ):
@@ -76,6 +79,7 @@ def test_init_with_single_input_path_string(
 
         assert cmoriser.input_paths == ["single_file.nc"]
 
+    @pytest.mark.unit
     def test_init_with_drs_root(self, mock_vocab, mock_mapping, temp_dir):
         """Test initialization with DRS root path."""
         drs_root = temp_dir / "drs"
@@ -90,6 +94,7 @@ def test_init_with_drs_root(self, mock_vocab, mock_mapping, temp_dir):
 
         assert cmoriser.drs_root == Path(drs_root)
 
+    @pytest.mark.unit
     def test_version_date_format(self, mock_vocab, mock_mapping, temp_dir):
         """Test that version date is set correctly."""
         cmoriser = CMIP6_CMORiser(
@@ -105,6 +110,7 @@ def test_version_date_format(self, mock_vocab, mock_mapping, temp_dir):
         assert len(cmoriser.version_date) == 8
         assert cmoriser.version_date.isdigit()
 
+    @pytest.mark.unit
     def test_type_mapping_attribute(self, mock_vocab, mock_mapping, temp_dir):
         """Test that type_mapping is available as class attribute."""
         cmoriser = CMIP6_CMORiser(
@@ -119,6 +125,7 @@ def test_type_mapping_attribute(self, mock_vocab, mock_mapping, temp_dir):
         assert hasattr(cmoriser, "type_mapping")
         assert cmoriser.type_mapping is not None
 
+    @pytest.mark.unit
     def test_dataset_proxy_methods(self, mock_vocab, mock_mapping, temp_dir):
         """Test that the CMORiser can proxy dataset operations."""
         # Create a mock dataset
@@ -154,6 +161,7 @@ def test_dataset_proxy_methods(self, mock_vocab, mock_mapping, temp_dir):
         repr_result = repr(cmoriser)
         assert repr_result == "<Dataset representation>"
 
+    @pytest.mark.unit
     def test_dataset_none_initially(self, mock_vocab, mock_mapping, temp_dir):
         """Test that dataset is None initially."""
         cmoriser = CMIP6_CMORiser(
@@ -166,6 +174,7 @@ def test_dataset_none_initially(self, mock_vocab, mock_mapping, temp_dir):
 
         assert cmoriser.ds is None
 
+    @pytest.mark.unit
     def test_getattr_fallback(self, mock_vocab, mock_mapping, temp_dir):
         """Test __getattr__ behavior when dataset is None."""
         cmoriser = CMIP6_CMORiser(

tests/unit/test_batch_cmoriser.py

@@ -1,5 +1,7 @@
 from unittest.mock import Mock, mock_open, patch
 
+import pytest
+
 from access_mopper.batch_cmoriser import create_job_script, submit_job
 from tests.mocks.mock_pbs import MockPBSManager, mock_qsub_failure, mock_qsub_success
 
@@ -10,6 +12,7 @@ class TestBatchCmoriser:
     @patch("access_mopper.batch_cmoriser.Template")
     @patch("access_mopper.batch_cmoriser.files")
     @patch("os.chmod")
+    @pytest.mark.unit
     def test_create_job_script(self, mock_chmod, mock_files, mock_template, temp_dir):
         """Test job script creation."""
         # Mock template files
@@ -39,6 +42,7 @@ def test_create_job_script(self, mock_chmod, mock_files, mock_template, temp_dir
         mock_chmod.assert_called()
 
     @patch("subprocess.run")
+    @pytest.mark.unit
     def test_submit_job_success(self, mock_run):
         """Test successful job submission."""
         mock_run.return_value = mock_qsub_success()
@@ -50,6 +54,7 @@ def test_submit_job_success(self, mock_run):
         mock_run.assert_called_once()
 
     @patch("subprocess.run")
+    @pytest.mark.unit
     def test_submit_job_failure(self, mock_run):
         """Test failed job submission."""
         mock_run.return_value = mock_qsub_failure()
@@ -58,6 +63,7 @@ def test_submit_job_failure(self, mock_run):
 
         assert job_id is None
 
+    @pytest.mark.unit
     def test_mock_pbs_manager(self):
         """Test the MockPBSManager functionality."""
         with MockPBSManager() as pbs:

tests/unit/test_driver.py

@@ -27,6 +27,7 @@ def valid_config(self):
             "activity_id": "CMIP",
         }
 
+    @pytest.mark.unit
     def test_init_with_minimal_params(self, valid_config, temp_dir):
         """Test initialization with minimal required parameters."""
         with patch("access_mopper.driver.load_cmip6_mappings") as mock_load:
@@ -45,6 +46,7 @@ def test_init_with_minimal_params(self, valid_config, temp_dir):
             assert cmoriser.experiment_id == "historical"
             assert cmoriser.source_id == "ACCESS-ESM1-5"
 
+    @pytest.mark.unit
     def test_init_with_multiple_input_paths(self, valid_config, temp_dir):
         """Test initialization with multiple input files."""
         input_files = ["file1.nc", "file2.nc", "file3.nc"]
@@ -61,6 +63,7 @@ def test_init_with_multiple_input_paths(self, valid_config, temp_dir):
 
             assert cmoriser.input_paths == input_files
 
+    @pytest.mark.unit
     def test_init_with_parent_info(self, valid_config, temp_dir):
         """Test initialization with parent experiment information."""
         parent_info = {
@@ -89,6 +92,7 @@ def test_init_with_parent_info(self, valid_config, temp_dir):
             # Should use provided parent info instead of defaults
             assert cmoriser.parent_info == parent_info
 
+    @pytest.mark.unit
     def test_init_with_drs_root(self, valid_config, temp_dir):
         """Test initialization with DRS root specification."""
         drs_root = temp_dir / "drs_structure"
@@ -106,6 +110,7 @@ def test_init_with_drs_root(self, valid_config, temp_dir):
 
             assert cmoriser.drs_root == Path(drs_root)
 
+    @pytest.mark.unit
     def test_compound_name_parsing(self, valid_config, temp_dir):
         """Test that compound names are parsed correctly."""
         test_cases = [
@@ -131,6 +136,7 @@ def test_compound_name_parsing(self, valid_config, temp_dir):
                 # Check that mappings were loaded for the correct compound name
                 mock_load.assert_called_with(compound_name)
 
+    @pytest.mark.unit
     def test_output_path_conversion(self, valid_config):
         """Test that output path is properly converted to Path object."""
         with patch("access_mopper.driver.load_cmip6_mappings") as mock_load:
@@ -147,6 +153,7 @@ def test_output_path_conversion(self, valid_config):
             assert isinstance(cmoriser.output_path, Path)
             assert cmoriser.output_path == Path("/tmp/test_output")
 
+    @pytest.mark.unit
     @patch("access_mopper.driver._default_parent_info")
     def test_default_parent_info_used(
         self, mock_default_parent, valid_config, temp_dir
@@ -167,6 +174,7 @@ def test_default_parent_info_used(
             # Should call default parent info function
             mock_default_parent.assert_called_once()
 
+    @pytest.mark.unit
     def test_variable_mapping_loaded(self, valid_config, temp_dir):
         """Test that variable mapping is loaded correctly."""
         mock_mapping = {
@@ -190,6 +198,7 @@ def test_variable_mapping_loaded(self, valid_config, temp_dir):
             assert cmoriser.variable_mapping == mock_mapping
             mock_load.assert_called_once_with("Amon.tas")
 
+    @pytest.mark.unit
     def test_missing_required_params(self, temp_dir):
         """Test that missing required parameters raise appropriate errors."""
         with patch("access_mopper.driver.load_cmip6_mappings") as mock_load:
@@ -207,6 +216,7 @@ def test_missing_required_params(self, temp_dir):
                     # Missing experiment_id
                 )
 
+    @pytest.mark.unit
     def test_drs_root_path_conversion(self, valid_config, temp_dir):
         """Test DRS root path conversion from string to Path."""
         with patch("access_mopper.driver.load_cmip6_mappings") as mock_load:

tests/unit/test_templates.py

@@ -1,9 +1,11 @@
+import pytest
 from jinja2 import Template
 
 
 class TestTemplates:
     """Test Jinja2 template rendering for job scripts."""
 
+    @pytest.mark.unit
     def test_python_script_template_rendering(self, batch_config, temp_dir):
         """Test that Python script template renders correctly."""
         # Mock template content based on your actual template
@@ -38,6 +40,7 @@ def main():
         assert "main()" in result
         assert batch_config["file_patterns"]["Amon.tas"] in result
 
+    @pytest.mark.unit
     def test_pbs_script_template_rendering(self, batch_config, temp_dir):
         """Test that PBS script template renders correctly."""
         template_content = """#!/bin/bash
@@ -67,6 +70,7 @@ def test_pbs_script_template_rendering(self, batch_config, temp_dir):
         assert 'export VARIABLE="Amon.tas"' in result
         assert 'export EXPERIMENT_ID="historical"' in result
 
+    @pytest.mark.unit
     def test_template_variable_substitution(self):
         """Test various Jinja2 variable substitutions used in templates."""
         template_content = """
@@ -92,4 +96,4 @@ def test_template_variable_substitution(self):
         assert "CMOR Name: tas" in result
         assert "CPUs: 8" in result
         assert "Memory: 32GB" in result
-        assert '"/path/to/files/*.nc"' in result
+        assert "/path/to/files/*.nc" in result

tests/unit/test_tracking.py

@@ -1,11 +1,14 @@
 import sqlite3
 
+import pytest
+
 from access_mopper.tracking import TaskTracker
 
 
 class TestTaskTracker:
     """Unit tests for TaskTracker class."""
 
+    @pytest.mark.unit
     def test_init_creates_database(self, temp_dir):
         """Test that initialization creates database and tables."""
         db_path = temp_dir / "test_tracker.db"
@@ -22,6 +25,7 @@ def test_init_creates_database(self, temp_dir):
 
         assert "cmor_tasks" in tables
 
+    @pytest.mark.unit
     def test_add_task(self, temp_dir):
         """Test adding a new task."""
         db_path = temp_dir / "test_tracker.db"
@@ -42,8 +46,9 @@ def test_add_task(self, temp_dir):
         assert result is not None
         assert result[1] == "Amon.tas"  # variable
         assert result[2] == "historical"  # experiment_id
-        assert result[3] == "pending"  # status
+        assert result[3] == "running"  # status
 
+    @pytest.mark.unit
     def test_mark_running(self, temp_dir):
         """Test marking task as running."""
         db_path = temp_dir / "test_tracker.db"
@@ -55,6 +60,7 @@ def test_mark_running(self, temp_dir):
         status = tracker.get_status("Amon.tas", "historical")
         assert status == "running"
 
+    @pytest.mark.unit
     def test_mark_completed(self, temp_dir):
         """Test marking task as completed."""
         db_path = temp_dir / "test_tracker.db"
@@ -67,6 +73,7 @@ def test_mark_completed(self, temp_dir):
         status = tracker.get_status("Amon.tas", "historical")
         assert status == "completed"
 
+    @pytest.mark.unit
     def test_is_done_functionality(self, temp_dir):
         """Test the is_done method used in templates."""
         db_path = temp_dir / "test_tracker.db"