streamline test class (#109)

* added base test parent class for cleaner code

* modified test_marsfiles and test_marsinterp to use base_test

* modified tests for marscal marsformat marsplot

* modified test_marsvars for base_test

* adjusted short time lengths of dummy test files to work with test_marsfiles

* cd to tests directory for actions

Author: rurata

.github/workflows/marscalendar_test.yml

@@ -49,4 +49,6 @@ jobs:
         run: pip install -e .
       # Run the tests
       - name: Run MarsCalendar tests
-        run: python -m unittest -v tests/test_marscalendar.py
+        run: |
+          cd tests
+          python -m unittest -v test_marscalendar.py

.github/workflows/marsformat_test.yml

@@ -82,7 +82,8 @@ jobs:
       # Run the integration tests with cleanup between tests
       - name: Run MarsFormat tests
         run: |
-          python -m unittest -v tests/test_marsformat.py
+          cd tests
+          python -m unittest -v test_marsformat.py
       # Clean up temporary files to avoid disk space issues - OS specific
       - name: Clean up temp files (Unix)
         if: runner.os != 'Windows' && always()

.github/workflows/marsplot_test.yml

@@ -82,7 +82,8 @@ jobs:
       # Run the integration tests with cleanup between tests
       - name: Run MarsPlot tests
         run: |
-          python -m unittest -v tests/test_marsplot.py
+          cd tests
+          python -m unittest -v test_marsplot.py
       # Clean up temporary files to avoid disk space issues - OS specific
       - name: Clean up temp files (Unix)
         if: runner.os != 'Windows' && always()

.github/workflows/marspull_test.yml

@@ -53,4 +53,6 @@ jobs:
 
       # Run the tests
       - name: Run MarsPull tests
-        run: python -m unittest -v tests/test_marspull.py
+        run: |
+          cd tests
+          python -m unittest -v test_marspull.py

tests/base_test.py

@@ -0,0 +1,118 @@
+#!/usr/bin/env python3
+"""
+Shared test class methods and functions
+"""
+
+import os
+import sys
+import unittest
+import shutil
+import subprocess
+import tempfile
+import glob
+import numpy as np
+from netCDF4 import Dataset
+
+class BaseTestCase(unittest.TestCase):
+    """Base class for integration tests with common setup methods"""
+    
+    PREFIX = "Default_test_"
+    FILESCRIPT = "create_ames_gcm_files.py"
+    SHORTFILE = "short"
+
+    # Verify files were created
+    expected_files = [
+        '01336.atmos_average.nc',
+        '01336.atmos_average_pstd_c48.nc',
+        '01336.atmos_daily.nc',
+        '01336.atmos_diurn.nc',
+        '01336.atmos_diurn_pstd.nc',
+        '01336.fixed.nc'
+    ]
+    # Remove files created by the tests
+    output_patterns = [
+    ]
+
+    @classmethod
+    def setUpClass(cls):
+        """Set up the test environment"""
+        # Create a temporary directory for the tests
+        cls.test_dir = tempfile.mkdtemp(prefix=cls.PREFIX)
+        print(f"Created temporary test directory: {cls.test_dir}")
+        # Project root directory
+        cls.project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+        print(f"Project root directory: {cls.project_root}")
+        # Create test files
+        cls.create_test_files()
+
+    @classmethod
+    def create_test_files(cls):
+        """Create test netCDF files using create_ames_gcm_files.py"""
+        # Get path to create_ames_gcm_files.py script
+        create_files_script = os.path.join(cls.project_root, "tests", cls.FILESCRIPT)
+
+        # Execute the script to create test files - Important: pass the test_dir as argument
+        cmd = [sys.executable, create_files_script, cls.test_dir, cls.SHORTFILE]
+
+        # Print the command being executed
+        print(f"Creating test files with command: {' '.join(cmd)}")
+
+        try:
+            result = subprocess.run(
+                cmd,
+                capture_output=True,
+                text=True,
+                cwd=cls.test_dir  # Run in the test directory to ensure files are created there
+            )
+
+            # Print output for debugging
+            print(f"File creation STDOUT: {result.stdout}")
+            print(f"File creation STDERR: {result.stderr}")
+
+            if result.returncode != 0:
+                raise Exception(f"Failed to create test files: {result.stderr}")
+
+        except Exception as e:
+            raise Exception(f"Error running create_ames_gcm_files.py: {e}")
+
+        # List files in the temp directory to debug
+        print(f"Files in test directory after creation: {os.listdir(cls.test_dir)}")
+
+        for filename in cls.expected_files:
+            filepath = os.path.join(cls.test_dir, filename)
+            if not os.path.exists(filepath):
+                raise Exception(f"Test file {filename} was not created in {cls.test_dir}")
+            else:
+                print(f"Confirmed test file exists: {filepath}")
+
+    def setUp(self):
+        """Change to temporary directory before each test"""
+        os.chdir(self.test_dir)
+        print(f"Changed to test directory: {os.getcwd()}")
+
+    def tearDown(self):
+        """Clean up after each test"""
+        # Clean up any generated output files after each test but keep input files
+
+        for pattern in self.output_patterns:
+            for file_path in glob.glob(os.path.join(self.test_dir, pattern)):
+                try:
+                    os.remove(file_path)
+                    print(f"Removed file: {file_path}")
+                except Exception as e:
+                    print(f"Warning: Could not remove file {file_path}: {e}")
+
+        # Return to test_dir
+        os.chdir(self.test_dir)
+
+    @classmethod
+    def tearDownClass(cls):
+        """Clean up the test environment"""
+        try:
+            # List files in temp directory before deleting to debug
+            print(f"Files in test directory before cleanup: {os.listdir(cls.test_dir)}")
+            shutil.rmtree(cls.test_dir, ignore_errors=True)
+            print(f"Removed test directory: {cls.test_dir}")
+        except Exception as e:
+            print(f"Warning: Could not remove test directory {cls.test_dir}: {e}")
+

tests/create_ames_gcm_files.py

@@ -169,7 +169,7 @@ def create_mgcm_atmos_average(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 5
     else:
         len_time = 133
 
@@ -287,16 +287,16 @@ def create_mgcm_atmos_average(short=False):
 
     dst_num_micro_var = nc_file.createVariable('dst_num_micro', 'f4', ('time', 'pfull', 'lat', 'lon'))
     dst_num_micro_var.long_name = 'dust_number'
-    dst_num_micro_var[:] = np.random.uniform(-3.8e-15, 6.3e+10, size=(133, 30, 48, 96))
+    dst_num_micro_var[:] = np.random.uniform(-3.8e-15, 6.3e+10, size=(len_time, 30, 48, 96))
 
     ice_mass_micro_var = nc_file.createVariable('ice_mass_micro', 'f4', ('time', 'pfull', 'lat', 'lon'))
     ice_mass_micro_var.long_name = 'ice_mass'
-    ice_mass_micro_var[:] = np.random.uniform(-5.8e-34, 3.1e-03, size=(133, 30, 48, 96))
+    ice_mass_micro_var[:] = np.random.uniform(-5.8e-34, 3.1e-03, size=(len_time, 30, 48, 96))
 
     omega_var = nc_file.createVariable('omega', 'f4', ('time', 'pfull', 'lat', 'lon'))
     omega_var.long_name = 'vertical wind'
     omega_var.units = 'Pa/s'
-    omega_var[:] = np.random.uniform(-0.045597, 0.0806756, size=(133, 30, 48, 96))
+    omega_var[:] = np.random.uniform(-0.045597, 0.0806756, size=(len_time, 30, 48, 96))
 
     ps_var = nc_file.createVariable('ps', 'f4', ('time', 'lat', 'lon'))
     ps_var.long_name = 'surface pressure'
@@ -342,7 +342,7 @@ def create_mgcm_atmos_daily(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 40
     else:
         len_time = 2672
 
@@ -357,7 +357,10 @@ def create_mgcm_atmos_daily(short=False):
     time_var = nc_file.createVariable('time', 'f4', ('time',))
     time_var.long_name = 'time'
     time_var.units = 'days'
-    time_var[:] = np.linspace(1336.2, 2004.0, len_time)
+    if short:
+        time_var[:] = np.linspace(1336.2, 1336.2+float(len_time)/4., len_time)
+    else:
+        time_var[:] = np.linspace(1336.2, 2004.0, len_time)
 
     lat_var = nc_file.createVariable('lat', 'f4', ('lat',))
     lat_var.long_name = 'latitude'
@@ -405,8 +408,11 @@ def create_mgcm_atmos_daily(short=False):
     areo_var = nc_file.createVariable('areo', 'f4', ('time', 'scalar_axis'))
     areo_var.long_name = 'areo'
     areo_var.units = 'degrees'
-    areo_vals = np.linspace(720.3, 1079.8, len_time)
-    areo_data = np.zeros((len_time, 1))  # Create a 2D array with shape (133, 1)
+    if short:
+        areo_vals = np.linspace(720.3, 720.3+0.538*float(len_time)/4., len_time)
+    else:
+        areo_vals = np.linspace(720.3, 1079.8, len_time)
+    areo_data = np.zeros((len_time, 1))  # Create a 2D array with shape (len_time, 1)
     for i in range(len_time):
         areo_data[i, 0] = areo_vals[i]
     areo_var[:] = areo_data
@@ -430,7 +436,7 @@ def create_mgcm_atmos_average_pstd(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 5
     else:
         len_time = 133
 
@@ -508,22 +514,22 @@ def create_mgcm_atmos_average_pstd(short=False):
     theta_var = nc_file.createVariable('theta', 'f4', ('time', 'pstd', 'lat', 'lon'))
     theta_var.long_name = 'Potential temperature'
     theta_var.units = 'K'
-    theta_var[:] = np.random.uniform(104.113, 3895.69, size=(133, 44, 48, 96))
+    theta_var[:] = np.random.uniform(104.113, 3895.69, size=(len_time, 44, 48, 96))
 
     rho_var = nc_file.createVariable('rho', 'f4', ('time', 'pstd', 'lat', 'lon'))
     rho_var.long_name = 'Density'
     rho_var.units = 'kg/m^3'
-    rho_var[:] = np.random.uniform(7.05091e-07, 0.0668856, size=(133, 44, 48, 96))
+    rho_var[:] = np.random.uniform(7.05091e-07, 0.0668856, size=(len_time, 44, 48, 96))
 
     omega_var = nc_file.createVariable('omega', 'f4', ('time', 'pstd', 'lat', 'lon'))
     omega_var.long_name = 'vertical wind'
     omega_var.units = 'Pa/s'
-    omega_var[:] = np.random.uniform(-0.045597, 0.0806756, size=(133, 44, 48, 96))
+    omega_var[:] = np.random.uniform(-0.045597, 0.0806756, size=(len_time, 44, 48, 96))
 
     w_var = nc_file.createVariable('w', 'f4', ('time', 'pstd', 'lat', 'lon'))
     w_var.long_name = 'w'
     w_var.units = 'm/s'
-    w_var[:] = np.random.uniform(-2.02603, 1.58804, size=(133, 44, 48, 96))
+    w_var[:] = np.random.uniform(-2.02603, 1.58804, size=(len_time, 44, 48, 96))
 
     ps_var = nc_file.createVariable('ps', 'f4', ('time', 'lat', 'lon'))
     ps_var.long_name = 'surface pressure'
@@ -569,7 +575,7 @@ def create_mgcm_atmos_diurn_pstd(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 5
     else:
         len_time = 133
 
@@ -662,7 +668,7 @@ def create_mgcm_atmos_diurn(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 5
     else:
         len_time = 133
 
@@ -773,7 +779,7 @@ def create_mgcm_atmos_average_pstd_c48(short=False):
 
     # Shorten file length if wanted
     if short:
-        len_time = 2
+        len_time = 5
     else:
         len_time = 133
 

tests/test_marscalendar.py

@@ -14,31 +14,14 @@
 import argparse
 import subprocess
 import re
+from base_test import BaseTestCase
 
-class TestMarsCalendar(unittest.TestCase):
+class TestMarsCalendar(BaseTestCase):
     """Integration test suite for MarsCalendar"""
-    
-    @classmethod
-    def setUpClass(cls):
-        """Set up the test environment"""
-        # Create a temporary directory in the user's home directory
-        cls.test_dir = os.path.join(os.path.expanduser('~'), 'MarsCalendar_test')
-        os.makedirs(cls.test_dir, exist_ok=True)
-        
-        # Project root directory
-        cls.project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-    
-    def setUp(self):
-        """Change to temporary directory before each test"""
-        os.chdir(self.test_dir)
-    
-    @classmethod
-    def tearDownClass(cls):
-        """Clean up the test environment"""
-        try:
-            shutil.rmtree(cls.test_dir, ignore_errors=True)
-        except Exception:
-            print(f"Warning: Could not remove test directory {cls.test_dir}")
+
+    PREFIX = "MarsCalendar_test_"
+    FILESCRIPT = "create_ames_gcm_files.py"
+    SHORTFILE = "short"
 
     def run_mars_calendar(self, args):
         """