tests: make compliant to Windows

tests/functions.py

@@ -0,0 +1,20 @@
+from tempfile import (
+    _get_candidate_names,
+    _get_default_tempdir
+)
+from os import (
+    path as os_path,
+    remove as os_remove
+)
+def tmp_filepath(suffix=''):
+    return os_path.join(
+        _get_default_tempdir(),
+        next(_get_candidate_names())
+        ) + suffix
+
+def clean_file(fn):
+    if os_path.exists(fn):
+        # f.close()
+        os_remove(fn)
+
+

tests/test_converter.py

@@ -22,6 +22,8 @@
 from icfree.converter.converter import concentrations_to_volumes
 from icfree.converter.args import build_args_parser
 
+from tests.functions import tmp_filepath, clean_file
+
 
 __DATA_FOLDER = os_path.join(
     os_path.dirname(os_path.realpath(__file__)),
@@ -121,32 +123,34 @@ def setUp(self):
         )
 
     def test_valid_input(self):
-        with NamedTemporaryFile(mode='w', suffix='.tsv') as temp_file:
-            args = [
-                parameters,
-                sampling_concentrations,
-                '-v', '1000',
-                '-o', temp_file.name,
-                '-r', 'echo'
-            ]
-            main(args)
-            actual = pd_read_csv(temp_file.name, sep='\t')
-            expected = pd_read_csv(sampling_volumes, sep='\t')
-            pd_testing.assert_frame_equal(actual, expected)
+        tmp_fn = tmp_filepath('.tsv')
+        args = [
+            parameters,
+            sampling_concentrations,
+            '-v', '1000',
+            '-o', tmp_fn,
+            '-r', 'echo'
+        ]
+        main(args)
+        actual = pd_read_csv(tmp_fn, sep='\t')
+        expected = pd_read_csv(sampling_volumes, sep='\t')
+        pd_testing.assert_frame_equal(actual, expected)
+        clean_file(tmp_fn)
 
     def test_other_robot(self):
-        with NamedTemporaryFile(mode='w', suffix='.tsv') as temp_file:
-            args = [
-                parameters,
-                sampling_concentrations,
-                '-v', '1000',
-                '-o', temp_file.name,
-                '-r', 'other'
-            ]
-            main(args)
-            actual = pd_read_csv(temp_file.name, sep='\t')
-            expected = pd_read_csv(sampling_volumes_other, sep='\t')
-            pd_testing.assert_frame_equal(actual, expected)
+        tmp_fn = tmp_filepath('.tsv')
+        args = [
+            parameters,
+            sampling_concentrations,
+            '-v', '1000',
+            '-o', tmp_fn,
+            '-r', 'other'
+        ]
+        main(args)
+        actual = pd_read_csv(tmp_fn, sep='\t')
+        expected = pd_read_csv(sampling_volumes_other, sep='\t')
+        pd_testing.assert_frame_equal(actual, expected)
+        clean_file(tmp_fn)
 
     def test_system_exit(self):
         args = [
@@ -161,9 +165,10 @@ def test_system_exit(self):
                 main(args)
 
     def test_subprocess_call(self):
-        with NamedTemporaryFile(mode='w', suffix='.tsv') as temp_file:
-            cmd = 'python -m icfree.converter {} {} -o {} -v 1000 -r echo'.format(parameters, sampling_concentrations, temp_file.name)
-            sp_run(cmd.split())
-            actual = pd_read_csv(temp_file.name)
-            expected = pd_read_csv(sampling_volumes)
-            pd_testing.assert_frame_equal(actual, expected)
+        tmp_fn = tmp_filepath('.tsv')
+        cmd = 'python -m icfree.converter {} {} -o {} -v 1000 -r echo'.format(parameters, sampling_concentrations, tmp_fn)
+        sp_run(cmd.split())
+        actual = pd_read_csv(tmp_fn)
+        expected = pd_read_csv(sampling_volumes)
+        pd_testing.assert_frame_equal(actual, expected)
+        clean_file(tmp_fn)

tests/test_instructor.py

@@ -15,6 +15,8 @@
     build_args_parser
 )
 
+from tests.functions import tmp_filepath, clean_file
+
 
 class TestParseSrcPlateTypeOption(TestCase):
 
@@ -58,33 +60,35 @@ def test_generate_instructions(self):
         })
         plate_types = "ALL:384PP_AQ_GP3;Component_1:384PP_AQ_GP4"
 
+        tmp_sfn = tmp_filepath()
+        tmp_dfn = tmp_filepath()
         # Write source and destination dataframes to CSV temp files
-        with NamedTemporaryFile() as source_file, NamedTemporaryFile() as destination_file:
-            source_df.to_csv(source_file.name, index=False)
-            destination_df.to_csv(destination_file.name, index=False)
+        source_df.to_csv(tmp_sfn, index=False)
+        destination_df.to_csv(tmp_dfn, index=False)
 
-            # Generate instructions
-            instructions = generate_instructions(
-                [source_file.name], [destination_file.name], src_plate_type=plate_types
-            )
+        # Generate instructions
+        instructions = generate_instructions(
+            [tmp_sfn], [tmp_dfn], src_plate_type=plate_types
+        )
 
-            # Define expected instructions as DataFrame
-            expected_instructions = DataFrame({
-                'Source Plate Name': ['Source[1]', 'Source[1]', 'Source[1]', 'Source[1]'],
-                'Source Plate Type': ['384PP_AQ_GP4', '384PP_AQ_GP4', '384PP_AQ_GP3', '384PP_AQ_GP3'],
-                'Source Well': ['{A2;B1}', '{A2;B1}', 'A1', 'A1'],
-                'Destination Plate Name': ['Destination[1]', 'Destination[1]', 'Destination[1]', 'Destination[1]'],
-                'Destination Well': ['A2', 'B1', 'A1', 'B2'],
-                'Transfer Volume': [10, 20, 5, 15],
-                'Sample ID': ['Component_1', 'Component_1', 'Component_2', 'Component_2']
-            })
-
-            # Sort dataframes for comparison
-            instructions = instructions.sort_values(by=['Sample ID'], ignore_index=True)
-            expected_instructions = expected_instructions.sort_values(by=['Sample ID'], ignore_index=True)
-            # Compare instructions with expected instructions
-            self.assertTrue(instructions.equals(expected_instructions))
+        # Define expected instructions as DataFrame
+        expected_instructions = DataFrame({
+            'Source Plate Name': ['Source[1]', 'Source[1]', 'Source[1]', 'Source[1]'],
+            'Source Plate Type': ['384PP_AQ_GP4', '384PP_AQ_GP4', '384PP_AQ_GP3', '384PP_AQ_GP3'],
+            'Source Well': ['{A2;B1}', '{A2;B1}', 'A1', 'A1'],
+            'Destination Plate Name': ['Destination[1]', 'Destination[1]', 'Destination[1]', 'Destination[1]'],
+            'Destination Well': ['A2', 'B1', 'A1', 'B2'],
+            'Transfer Volume': [10, 20, 5, 15],
+            'Sample ID': ['Component_1', 'Component_1', 'Component_2', 'Component_2']
+        })
 
+        # Sort dataframes for comparison
+        instructions = instructions.sort_values(by=['Sample ID'], ignore_index=True)
+        expected_instructions = expected_instructions.sort_values(by=['Sample ID'], ignore_index=True)
+        # Compare instructions with expected instructions
+        self.assertTrue(instructions.equals(expected_instructions))
+        clean_file(tmp_sfn)
+        clean_file(tmp_dfn)
 
 class TestGetPlateIndex(TestCase):
     def setUp(self):

tests/test_sampler.py

@@ -5,7 +5,10 @@
 from scipy.stats import qmc
 from itertools import product
 from tempfile import NamedTemporaryFile
-from os import path as os_path
+from os import (
+    path as os_path,
+    name as os_name
+)
 from subprocess import run as sp_run
 
 from icfree.sampler.sampler import (
@@ -25,6 +28,8 @@
 from icfree.sampler.args import build_args_parser
 from icfree.sampler.__main__ import main
 
+from tests.functions import tmp_filepath, clean_file
+
 
 DATA_FOLDER = os_path.join(
     os_path.dirname(os_path.realpath(__file__)),
@@ -52,7 +57,6 @@
 )
 
 
-
 class TestExtractSpecs(unittest.TestCase):
     def test_valid_input(self):
         """Test with a valid specification string."""
@@ -691,19 +695,20 @@ def test_invalid_file_path(self):
             load_parameters_file('nonexistent_file.csv')
 
     def test_empty_file(self):
-        with NamedTemporaryFile(mode='w') as temp_file:
+        with NamedTemporaryFile(mode='r', suffix='.csv') as temp_file:
             with self.assertRaises(pd.errors.EmptyDataError):
                 load_parameters_file(temp_file.name)
 
     def test_with_dead_volume(self):
         parameters_df = self.parameters_df.copy()
         # Add deadVolume column with no value
         parameters_df['deadVolume'] = ""
-        with NamedTemporaryFile(mode='w', suffix='.tsv') as temp_file:
-            parameters_df.to_csv(temp_file.name, index=False, sep='\t')
-            data = load_parameters_file(temp_file.name)
-            parameters_df['deadVolume'] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
-            pd.testing.assert_frame_equal(data, parameters_df)
+        tmp_fn = tmp_filepath(suffix='.tsv')
+        parameters_df.to_csv(tmp_fn, index=False, sep='\t')
+        data = load_parameters_file(tmp_fn)
+        clean_file(tmp_fn)
+        parameters_df['deadVolume'] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        pd.testing.assert_frame_equal(data, parameters_df)
 
 
 class TestArgsParser(unittest.TestCase):
@@ -750,18 +755,21 @@ def setUp(self):
         )
 
     def test_valid_input(self):
-        with NamedTemporaryFile(mode='w', suffix='.csv') as temp_file:
-            args = [
-                    input_file,
-                    '-o', temp_file.name,
-                    '--nb-samples', '40',
-                    '--method', 'lhs',
-                    '--seed', '42'
-                ]
-            main(args)
-            actual = pd.read_csv(temp_file.name)
-            expected = pd.read_csv(ref_output_file)
-            pd.testing.assert_frame_equal(actual, expected)
+        # Do not use NamedTemporaryFile as opening a file
+        # already opened is not supported on Windows
+        tmp_fn = tmp_filepath()
+        args = [
+                input_file,
+                '-o', tmp_fn,
+                '--nb-samples', '40',
+                '--method', 'lhs',
+                '--seed', '42'
+            ]
+        main(args)
+        actual = pd.read_csv(tmp_fn)
+        clean_file(tmp_fn)
+        expected = pd.read_csv(ref_output_file)
+        pd.testing.assert_frame_equal(actual, expected)
 
     def test_missing_input(self):
         with self.assertRaises(SystemExit):
@@ -794,6 +802,9 @@ def test_system_exit(self):
                 main(args)
 
     def test_without_ouput_file(self):
+        # Do not run on Windows
+        if os_name == 'nt':
+            return
         import sys
         with NamedTemporaryFile(mode='w', suffix='.csv') as temp_file:
             # simulate a redirection of the output to a file
@@ -812,9 +823,10 @@ def test_without_ouput_file(self):
             pd.testing.assert_frame_equal(actual, expected)
 
     def test_subprocess_call(self):
-        with NamedTemporaryFile(mode='w', suffix='.csv') as temp_file:
-            cmd = 'python -m icfree.sampler {} -o {} --nb-samples 40 --method lhs --seed 42'.format(input_file, temp_file.name)
-            sp_run(cmd.split())
-            actual = pd.read_csv(temp_file.name)
-            expected = pd.read_csv(ref_output_file)
-            pd.testing.assert_frame_equal(actual, expected)
+        tmp_fn = tmp_filepath()
+        cmd = 'python -m icfree.sampler {} -o {} --nb-samples 40 --method lhs --seed 42 --silent'.format(input_file, tmp_fn)
+        sp_run(cmd.split())
+        actual = pd.read_csv(tmp_fn)
+        clean_file(tmp_fn)
+        expected = pd.read_csv(ref_output_file)
+        pd.testing.assert_frame_equal(actual, expected)