implemented tox to run tests

soar-telescope · Jul 24, 2024 · cd21d15 · cd21d15
1 parent bc3ab81
commit cd21d15
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Showing 7 changed files with 57 additions and 33 deletions.
diff --git a/goodman_pipeline/core/tests/test_core.py b/goodman_pipeline/core/tests/test_core.py
@@ -232,8 +232,8 @@ class ClassifySpectroscopicData(TestCase):
 
     def setUp(self):
         self.path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/test_classify_spectroscopic');
+            os.path.dirname(__file__),
+            '../../data/test_data/test_classify_spectroscopic');
         if not os.path.isdir(self.path):
             os.mkdir(self.path)
 
@@ -1366,7 +1366,7 @@ def setUp(self):
         # expected master flat to be retrieved by get_best_flat
         self.reference_flat_name = 'master_flat_1200m2_0.84_dome.fits'
         # location of sample flats
-        self.flat_path = 'goodman_pipeline/data/test_data/master_flat'
+        self.flat_path = os.path.join(os.path.dirname(__file__), '../../data/test_data/master_flat')
         slit = re.sub('[A-Za-z" ]',
                       '',
                       self.master_flat.header['SLIT'])
@@ -1761,8 +1761,8 @@ class ReferenceDataTest(TestCase):
 
     def setUp(self):
         self.rd = ReferenceData(
-            reference_dir=os.path.join(os.getcwd(),
-                                       'goodman_pipeline/data/ref_comp'))
+            reference_dir=os.path.join(os.path.dirname(__file__),
+                                       '../../data/ref_comp'))
         self.ccd = CCDData(data=np.ones((800, 2000)),
                            meta=fits.Header(),
                            unit='adu')
@@ -2037,8 +2037,8 @@ def setUp(self):
                        'FALSE']], columns=columns)]
 
         self.reference_data = ReferenceData(
-            reference_dir=os.path.join(os.getcwd(),
-                                       'goodman_pipeline/data/ref_comp'))
+            reference_dir=os.path.join(os.path.dirname(__file__),
+                                       '../../data/ref_comp'))
 
     def test_search_comp_group(self):
         result = search_comp_group(

diff --git a/goodman_pipeline/images/tests/test_data_classifier.py b/goodman_pipeline/images/tests/test_data_classifier.py
@@ -16,8 +16,8 @@ class DataClassifierTests(TestCase):
 
     def setUp(self):
         self.raw_path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/classify-data')
+            os.path.dirname(__file__),
+            '../../data/test_data/classify-data')
 
         if not os.path.isdir(self.raw_path):
             os.mkdir(self.raw_path)

diff --git a/goodman_pipeline/images/tests/test_night_organizer.py b/goodman_pipeline/images/tests/test_night_organizer.py
@@ -111,8 +111,8 @@ class NightOrganizerTest(TestCase):
 
     def setUp(self):
         self.full_path = os.path.join(
-            os.getcwd(),
-            'goodman_pipeline/data/test_data/night-organizer-test')
+            os.path.dirname(__file__),
+            '../../data/test_data/night-organizer-test')
 
         if not os.path.isdir(self.full_path):
             os.mkdir(self.full_path)

diff --git a/goodman_pipeline/spectroscopy/tests/test_redspec.py b/goodman_pipeline/spectroscopy/tests/test_redspec.py
@@ -77,8 +77,8 @@ def test_reference_dir_does_not_exists(self):
 
         args = get_args(arguments=arguments)
         self.assertTrue(os.path.exists(
-            os.path.join(os.getcwd(),
-                         'goodman_pipeline/testing/reference_files')))
+            os.path.join(os.path.dirname(__file__),
+                         '../../testing/reference_files')))
         self.assertTrue(os.path.isabs(args.reference_dir))
 
     def test_reference_dir_os_error(self):
@@ -114,8 +114,11 @@ def test_get_args():
     args = get_args(arguments)
 
     assert isinstance(args, argparse.Namespace)
+    assert os.path.normpath(args.source) == os.getcwd()
+    assert os.path.normpath(args.destination) == os.getcwd()
     assert args.pattern == 'test-pattern'
-    return args
+    assert args.output_prefix == 'w'
+    assert args.extraction_type == 'fractional'
 
 
 class TestMainApp(TestCase):
@@ -141,7 +144,3 @@ def test___call___with_valid_arguments(self):
                      '--extraction', 'fractional']
         args = get_args(arguments=arguments)
         self.assertRaises(SystemExit, self.main_app, args)
-
-
-if __name__ == '__main__':
-    test_get_args()
diff --git a/goodman_pipeline/spectroscopy/tests/test_wavelength.py b/goodman_pipeline/spectroscopy/tests/test_wavelength.py
@@ -21,12 +21,12 @@ class WavelengthCalibrationTests(TestCase):
 
     def setUp(self):
         self.file_list = []
-        argument_list = ['--data-path', os.getcwd(),
-                         '--proc-path', os.getcwd(),
+        argument_list = ['--data-path', os.path.dirname(__file__),
+                         '--proc-path', os.path.dirname(__file__),
                          '--search-pattern', 'cfzsto',
                          '--output-prefix', 'w',
                          '--extraction', 'fractional',
-                         '--reference-files', 'data/ref_comp',
+                         '--reference-files', os.path.join(os.path.dirname(__file__), '../../data/ref_comp'),
                          '--max-targets', '3',
                          ]
         arguments = get_args(argument_list)
@@ -155,7 +155,7 @@ def test___call___method_one_comparison_lamps(self):
         json_output = self.wc(ccd=self.ccd,
                               comp_list=[self.lamp],
                               save_data_to='',
-                              reference_data='goodman_pipeline/data/ref_comp',
+                              reference_data=os.path.join(os.path.dirname(__file__), '../../data/ref_comp'),
                               json_output=True)
 
         self.assertEqual(json_output['error'], 'Unable to obtain wavelength solution')
@@ -170,19 +170,19 @@ def test___call___method_no_match_found(self):
                           self.ccd,
                           [self.lamp],
                           '',
-                          'goodman_pipeline/data/ref_comp')
+                          os.path.join(os.path.dirname(__file__), '../../data/ref_comp'))
 
     def test___call___method_one_solution(self):
-        file_path = os.path.join(os.getcwd(),
-                                 'goodman_pipeline/data/ref_comp',
+        file_path = os.path.join(os.path.dirname(__file__),
+                                 '../../data/ref_comp',
                                  'goodman_comp_1200M2_FeHeAr.fits')
         ref_lamp = CCDData.read(file_path, unit='adu')
         lamp_ccd = write_fits(ref_lamp, os.path.join(os.getcwd(), 'test_comparison_lamp.fits'), )
         self.file_list.append('test_comparison_lamp.fits')
         json_output = self.wc(ccd=self.ccd,
                               comp_list=[lamp_ccd],
                               save_data_to='',
-                              reference_data='goodman_pipeline/data/ref_comp',
+                              reference_data=os.path.join(os.path.dirname(__file__), '../../data/ref_comp'),
                               json_output=True)
         # print(json.dumps(json_output, indent=4))
         self.assertEqual(len(json_output['wavelength_solution']), 1)
@@ -191,11 +191,11 @@ def test___call___method_one_solution(self):
             self.file_list.append(_solution['reference_lamp'])
 
     def test___call___method_two_solution(self):
-        file_path_1 = os.path.join(os.getcwd(),
-                                   'goodman_pipeline/data/ref_comp',
+        file_path_1 = os.path.join(os.path.dirname(__file__),
+                                   '../../data/ref_comp',
                                    'goodman_comp_1200M2_FeHeAr.fits')
-        file_path_2 = os.path.join(os.getcwd(),
-                                   'goodman_pipeline/data/ref_comp',
+        file_path_2 = os.path.join(os.path.dirname(__file__),
+                                   '../../data/ref_comp',
                                    'goodman_comp_1200M2_CuHeAr.fits')
         ref_lamp_1 = CCDData.read(file_path_1, unit='adu')
         ref_lamp_2 = CCDData.read(file_path_2, unit='adu')
@@ -207,7 +207,7 @@ def test___call___method_two_solution(self):
         json_output = self.wc(ccd=self.ccd,
                               comp_list=[lamp_ccd_1, lamp_ccd_2],
                               save_data_to='',
-                              reference_data='goodman_pipeline/data/ref_comp',
+                              reference_data=os.path.join(os.path.dirname(__file__), '../../data/ref_comp'),
                               json_output=True)
         # print(json.dumps(json_output, indent=4))
         self.assertEqual(len(json_output['wavelength_solution']), 2)

diff --git a/pyproject.toml b/pyproject.toml
@@ -66,8 +66,8 @@ dependencies = [
 "Source" = "https://github.com/soar-telescope/goodman_pipeline"
 
 [project.scripts]
-redccd = "goodman_pipeline.scripts.redccd"
-redspec = "goodman_pipeline.scripts.redspec"
+redccd = "goodman_pipeline.scripts.redccd:__main__"
+redspec = "goodman_pipeline.scripts.redspec:__main__"
 
 
 [tool.setuptools]

diff --git a/tox.ini b/tox.ini
@@ -0,0 +1,25 @@
+[tox]
+envlist = 
+    py{38, 39, 310, 311, 312}-test{,-cov}
+
+isolated_build = true
+
+[testenv]
+setenv = 
+    MPLBACKEND=agg
+allowlist_externals = *
+
+passenv = HOME,WINDIR,LC_ALL,LC_CTYPE,CC,CI
+
+changedir = .tmp/{envname}
+
+description = 
+    run tests
+    cov: also test coverage
+
+deps =
+    cov: pytest-cov
+
+commands =
+    pytest '{toxinidir}/goodman_pipeline' {posargs}
+    cov: pytest --cov goodman_pipeline --cov-config='{toxinidir}/setup.cfg' {posargs}