dropping nose tests from circle ci (all in pytest now)

.circleci/config.yml

@@ -39,31 +39,6 @@ jobs:
             - "/home/venv"
           key:  deps1-{{ .Branch }}-{{ checksum "/home/ciftify/cifti_requirements.txt" }}
 
-  nose:
-    docker:
-      - image: mmanogaran/ciftify_ci:0.1
-    environment:
-      NOSE_XUNIT_FILE: /home/outputs/nose/nose_result.xml
-    steps:
-      - restore_cache:
-          keys:
-            - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
-      - restore_cache:
-          keys:
-            - deps1-{{ .Branch }}-{{ checksum "/home/ciftify/cifti_requirements.txt" }}
-            - deps1
-      - run:
-          name: run tests
-          command: |
-            source  /home/venv/bin/activate
-            mkdir -p /home/outputs/nose/
-            nosetests --with-xunit -w /homeciftify
-      - store_artifacts:
-          path: /home/outputs/nose
-          destination: nose
-      - store_test_results:
-          path: /home/outputs
-
   pytest:
     docker:
       - image: mmanogaran/ciftify_ci:0.1

tests/test_cifti_vis_map.py

@@ -3,7 +3,7 @@
 import importlib
 import random
 
-from mock import patch
+from unittest.mock import patch
 
 vis_map = importlib.import_module('ciftify.bin.cifti_vis_map')
 

tests/test_cifti_vis_recon_all.py

@@ -3,23 +3,22 @@
 import logging
 import importlib
 import random
+import pytest
 
-from mock import patch, MagicMock, mock_open
-from nose.tools import raises
+from unittest.mock import patch, MagicMock, mock_open
 
 recon = importlib.import_module('ciftify.bin.cifti_vis_recon_all')
 
 logging.disable(logging.CRITICAL)
 
 class TestUserSettings(unittest.TestCase):
 
-    @raises(SystemExit)
     def test_exits_gracefully_when_user_supplies_undefined_qc_mode(self):
         arguments = {'<subject>': 'some_subject',
                      '<QCmode>': 'new_mode',
                      '--temp-dir': None}
-        recon.UserSettings(arguments)
-        assert False
+        with pytest.raises(SystemExit):
+            recon.UserSettings(arguments)
 
 class TestModifyTemplateContents(unittest.TestCase):
 

tests/test_ciftify_clean_image.py

@@ -9,8 +9,8 @@
 import pandas as pd
 import json
 
-from nose.tools import raises
-from mock import patch
+import pytest
+from unittest.mock import patch
 
 from nibabel import Nifti1Image
 import numpy as np
@@ -72,7 +72,6 @@ def test_that_updated_arg_is_present(self, mock_readable, mock_writable, mock_js
         assert settings.detrend == True, "detrend not set to config val"
 
 
-    @raises(SystemExit)
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
     @patch('ciftify.utils.check_output_writable', return_value = True)
     def test_exist_gracefully_if_json_not_readable(self, mock_readable, mock_writable):
@@ -82,23 +81,20 @@ def test_exist_gracefully_if_json_not_readable(self, mock_readable, mock_writabl
         missing_json = '/wrong/path/missing.json'
         arguments['--clean-config'] = missing_json
 
-
-        settings = ciftify_clean_img.UserSettings(arguments)
-
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
 
 
-    @raises(SystemExit)
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
     @patch('ciftify.utils.check_output_writable', return_value = True)
     def test_exists_gracefully_if_input_is_gifti(self, mock_readable, mock_writable):
 
 
         arguments = copy.deepcopy(self.docopt_args)
         arguments['<func_input>'] = '/path/to/input/func.L.func.gii'
-        settings = ciftify_clean_img.UserSettings(arguments)
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
 
-        assert False
 
 
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
@@ -123,14 +119,13 @@ def test_nifti_input_returned_correctly(self, mock_readable, mock_writable):
         assert settings.func.path == '/path/to/input/myfunc.nii.gz'
 
 
-    @raises(SystemExit)
     def test_exists_gracefully_if_output_not_writable(self):
 
         wrong_func = '/wrong/path/to/input/myfunc.nii.gz'
         arguments = copy.deepcopy(self.docopt_args)
         arguments['<func_input>'] = wrong_func
-        settings = ciftify_clean_img.UserSettings(arguments)
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
 
 
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
@@ -153,16 +148,15 @@ def test_proper_output_returned_for_cifti(self, mock_readable, mock_writable):
         settings = ciftify_clean_img.UserSettings(arguments)
         assert settings.output_func == '/path/to/input/myfunc_clean_s0.dtseries.nii'
 
-    @raises(SystemExit)
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
     @patch('ciftify.utils.check_output_writable', return_value = True)
     def test_exits_when_confounds_tsv_not_given(self, mock_readable, mock_writable):
 
         arguments = copy.deepcopy(self.docopt_args)
         arguments['--cf-cols'] = 'one,two,three'
         arguments['--confounds-tsv'] = None
-        settings = ciftify_clean_img.UserSettings(arguments)
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
 
     @patch('pandas.read_csv', return_value = pd.DataFrame(columns = ['one', 'two', 'three']))
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
@@ -214,18 +208,18 @@ def test_bandpass_filter_returns_float_if_float(self, mock_readable, mock_writab
         assert settings.high_pass == 3.14
 
 
-    @raises(SystemExit)
+
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
     @patch('ciftify.utils.check_output_writable', return_value = True)
     def test_exists_gracefully_if_filter_not_float(self, mock_readable, mock_writable):
 
         arguments = copy.deepcopy(self.docopt_args)
         arguments['--high-pass'] = 'three'
-        settings = ciftify_clean_img.UserSettings(arguments)
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
+
 
 
-    @raises(SystemExit)
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)
     @patch('ciftify.utils.check_output_writable', return_value = True)
     def test_exists_gracefully_if_surfaces_not_present(self, mock_readable, mock_writable):
@@ -234,9 +228,8 @@ def test_exists_gracefully_if_surfaces_not_present(self, mock_readable, mock_wri
         arguments['<func_input>'] = '/path/to/input/myfunc.dtseries.nii'
         arguments['--smooth-fwhm'] = 8
         arguments['--left-surface'] = None
-
-        settings = ciftify_clean_img.UserSettings(arguments)
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_clean_img.UserSettings(arguments)
 
 
     @patch('ciftify.utils.check_input_readable', side_effect = _check_input_readble_side_effect)

tests/test_ciftify_recon_all.py

@@ -6,8 +6,8 @@
 import os
 from docopt import docopt
 
-from mock import patch
-from nose.tools import raises
+from unittest.mock import patch
+import pytest
 import ciftify.utils
 
 logging.disable(logging.CRITICAL)
@@ -224,7 +224,7 @@ def test_fs_root_dir_set_to_user_value_when_given(self, mock_exists,
 
         assert settings.fs_root_dir == self.arguments['--fs-subjects-dir']
 
-    @raises(SystemExit)
+
     @patch('ciftify.config.find_ciftify_global')
     @patch('ciftify.config.find_freesurfer_data')
     @patch('os.path.exists')
@@ -241,10 +241,9 @@ def test_exits_when_no_fs_dir_given_and_cannot_find_shell_value(self,
         args_copy['--fs-subjects-dir'] = None
         # Just in case the shell environment has the variable set...
         mock_fs.return_value = None
+        with pytest.raises(SystemExit):
+            settings = ciftify_recon_all.Settings(args_copy)
 
-        settings = ciftify_recon_all.Settings(args_copy)
-        # Should never reach this line
-        assert False
 
     @patch('ciftify.config.find_ciftify_global')
     @patch('ciftify.bin.ciftify_recon_all.WorkFlowSettings._WorkFlowSettings__read_settings')
@@ -309,7 +308,6 @@ def test_msm_config_set_to_default_when_user_config_not_given(self,
 
         assert settings.msm_config is not None
 
-    @raises(SystemExit)
     @patch('ciftify.config.find_ciftify_global')
     @patch('os.path.exists')
     def test_sys_exit_raised_when_user_msm_config_doesnt_exist(self, mock_exists,
@@ -326,11 +324,10 @@ def test_sys_exit_raised_when_user_msm_config_doesnt_exist(self, mock_exists,
         args['--surf-reg'] = 'MSMSulc'
         args['--MSM-config'] = user_config
 
-        settings = ciftify_recon_all.Settings(args)
-        # Test should never reach this line
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_recon_all.Settings(args)
+
 
-    @raises(SystemExit)
     @patch('ciftify.config.find_ciftify_global')
     @patch('os.path.exists')
     def test_sys_exit_raised_when_nonlin_xfm_given_alone(self, mock_exists,
@@ -340,11 +337,10 @@ def test_sys_exit_raised_when_nonlin_xfm_given_alone(self, mock_exists,
         mock_exists.side_effect = lambda path: False if path == self.subworkdir else True
         args = copy.deepcopy(self.arguments)
         args['--read-non-lin-xfm'] = '/some/file'
-        settings = ciftify_recon_all.Settings(args)
-        # Test should never reach this line
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_recon_all.Settings(args)
+
 
-    @raises(SystemExit)
     @patch('ciftify.config.find_ciftify_global')
     @patch('os.path.exists')
     def test_sys_exit_raised_when_lin_xfm_given_alone(self, mock_exists,
@@ -354,9 +350,9 @@ def test_sys_exit_raised_when_lin_xfm_given_alone(self, mock_exists,
         mock_exists.side_effect = lambda path: False if path == self.subworkdir else True
         args = copy.deepcopy(self.arguments)
         args['--read-lin-premat'] = '/some/file'
-        settings = ciftify_recon_all.Settings(args)
-        # Test should never reach this line
-        assert False
+        with pytest.raises(SystemExit):
+            settings = ciftify_recon_all.Settings(args)
+
 
     @patch('ciftify.utils.check_input_readable')
     @patch('os.path.exists')

tests/test_config.py

@@ -5,8 +5,8 @@
 from subprocess import CalledProcessError
 import pkg_resources
 
-from mock import patch
-from nose.tools import raises
+from unittest.mock import patch
+import pytest
 
 import ciftify.config
 
@@ -94,21 +94,19 @@ def test_workbench_path_new_line_is_removed(self, mock_out):
 
 class TestWBCommandVersion(unittest.TestCase):
 
-    @raises(EnvironmentError)
     @patch('ciftify.config.find_workbench')
     def test_error_raised_if_not_found(self, mock_find):
         mock_find.return_value = None
-
-        version = ciftify.config.wb_command_version()
+        with pytest.raises(EnvironmentError):
+            version = ciftify.config.wb_command_version()
 
 class TestFreesurferVersion(unittest.TestCase):
 
-    @raises(EnvironmentError)
     @patch('ciftify.config.find_freesurfer')
     def test_raises_error_when_not_found(self, mock_find):
         mock_find.return_value = None
-
-        version = ciftify.config.freesurfer_version()
+        with pytest.raises(EnvironmentError):
+            version = ciftify.config.freesurfer_version()
 
     @patch('ciftify.config.find_freesurfer')
     def test_doesnt_crash_if_build_stamp_txt_not_found(self, mock_find):
@@ -162,12 +160,11 @@ def test_returns_none_if_fsldir_unset_and_which_fails(self, mock_which):
 
 class TestFSLVersion(unittest.TestCase):
 
-    @raises(EnvironmentError)
     @patch('ciftify.config.find_fsl')
     def test_raises_error_when_not_found(self, mock_find):
         mock_find.return_value = None
-
-        version = ciftify.config.fsl_version()
+        with pytest.raises(EnvironmentError):
+            version = ciftify.config.fsl_version()
 
     @patch('ciftify.config.find_fsl')
     def test_doesnt_crash_if_version_info_not_found(self, mock_find):

tests/test_html.py

@@ -3,7 +3,7 @@
 import sys
 import unittest
 
-from mock import MagicMock, mock_open, patch
+from unittest.mock import MagicMock, mock_open, patch
 
 from ciftify import html
 import ciftify.qc_config

tests/test_niio.py

@@ -5,8 +5,8 @@
 import shutil
 import random
 
-from nose.tools import raises
-from mock import patch
+import pytest
+from unittest.mock import patch
 
 import ciftify.niio as niio
 
@@ -83,37 +83,30 @@ def test_returns_basename_even_when_full_path_given(self):
         assert mr_type == 'cifti'
         assert mr_base == 'subject1_data'
 
-    @raises(SystemExit)
     def test_raises_exception_with_unrecognized_filetype(self):
         file_name = 'subject1_data.txt'
-
-        mr_type, mr_base = niio.determine_filetype(file_name)
+        with pytest.raises(SystemExit):
+            mr_type, mr_base = niio.determine_filetype(file_name)
 
 class TestLoadNii(unittest.TestCase):
 
-    @raises(SystemExit)
     def test_exits_gracefully_if_nifti_cannot_be_read(self):
         path = '/some/path/fake_nifti.nii.gz'
+        with pytest.raises(SystemExit):
+            niio.load_nifti(path)
 
-        niio.load_nifti(path)
-
-        # Should never reach here
-        assert False
 
 class TestLoadCifti(unittest.TestCase):
 
-    @raises(SystemExit)
     def test_exits_gracefully_if_cifti_cannot_be_read(self):
         path = '/some/path/subject.data.dscalar.nii'
+        with pytest.raises(SystemExit):
+            niio.load_cifti(path)
 
-        niio.load_cifti(path)
-        assert False
 
 class TestLoadGiiData(unittest.TestCase):
 
-    @raises(SystemExit)
     def test_exits_gracefully_if_gifti_cannot_be_read(self):
         path = '/some/path/subject.data.shape.gii'
-
-        niio.load_gii_data(path)
-        assert False
+        with pytest.raises(SystemExit):
+            niio.load_gii_data(path)