Merge pull request #828 from arnaudbore/rename_convert_scripts

Rename convert scripts

scripts/legacy/scil_convert_gradients_fsl_to_mrtrix.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_gradients_convert_fsl_to_mrtrix import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_gradients_convert_fsl_to_mrtrix.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_convert_gradients_fsl_to_mrtrix.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_convert_gradients_mrtrix_to_fsl.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_gradients_convert_mrtrix_to_fsl import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_gradients_convert_mrtrix_to_fsl.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_convert_gradients_mrtrix_to_fsl.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_convert_rgb.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_rgb_convert import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_rgb_convert.py.
+Now, all our scripts using metrics or reconstructions start
+with scil_reconst_...!
+
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_convert_rgb.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_convert_tractogram.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_tractogram_convert import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_tractogram_convert.py.
+Now, all our scripts using tractogram start with scil_tractogram_...!
+
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_convert_tractogram.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/tests/test_convert_gradients_fsl_to_mrtrix.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_convert_gradients_fsl_to_mrtrix.py', '--help')
+    assert ret.success

scripts/legacy/tests/test_convert_gradients_mrtrix_to_fsl.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_convert_gradients_mrtrix_to_fsl.py', '--help')
+    assert ret.success

scripts/legacy/tests/test_convert_rgb.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_convert_rgb.py', '--help')
+    assert ret.success

scripts/legacy/tests/test_convert_tractogram.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_convert_tractogram.py', '--help')
+    assert ret.success

scripts/tests/test_convert_gradients_fsl_to_mrtrix.py → scripts/tests/test_gradients_convert_fsl_to_mrtrix.py

@@ -12,7 +12,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_convert_gradients_fsl_to_mrtrix.py',
+    ret = script_runner.run('scil_gradients_convert_fsl_to_mrtrix.py',
                             '--help')
     assert ret.success
 
@@ -23,6 +23,6 @@ def test_execution_processing(script_runner):
                            '1000.bval')
     in_bvec = os.path.join(get_home(), 'processing',
                            '1000.bvec')
-    ret = script_runner.run('scil_convert_gradients_fsl_to_mrtrix.py',
+    ret = script_runner.run('scil_gradients_convert_fsl_to_mrtrix.py',
                             in_bval, in_bvec, '1000.b')
     assert ret.success

scripts/tests/test_convert_gradients_mrtrix_to_fsl.py → scripts/tests/test_gradients_convert_mrtrix_to_fsl.py

@@ -12,7 +12,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_convert_gradients_mrtrix_to_fsl.py',
+    ret = script_runner.run('scil_gradients_convert_mrtrix_to_fsl.py',
                             '--help')
     assert ret.success
 
@@ -21,6 +21,6 @@ def test_execution_processing(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_encoding = os.path.join(get_home(), 'processing',
                                '1000.b')
-    ret = script_runner.run('scil_convert_gradients_mrtrix_to_fsl.py',
+    ret = script_runner.run('scil_gradients_convert_mrtrix_to_fsl.py',
                             in_encoding, '1000.bval', '1000.bvec')
     assert ret.success

scripts/tests/test_convert_rgb.py → scripts/tests/test_rgb_convert.py

@@ -13,13 +13,14 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_convert_rgb.py', '--help')
+    ret = script_runner.run('scil_rgb_convert.py', '--help')
     assert ret.success
 
 
 def test_execution_others(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img = os.path.join(get_home(), 'others',
                           'rgb.nii.gz')
-    ret = script_runner.run('scil_convert_rgb.py', in_img, 'rgb_4D.nii.gz')
+    ret = script_runner.run('scil_rgb_convert.py',
+                            in_img, 'rgb_4D.nii.gz')
     assert ret.success

scripts/tests/test_convert_tractogram.py → scripts/tests/test_tractogram_convert.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_convert_tractogram.py', '--help')
+    ret = script_runner.run('scil_tractogram_convert.py', '--help')
     assert ret.success
 
 
@@ -23,6 +23,6 @@ def test_execution_surface_vtk_fib(script_runner):
                           'gyri_fanning.fib')
     in_fa = os.path.join(get_home(), 'surface_vtk_fib',
                          'fa.nii.gz')
-    ret = script_runner.run('scil_convert_tractogram.py', in_fib,
+    ret = script_runner.run('scil_tractogram_convert.py', in_fib,
                             'gyri_fanning.trk', '--reference', in_fa)
     assert ret.success