Merge pull request #833 from EmmaRenauld/add_legacy_test_help

Add legacy test (help)

README.md

@@ -35,7 +35,6 @@ In order to install the library and scripts flawlessly (we hope), please follow
 pip install packaging>=19.0
 pip install numpy==1.23.*
 pip install Cython==0.29.*
-pip install -e . 
 ```
 
 The library and scripts can be installed locally by using:
@@ -49,6 +48,11 @@ export SCILPY_LEGACY='False'
 pip install -e .
 ```
 
+(Then, without the legacy scripts, if you want to use pytest, use:)
+```
+pytest --ignore=scripts/legacy
+```
+
 On Linux, most likely you will have to install libraries for COMMIT/AMICO
 ```
 sudo apt install libblas-dev liblapack-dev

scripts/legacy/scil_split_dwi.py → scripts/legacy/scil_split_image.py

@@ -11,7 +11,7 @@
 """
 
 
-@deprecate_script("scil_split_dwi.py", DEPRECATION_MSG, '1.7.0')
+@deprecate_script("scil_split_image.py", DEPRECATION_MSG, '1.7.0')
 def main():
     new_main()
 

scripts/legacy/scil_swap_gradients.py → scripts/legacy/scil_swap_gradient_axis.py

@@ -12,7 +12,7 @@
 """
 
 
-@deprecate_script("scil_swap_gradients.py", DEPRECATION_MSG, '1.7.0')
+@deprecate_script("scil_swap_gradient_axis.py", DEPRECATION_MSG, '1.7.0')
 def main():
     new_main()
 

scripts/legacy/tests/test_add_tracking_mask_to_pft_maps.py

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

scripts/legacy/tests/test_apply_bias_field_on_dwi.py

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

scripts/legacy/tests/test_apply_transform_to_tractogram.py

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

scripts/legacy/tests/test_combine_labels.py

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

scripts/legacy/tests/test_compare_connectivity.py

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

scripts/legacy/tests/test_compute_connectivity.py

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

scripts/legacy/tests/test_compute_local_tracking.py

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

scripts/legacy/tests/test_compute_local_tracking_dev.py

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

scripts/legacy/tests/test_compute_maps_for_particle_filter_tracking.py

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

scripts/legacy/tests/test_compute_pft.py

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

scripts/legacy/tests/test_compute_powder_average.py

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

scripts/legacy/tests/test_concatenate_dwi.py

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

scripts/legacy/tests/test_dilate_labels.py

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

scripts/legacy/tests/test_evaluate_connectivity_graph_measures.py

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

scripts/legacy/tests/test_evaluate_connectivity_pairwise_agreement_measures.py

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

scripts/legacy/tests/test_extract_b0.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_extract_b0.py', '--help')
+    assert ret.success

scripts/legacy/tests/test_extract_dwi_shell.py

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

scripts/legacy/tests/test_filter_connectivity.py

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

scripts/legacy/tests/test_filter_tractogram.py

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

scripts/legacy/tests/test_flip_gradients.py

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

scripts/legacy/tests/test_flip_streamlines.py

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

scripts/legacy/tests/test_normalize_connectivity.py

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

scripts/legacy/tests/test_print_connectivity_filenames.py

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

scripts/legacy/tests/test_register_tractogram.py

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

scripts/legacy/tests/test_remove_labels.py

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

scripts/legacy/tests/test_reorder_connectivity.py

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

scripts/legacy/tests/test_resample_bvals.py

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

scripts/legacy/tests/test_resample_tractogram.py

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

scripts/legacy/tests/test_shuffle_streamlines.py

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

scripts/legacy/tests/test_split_image.py

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

scripts/legacy/tests/test_split_tractogram.py

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

scripts/legacy/tests/test_split_volume_by_ids.py

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

scripts/legacy/tests/test_split_volume_by_labels.py

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

scripts/legacy/tests/test_streamlines_math.py

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

scripts/legacy/tests/test_swap_gradient_axis.py

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