Merge pull request #137 from kostrykin/update-deprecated-and-rename

Update deprecated and rename
BMCV · Oct 4, 2024 · 5bf3d88 · 5bf3d88
2 parents 2266053 + e1acdbe
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diff --git a/...sor_feature_dimension_reduction/.shed.yml → ...sor_feature_dimension_reduction/.shed.yml b/...sor_feature_dimension_reduction/.shed.yml → ...sor_feature_dimension_reduction/.shed.yml
diff --git a/.../3d_tensor_feature_dimension_reduction.py → .../3d_tensor_feature_dimension_reduction.py b/.../3d_tensor_feature_dimension_reduction.py → .../3d_tensor_feature_dimension_reduction.py
diff --git a/...3d_tensor_feature_dimension_reduction.xml → ...3d_tensor_feature_dimension_reduction.xml b/...3d_tensor_feature_dimension_reduction.xml → ...3d_tensor_feature_dimension_reduction.xml
diff --git a/...e_dimension_reduction/test-data/tensor.h5 → ...e_dimension_reduction/test-data/tensor.h5 b/...e_dimension_reduction/test-data/tensor.h5 → ...e_dimension_reduction/test-data/tensor.h5
diff --git a/...imension_reduction/test-data/tensor_r.tif → ...imension_reduction/test-data/tensor_r.tif b/...imension_reduction/test-data/tensor_r.tif → ...imension_reduction/test-data/tensor_r.tif
diff --git a/tools/curl_post/.shed.yml → deprecated/tools/curl_post/.shed.yml b/tools/curl_post/.shed.yml → deprecated/tools/curl_post/.shed.yml
diff --git a/tools/curl_post/curl_post.xml → deprecated/tools/curl_post/curl_post.xml b/tools/curl_post/curl_post.xml → deprecated/tools/curl_post/curl_post.xml
diff --git a/tools/curl_post/test-data/curl.txt → ...ecated/tools/curl_post/test-data/curl.txt b/tools/curl_post/test-data/curl.txt → ...ecated/tools/curl_post/test-data/curl.txt
diff --git a/tools/curl_post/test-data/sample_seg.tif → .../tools/curl_post/test-data/sample_seg.tif b/tools/curl_post/test-data/sample_seg.tif → .../tools/curl_post/test-data/sample_seg.tif
diff --git a/tools/points2binaryimage/.shed.yml → ...ecated/tools/points2binaryimage/.shed.yml b/tools/points2binaryimage/.shed.yml → ...ecated/tools/points2binaryimage/.shed.yml
diff --git a/tools/points2binaryimage/creators.xml → ...ted/tools/points2binaryimage/creators.xml b/tools/points2binaryimage/creators.xml → ...ted/tools/points2binaryimage/creators.xml
diff --git a/.../points2binaryimage/points2binaryimage.py → .../points2binaryimage/points2binaryimage.py b/.../points2binaryimage/points2binaryimage.py → .../points2binaryimage/points2binaryimage.py
diff --git a/...points2binaryimage/points2binaryimage.xml → ...points2binaryimage/points2binaryimage.xml b/...points2binaryimage/points2binaryimage.xml → ...points2binaryimage/points2binaryimage.xml
diff --git a/...s/points2binaryimage/test-data/input1.tsv → ...s/points2binaryimage/test-data/input1.tsv b/...s/points2binaryimage/test-data/input1.tsv → ...s/points2binaryimage/test-data/input1.tsv
diff --git a/...s/points2binaryimage/test-data/input2.tsv → ...s/points2binaryimage/test-data/input2.tsv b/...s/points2binaryimage/test-data/input2.tsv → ...s/points2binaryimage/test-data/input2.tsv
diff --git a/.../points2binaryimage/test-data/output1.tif → .../points2binaryimage/test-data/output1.tif b/.../points2binaryimage/test-data/output1.tif → .../points2binaryimage/test-data/output1.tif
diff --git a/.../points2binaryimage/test-data/output2.tif → .../points2binaryimage/test-data/output2.tif b/.../points2binaryimage/test-data/output2.tif → .../points2binaryimage/test-data/output2.tif
diff --git a/tools/points2binaryimage/tests.xml → ...ecated/tools/points2binaryimage/tests.xml b/tools/points2binaryimage/tests.xml → ...ecated/tools/points2binaryimage/tests.xml
diff --git a/tools/roi2binaryimage/WARNING → deprecated/tools/roi2binaryimage/WARNING b/tools/roi2binaryimage/WARNING → deprecated/tools/roi2binaryimage/WARNING
diff --git a/tools/roi2binaryimage/roi2binaryimage.py → .../tools/roi2binaryimage/roi2binaryimage.py b/tools/roi2binaryimage/roi2binaryimage.py → .../tools/roi2binaryimage/roi2binaryimage.py
diff --git a/tools/roi2binaryimage/test-data/1.roi → ...ted/tools/roi2binaryimage/test-data/1.roi b/tools/roi2binaryimage/test-data/1.roi → ...ted/tools/roi2binaryimage/test-data/1.roi
diff --git a/tools/color-deconvolution/.shed.yml → tools/color_deconvolution/.shed.yml b/tools/color-deconvolution/.shed.yml → tools/color_deconvolution/.shed.yml
diff --git a/...lor-deconvolution/color-deconvolution.xml → ...lor_deconvolution/color-deconvolution.xml b/...lor-deconvolution/color-deconvolution.xml → ...lor_deconvolution/color-deconvolution.xml
diff --git a/...olor-deconvolution/color_deconvolution.py → ...olor_deconvolution/color_deconvolution.py b/...olor-deconvolution/color_deconvolution.py → ...olor_deconvolution/color_deconvolution.py
diff --git a/...nvolution/test-data/galaxyIcon_noText.png → ...nvolution/test-data/galaxyIcon_noText.png b/...nvolution/test-data/galaxyIcon_noText.png → ...nvolution/test-data/galaxyIcon_noText.png
diff --git a/tools/mahotas-features/.shed.yml → tools/mahotas_features/.shed.yml b/tools/mahotas-features/.shed.yml → tools/mahotas_features/.shed.yml
diff --git a/tools/mahotas-features/mahotas_features.xml → tools/mahotas_features/mahotas_features.xml b/tools/mahotas-features/mahotas_features.xml → tools/mahotas_features/mahotas_features.xml
diff --git a/...s/mahotas-features/test-data/features.tsv → ...s/mahotas_features/test-data/features.tsv b/...s/mahotas-features/test-data/features.tsv → ...s/mahotas_features/test-data/features.tsv
diff --git a/...-features/test-data/galaxyIcon_noText.png → ..._features/test-data/galaxyIcon_noText.png b/...-features/test-data/galaxyIcon_noText.png → ..._features/test-data/galaxyIcon_noText.png
diff --git a/...s/visceral-evaluatesegmentation/.shed.yml → ...s/visceral_evaluatesegmentation/.shed.yml b/...s/visceral-evaluatesegmentation/.shed.yml → ...s/visceral_evaluatesegmentation/.shed.yml
diff --git a/...evaluatesegmentation/test-data/.gitignore → ...evaluatesegmentation/test-data/.gitignore b/...evaluatesegmentation/test-data/.gitignore → ...evaluatesegmentation/test-data/.gitignore
diff --git a/...al-evaluatesegmentation/test-data/out.xml → ...al_evaluatesegmentation/test-data/out.xml b/...al-evaluatesegmentation/test-data/out.xml → ...al_evaluatesegmentation/test-data/out.xml
diff --git a/...evaluatesegmentation/test-data/sample.png → ...evaluatesegmentation/test-data/sample.png b/...evaluatesegmentation/test-data/sample.png → ...evaluatesegmentation/test-data/sample.png
diff --git a/...ntation/visceral-evaluatesegmentation.xml → ...ntation/visceral-evaluatesegmentation.xml b/...ntation/visceral-evaluatesegmentation.xml → ...ntation/visceral-evaluatesegmentation.xml
diff --git a/util/README.md b/util/README.md
@@ -1,5 +1,13 @@
 # Utility scripts
 
+## Check tool directory names
+
+Verify that the path of all tools contains the name of the corresponding tool shed repository or the name of a tool suite.
+
+```bash
+./util/check_directory_names.py
+```
+
 ## Use case: An input TIFF file is too large
 
 Assuming that the TIFF file is an RGB file:

diff --git a/util/check_directory_names.py b/util/check_directory_names.py
@@ -0,0 +1,26 @@
+#!/bin/env python
+
+import glob
+import pathlib
+import yaml
+
+
+gia_root_path = pathlib.Path(__file__).resolve().parent.parent
+gia_root_dir_names = [gia_root_path.name] + [p.name for p in gia_root_path.parents if p.name != '']
+
+
+for path_str in glob.glob('./**/.shed.yml', recursive=True):
+
+    # Read the .shed.yml file:
+    shed_file_path = pathlib.Path(path_str).resolve()
+    with shed_file_path.open('r') as shed_file:
+        shed = yaml.safe_load(shed_file)
+        ts_repo_name = shed['name']
+
+    # Check that the toolshed repo name corresponds to one of the parent directory names:
+    parent_dir_names = frozenset(p.name for p in shed_file_path.parents if p.name != '') - frozenset(gia_root_dir_names)
+    if ts_repo_name not in parent_dir_names:
+        print(
+            f'{shed_file_path.relative_to(gia_root_path)}: '
+            f'{ts_repo_name} not in {", ".join(str(dir_name) for dir_name in parent_dir_names)}'
+        )