BUG: Fix CLI for slide-info and travis for deployment to pypi (#17)

- Fix CLI for slide-info and travis for deployment to pypi

Author: shaneahmed

.deepsource.toml

@@ -1,6 +1,6 @@
 version = 1
 
-test_patterns = ["*/tests/test_*.py"]
+test_patterns = ["tests/test_*.py"]
 
 [[analyzers]]
 name = "python"

docs/conf.py

@@ -119,15 +119,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 tag = False
 
@@ -22,3 +22,4 @@ test = pytest
 
 [tool:pytest]
 collect_ignore = ['setup.py']
+

setup.py

@@ -56,6 +56,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/tialab/tiatoolbox",
-    version="0.2.1",
+    version="0.2.2",
     zip_safe=False,
 )

tiatoolbox/__init__.py

@@ -6,7 +6,7 @@
 
 __author__ = """TIA Lab"""
 __email__ = "tialab@dcs.warwick.ac.uk"
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 
 if __name__ == "__main__":
     pass

tiatoolbox/cli.py

@@ -40,6 +40,7 @@ def main():
 )
 @click.option(
     "--mode",
+    default="show",
     help="'show' to display meta information only or 'save' to save "
     "the meta information, default=show",
 )
@@ -52,23 +53,43 @@ def main():
 def slide_info(wsi_input, output_dir, file_types, mode, workers=None):
     """Displays or saves WSI metadata"""
     file_types = tuple(file_types.split(", "))
+
     if os.path.isdir(wsi_input):
         files_all = utils.misc.grab_files_from_dir(
             input_path=wsi_input, file_types=file_types
         )
+        if output_dir is None and mode == "save":
+            input_dir, _, _ = utils.misc.split_path_name_ext(wsi_input)
+            output_dir = pathlib.Path(input_dir).joinpath("meta")
+
     elif os.path.isfile(wsi_input):
         files_all = [
             wsi_input,
         ]
+        if output_dir is None and mode == "save":
+            input_dir, _, _ = utils.misc.split_path_name_ext(wsi_input)
+            output_dir = pathlib.Path(input_dir).joinpath("..").joinpath("meta")
     else:
         raise ValueError("wsi_input path is not valid")
 
     print(files_all)
 
-    dataloader.slide_info.slide_info(
-        input_path=files_all, output_dir=output_dir, mode=mode, workers=workers,
+    slide_params = dataloader.slide_info.slide_info(
+        input_path=files_all, workers=workers,
     )
 
+    if mode == "show":
+        for slide_param in slide_params:
+            print(slide_param)
+
+    if mode == "save":
+        output_dir.mkdir(parents=True, exist_ok=True)
+        for slide_param in slide_params:
+            utils.misc.save_yaml(slide_param,
+                                 pathlib.Path(output_dir)
+                                 .joinpath(slide_param["file_name"] + ".yaml"))
+        print("Meta files saved at " + str(output_dir))
+
 
 @main.command()
 @click.option("--wsi_input", help="Path to WSI file")