Sophios yaml pip

setup.py

@@ -0,0 +1,59 @@
+import json
+from pathlib import Path
+from shutil import copytree, ignore_patterns
+from setuptools import setup, find_packages
+from setuptools.command.build_py import build_py as _build_py
+import versioneer
+
+
+class build_py(_build_py):
+    """build mode script"""
+
+    def run(self) -> None:
+        adapters_dir = Path(__file__).parent / 'cwl_adapters'
+        examples_dir = Path(__file__).parent / 'docs' / 'tutorials'
+        adapters_target_dir = Path(self.build_lib) / 'sophios/cwl_adapters'
+        examples_target_dir = Path(self.build_lib) / 'sophios/examples'
+        extlist = ['*.png', '*.md', '*.rst', '*.pyc', '__pycache__', '*.json']
+        copytree(adapters_dir, adapters_target_dir, dirs_exist_ok=True)
+        copytree(examples_dir, examples_target_dir, ignore=ignore_patterns(*extlist), dirs_exist_ok=True)
+        # Never overwrite user config
+        if not (Path.home() / 'wic').exists():
+            # config_path
+            config_path = Path.home() / 'wic'
+            # global config file in ~/wic
+            global_config_file = config_path / 'global_config.json'
+
+            # setup.py always gets executed in the project_root
+            config_file = Path(__file__).parent / 'src' / 'sophios' / 'config.json'
+            config = {}
+            # config_file can contain absolute or relative paths
+            with open(config_file, 'r', encoding='utf-8') as f:
+                config = json.load(f)
+            conf_tags = ['search_paths_cwl', 'search_paths_wic']
+            for tag in conf_tags:
+                for ns in config[tag]:
+                    abs_paths = [str(Path(path).absolute()) for path in config[tag][ns]]
+                    config[tag][ns] = abs_paths
+            config_path.mkdir(parents=True, exist_ok=True)
+            # write out the config file with paths
+            with open(global_config_file, 'w', encoding='utf-8') as f:
+                json.dump(config, f)
+
+        # Continue with the standard build process
+        super().run()
+
+
+setup(
+    name='sophios',
+    version=versioneer.get_version(),
+    packages=find_packages(where="src"),
+    package_dir={"": "src"},
+    include_package_data=True,
+    cmdclass={
+        'build_py': build_py,
+    },
+    package_data={
+        "sophios": ["cwl_adapters/*.cwl", "examples/*.wic"]
+    }
+)

src/sophios/input_output.py

@@ -186,8 +186,15 @@ def move_adapters_and_examples(config: Json) -> None:
     Args:
         config (Json): Json containing search path information
     """
-    adapters_dir = Path(__file__).parent.parent.parent / 'cwl_adapters'
-    examples_dir = Path(__file__).parent.parent.parent / 'docs' / 'tutorials'
+    # if the sophios installation is through pip package
+    pip_dir_name = 'sophios'
+    if str(Path(__file__).parent).endswith(pip_dir_name):
+        adapters_dir = Path(__file__).parent / 'cwl_adapters'
+        examples_dir = Path(__file__).parent / 'examples'
+    # when using dev/git install
+    else:
+        adapters_dir = Path(__file__).parent.parent.parent / 'cwl_adapters'
+        examples_dir = Path(__file__).parent.parent.parent / 'docs' / 'tutorials'
 
     extlist = ['*.png', '*.md', '*.rst', '*.pyc', '__pycache__', '*.json']
     # the default search paths will be the first entry in the 'global' namespace