account for pwd when installing through src (like CI)

setup.py

@@ -15,29 +15,52 @@ def run(self) -> None:
         # Custom post-installation actions go here
         # Never overwrite user config
         if not (Path.home() / 'wic').exists():
+            # proj_root_dir convention necessary for CI installation
+            proj_root_dir = 'workflow-inference-compiler'
             # config_path
             config_path = Path.home() / 'wic'
-            cwl_path = config_path / 'cwl_adapters'
-            wic_path = config_path / 'examples'
+            # global config file in ~/wic
             global_config_file = config_path / 'global_config.json'
-            extlist = ['*.png', '*.md', '*.rst', '*.pyc', '__pycache__', '*.json']
-            adapters_dir = Path(__file__).parent / 'cwl_adapters'
-            examples_dir = Path(__file__).parent / 'docs' / 'tutorials'
-            config_file = Path(__file__).parent / 'src' / 'sophios' / 'config_basic.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.home() / path) for path in config[tag][ns]]
-                    config[tag][ns] = abs_paths
-            # copy to config_path
-            copytree(adapters_dir, cwl_path)
-            copytree(examples_dir, wic_path, ignore=ignore_patterns(*extlist))
-            with open(global_config_file, 'w', encoding='utf-8') as f:
-                json.dump(config, f)
+
+            # if it is 'proj_root_dir' i.e, src installed with pip install ".[all]"
+            # or pip install ".[all_except_runner_src]"
+            if str(Path.cwd()).endswith(proj_root_dir):
+                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)
+            else:
+                cwl_path = config_path / 'cwl_adapters'
+                wic_path = config_path / 'examples'
+                extlist = ['*.png', '*.md', '*.rst', '*.pyc', '__pycache__', '*.json']
+                adapters_dir = Path(__file__).parent / 'cwl_adapters'
+                examples_dir = Path(__file__).parent / 'docs' / 'tutorials'
+                config_file = Path(__file__).parent / 'src' / 'sophios' / 'config_basic.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.home() / path) for path in config[tag][ns]]
+                        config[tag][ns] = abs_paths
+                # copy to config_path
+                copytree(adapters_dir, cwl_path)
+                copytree(examples_dir, wic_path, ignore=ignore_patterns(*extlist))
+                # write out the config file with paths
+                with open(global_config_file, 'w', encoding='utf-8') as f:
+                    json.dump(config, f)
 
 
 setup(