From dee1162d3a875b4759253c8462dfe8c0148df94c Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 7 Nov 2023 16:36:06 +0100
Subject: [PATCH 1/3] fix: replace relative paths for custom module with
 absolute ones in parse_yaml()

---
 junifer/api/parser.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/junifer/api/parser.py b/junifer/api/parser.py
index 56bccf9a4..97ecf3fc2 100644
--- a/junifer/api/parser.py
+++ b/junifer/api/parser.py
@@ -50,6 +50,8 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
         # Convert load modules to list
         if not isinstance(to_load, list):
             to_load = [to_load]
+        # Initialize list to have absolute paths for custom modules
+        final_to_load = []
         for t_module in to_load:
             if t_module.endswith(".py"):
                 logger.debug(f"Importing file: {t_module}")
@@ -65,9 +67,18 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                 module = importlib.util.module_from_spec(spec)  # type: ignore
                 sys.modules[t_module] = module
                 spec.loader.exec_module(module)  # type: ignore
+                # Add absolute path to final list
+                final_to_load.append(str(file_path.resolve()))
             else:
                 logger.info(f"Importing module: {t_module}")
                 importlib.import_module(t_module)
+                # Add module to final list
+                final_to_load.append(t_module)
+
+        # Replace modules to be loaded so that custom modules will take the
+        # absolute path. This was not the case as found in #224. Similar thing
+        # is done with the storage URI below.
+        contents["with"] = final_to_load
 
     # Compute path for the URI parameter in storage files that are relative
     # This is a tricky thing that appeared in #127. The problem is that
-- 
2.52.0


From f4f45d981bb3b7741e5bc1616d887a87a3b6db1d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 17 Nov 2023 10:55:47 +0100
Subject: [PATCH 2/3] chore: add changelog 224.bugfix

---
 docs/changes/newsfragments/224.bugfix | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/changes/newsfragments/224.bugfix

diff --git a/docs/changes/newsfragments/224.bugfix b/docs/changes/newsfragments/224.bugfix
new file mode 100644
index 000000000..ec0b01b64
--- /dev/null
+++ b/docs/changes/newsfragments/224.bugfix
@@ -0,0 +1 @@
+Make copying of assets in ``with`` block of YAML, relative to YAML and not to current working directory by `Fede Raimondo`_ and `Synchon Mandal`_
-- 
2.52.0


From 62567ad665d0398b6cb06e5a70a59686c6494e13 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 17 Nov 2023 11:32:10 +0100
Subject: [PATCH 3/3] fix: update parse_yaml() test

---
 junifer/api/tests/test_parser.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/junifer/api/tests/test_parser.py b/junifer/api/tests/test_parser.py
index bf5bcb58d..adad752c0 100644
--- a/junifer/api/tests/test_parser.py
+++ b/junifer/api/tests/test_parser.py
@@ -53,7 +53,7 @@ def test_parse_yaml_success_with_module_autoload(tmp_path: Path) -> None:
     assert "foo" in contents
     assert contents["foo"] == "bar"
     assert "with" in contents
-    assert contents["with"] == "numpy"
+    assert contents["with"] == ["numpy"]
     assert "numpy" in sys.modules
     assert "junifer.configs.wrong_config" not in sys.modules
 
-- 
2.52.0