docs/changes/newsfragments/127.bugfix

@@ -0,0 +1 @@
+Fix a bug in which relative storage URIs will be computed relative to the CWD and not to the location of the YAML file by `Fede Raimondo`_.

junifer/api/parser.py

@@ -71,4 +71,23 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                 logger.info(f"Importing module: {t_module}")
                 importlib.import_module(t_module)
 
+    # 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
+    # the path in the URI parameter is relative to YAML file, not to the
+    # current working directory. If we leave it as is in the contents
+    # dict, then it will be used later in the ``build`` function as is,
+    # which will be computed relative to the current working directory.
+    # The solution is to compute the absolute path and replace the
+    # relative path in the contents dict with the absolute path.
+
+    # Check if the storage file is defined
+    if "storage" in contents:
+        if "uri" in contents["storage"]:
+            # Check if the storage file is relative
+            uri_path = Path(contents["storage"]["uri"])
+            if not uri_path.is_absolute():
+                # Compute the absolute path
+                contents["storage"]["uri"] = str(
+                    (filepath.parent / uri_path).resolve()
+                )
     return contents

junifer/api/tests/test_parser.py

@@ -77,6 +77,28 @@ def test_parse_yaml_failure_with_multi_module_autoload(tmp_path: Path) -> None:
         parse_yaml(fname)
 
 
+def test_parse_yaml_with_wrong_path(tmp_path: Path) -> None:
+    """Test YAML parsing with wrong paths in with.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    t_tmp_path = tmp_path / "test_relative_with"
+    # Write yaml that includes a relative path
+    yaml_path = t_tmp_path / "yamls"
+    yaml_path.mkdir(exist_ok=True, parents=True)
+    yaml_fname = yaml_path / "test_parse_yaml_wrong_path.yaml"
+
+    yaml_fname.write_text("foo: bar\nwith:\n  -  missingt.py\n  - scipy\n")
+
+    # Check test file
+    with pytest.raises(ValueError, match="does not exist"):
+        parse_yaml(yaml_fname)
+
+
 def test_parse_yaml_relative_path(tmp_path: Path) -> None:
     """Test YAML parsing with relative paths in with.
 
@@ -135,3 +157,58 @@ def test_parse_yaml_absolute_path(tmp_path: Path) -> None:
 
     # Check test file
     parse_yaml(yaml_fname)
+
+
+def test_parse_storage_uri_relative(tmp_path: Path) -> None:
+    """Test YAML parsing with storage and relative URI.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
+    fname.write_text("foo: bar\nwith: numpy\nstorage:\n  uri: test.db\n")
+
+    contents = parse_yaml(fname)
+    assert "foo" in contents
+    assert contents["foo"] == "bar"
+    assert "storage" in contents
+    assert "uri" in contents["storage"]
+    assert contents["storage"]["uri"] == str(tmp_path / "test.db")
+
+    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
+    fname.write_text(
+        "foo: bar\nwith: numpy\nstorage:\n  uri: ../another/test.db\n"
+    )
+
+    contents = parse_yaml(fname)
+    assert "foo" in contents
+    assert contents["foo"] == "bar"
+    assert "storage" in contents
+    assert "uri" in contents["storage"]
+    assert contents["storage"]["uri"] == str(
+        (tmp_path / "../another/test.db").resolve()
+    )
+
+    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
+    fname.write_text(
+        "foo: bar\nwith: numpy\nstorage:\n  uri: /absolute/test.db\n"
+    )
+
+    contents = parse_yaml(fname)
+    assert "foo" in contents
+    assert contents["foo"] == "bar"
+    assert "storage" in contents
+    assert "uri" in contents["storage"]
+    assert contents["storage"]["uri"] == "/absolute/test.db"
+
+    # Just to trick coverage
+    fname = tmp_path / "test_parse_yaml_with_storage_uri.yaml"
+    fname.write_text("foo: bar\nwith: numpy\nstorage:\n  kind: SomeStorage\n")
+
+    contents = parse_yaml(fname)
+    assert "foo" in contents
+    assert contents["foo"] == "bar"
+    assert "storage" in contents