Release/2.3.1

.github/dependabot.yml

@@ -7,4 +7,9 @@ updates:
     # Check for updates once a week
     schedule:
       interval: "weekly"
+    # Group actions version bumps into a single PR
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
 

.github/workflows/linting.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout IMAS-Python sources
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           # until saxonche is available in 3.13
           # https://saxonica.plan.io/issues/6561

.github/workflows/publish.yml

@@ -10,11 +10,11 @@ jobs:
     name: Build distribution
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         # until saxonche is available in 3.13
         # https://saxonica.plan.io/issues/6561

.github/workflows/test_with_pytest.yml

@@ -14,11 +14,11 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Set up Python ${{ matrix.python-version }}
 
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version

docs/source/changelog.rst

@@ -3,6 +3,23 @@
 Changelog
 =========
 
+What's new in IMAS-Python 2.3.1
+-------------------------------
+
+Improvements
+''''''''''''
+
+- :merge:`140`: improve performance of ``hasattr()`` on IDS structures 
+- :merge:`139`: improve performance of :py:meth:`~imas.ids_toplevel.IDSToplevel.validate` for large arrays of structures
+
+Bugs
+''''
+
+- :issue:`146`: Fix creation of MDSplus models, regression since 2.2.0 when used together with IMAS-Core >= 5.6
+- Fix broken test (due to breaking change in xxhash>=4 dep)
+
+
+
 What's new in IMAS-Python 2.3.0
 -------------------------------
 

imas/backends/imas_core/mdsplus_model.py

@@ -12,7 +12,7 @@
 import time
 import uuid
 from pathlib import Path
-from subprocess import CalledProcessError, check_output
+from subprocess import STDOUT, CalledProcessError, check_output
 from zlib import crc32
 from packaging.version import Version
 
@@ -324,12 +324,19 @@ def create_mdsplus_model(cache_dir_path: Path) -> None:
                 "Could not determine CompileTree class in jTraverser.jar."
             )
         compiletree = compiletree_class.rpartition(".class")[0].replace("/", ".")
+        # only add option to suppress warning if the JVM supports it
+        native_access = ["--enable-native-access=ALL-UNNAMED"]
+        try:
+            check_output(["java", *native_access, "-version"], stderr=STDOUT)
+        except CalledProcessError:
+            native_access = []
         check_output(
             [
                 "java",
                 "-Xms1g",  # what do these do?
                 "-Xmx8g",  # what do these do?
                 "-XX:+UseG1GC",  # what do these do?
+                *native_access,
                 "-cp",
                 jarfile,
                 compiletree,
@@ -339,13 +346,14 @@ def create_mdsplus_model(cache_dir_path: Path) -> None:
             env={
                 "PATH": os.environ.get("PATH", ""),
                 "LD_LIBRARY_PATH": os.environ.get("LD_LIBRARY_PATH", ""),
-                get_mdsplus_model_var(): str(cache_dir_path),
+                # MDSplus locates models through '<tree>_path' (tree='ids')
+                "ids_path": str(cache_dir_path),
             },
         )
         # Touch a file to show that we have finished the model
         (cache_dir_path / "done.txt").touch()
     except CalledProcessError as e:
-        logger.error("Error making MDSPlus model in {path}", cache_dir_path)
+        logger.error("Error making MDSPlus model in %s", cache_dir_path)
         raise e
 
 

imas/ids_coordinates.py

@@ -81,7 +81,7 @@ def __init__(self, coordinate_spec: str) -> None:
                     logger.debug(
                         f"Ignoring invalid coordinate specifier {spec}", exc_info=True
                     )
-        self.references: "tuple[IDSPath]" = tuple(refs)
+        self.references: "tuple[IDSPath, ...]" = tuple(refs)
         """A tuple paths that this coordinate refers to.
         """
 
@@ -357,28 +357,29 @@ def _capture_goto_errors(self, dim, coordinate):
         IDSPath.goto().
         """
         did_capture = []
-        path = self._node._path
         try:
             yield did_capture
         except CoordinateLookupError as exc:
             raise ValidationError(exc.args[0])
         except IndexError as exc:
             # Can happen in IDSPath.goto when an invalid index is encountered.
             coordinate_refs = coordinate.format_refs(self._node)
+            path = self._node._path
             raise ValidationError(
                 f"Error while validating element `{path}`: dimension {dim + 1} has an "
                 f"invalid index for coordinate(s) {coordinate_refs}."
             ) from exc
         except Exception as exc:
             # Ignore all other exceptions and log them
             if "Unexpected index" in str(exc):
-                logger.debug(
-                    "Ignored AoS coordinate outside our tree (see IMAS-4675) of "
-                    "element `%s`, dimension %s, coordinate `%s`",
-                    path,
-                    dim,
-                    coordinate.references,
-                )
+                if logger.isEnabledFor(logging.DEBUG):
+                    logger.debug(
+                        "Ignored AoS coordinate outside our tree (see IMAS-4675) "
+                        "of element `%s`, dimension %s, coordinate `%s`",
+                        self._node._path,
+                        dim,
+                        coordinate.references,
+                    )
             else:
                 if self._node._version <= "3.38.1":
                     version_error = (
@@ -395,7 +396,7 @@ def _capture_goto_errors(self, dim, coordinate):
                     coordinate.references,
                     dim,
                     version_error,
-                    exc_info=1,
+                    exc_info=True,
                 )
             # Flag to the caller that an error was suppressed
             did_capture.append(1)

imas/ids_structure.py

@@ -57,7 +57,7 @@ def __init__(self, parent: IDSBase, metadata: IDSMetadata):
     def __getattr__(self, name):
         if name not in self._children:
             raise AttributeError(
-                f"IDS structure '{self._path}' has no attribute '{name}'"
+                f"IDS structure '{self.metadata.path_string}' has no attribute '{name}'"
             )
         # Create child node
         child_meta = self._children[name]

imas/test/test_hash.py

@@ -27,7 +27,7 @@ def test_hash_str1d(minimal):
         "multiple entries to test!",
     ]
     minimal.str_1d = string_list
-    hashes = list(map(xxh3_64_digest, string_list))
+    hashes = [xxh3_64_digest(s.encode("utf-8")) for s in string_list]
     expected = xxh3_64_digest(struct.pack("<Q", len(string_list)) + b"".join(hashes))
     assert expected == b"\x98\x011\x9dx+\x0e\xc0"
     assert imas.util.calc_hash(minimal.str_1d) == expected