imas-python 2.2.0__tar.gz → 2.3.1__tar.gz

imas_python-2.3.1/.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  # Enable version updates for Github Actions
+  - package-ecosystem: "github-actions"
+    # Look for `/.github/workflows` and `/action.yml` or `.yaml`
+    directory: "/"
+    # Check for updates once a week
+    schedule:
+      interval: "weekly"
+    # Group actions version bumps into a single PR
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
+

{imas_python-2.2.0 → imas_python-2.3.1}/.github/workflows/linting.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout IMAS-Python sources
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           # until saxonche is available in 3.13
           # https://saxonica.plan.io/issues/6561

{imas_python-2.2.0 → imas_python-2.3.1}/.github/workflows/publish.yml

@@ -10,11 +10,11 @@ jobs:
     name: Build distribution
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         # until saxonche is available in 3.13
         # https://saxonica.plan.io/issues/6561
@@ -25,7 +25,7 @@ jobs:
     - name: Build a binary wheel and a source tarball
       run: python3 -m build .
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v7
       with:
         name: python-package-distributions
         path: dist/
@@ -43,7 +43,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v8
       with:
         name: python-package-distributions
         path: dist/
@@ -63,7 +63,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v8
       with:
         name: python-package-distributions
         path: dist/

{imas_python-2.2.0 → imas_python-2.3.1}/.github/workflows/test_with_pytest.yml

@@ -14,11 +14,11 @@ jobs:
     
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Set up Python ${{ matrix.python-version }}
 
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -37,13 +37,13 @@ jobs:
           python -m pytest -n=auto --cov=imas --cov-report=term-missing --cov-report=xml:coverage.xml --cov-report=html:htmlcov --junit-xml=junit.xml
 
       - name: Upload coverage report ${{ matrix.python-version }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-report-${{ matrix.python-version }}
           path: htmlcov
 
       - name: Upload test report ${{ matrix.python-version }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: test-report-${{ matrix.python-version }}
           path: junit.xml

{imas_python-2.2.0 → imas_python-2.3.1}/.readthedocs.yml

@@ -20,4 +20,4 @@ python:
 sphinx:
   builder: html
   configuration: docs/source/conf.py
-  fail_on_warning: false
+  fail_on_warning: true

{imas_python-2.2.0/imas_python.egg-info → imas_python-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imas-python
-Version: 2.2.0
+Version: 2.3.1
 Summary: Pythonic wrappers for the IMAS Access Layer
 Author: ITER Organization
 Author-email: Karel Lucas van de Plassche <karelvandeplassche@gmail.com>, Daan van Vugt <dvanvugt@ignitioncomputing.com>, Maarten Sebregts <msebregts@ignitioncomputing.com>, imas-support@iter.org

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/changelog.rst

@@ -3,6 +3,72 @@
 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
+-------------------------------
+
+Features
+''''''''
+
+- :merge:`131`: introduce alias and units metadata in the :ref:`Identifiers` API
+- :merge:`104`: add a :py:func:`imas.db_entry.DBEntry.list_filled_paths` function (requires imas_core >= 5.7 for HDF5 backend)
+
+Improvements
+''''''''''''
+
+- :issue:`116`: migrate `magnetics` obsolescent fields (`method -> ip`, `bpol_probe -> b_field_pol_probe`) with a value during a 3to4 conversion 
+- :merge:`112`: include metadata variables when writing an IDS to a netCDF files with the function `to_xarray`, allowing to read back the IDS with a `get` (see :ref:`Store Xarray Datasets in IMAS-compatible netCDF file`)
+  - improve documentation w.r.t netcdf URI and UDA backend usage limitations and associated workarounds
+
+Bug fixes
+'''''''''
+
+- :issue:`118`: fix deprecation warning with copy keyword for __array__ implementation (Numpy > 2)
+- :issue:`117`: fix 3to4 conversion of name/identifier when identifier is empty
+- :merge:`105`: fix training data assets that failed loading
+
+  
+
+What's new in IMAS-Python 2.2.0
+-------------------------------
+
+Features
+''''''''
+- :issue:`44`: add `--convert-to-plasma-ids` option to `imas convert`  
+
+Improvements
+''''''''''''
+
+- :merge:`100`: remove legacy tool `extract_test_data` 
+- :merge:`98`: support MDSplus models configuration change introduced in imas_core >= 5.6
+- :issue:`97`: better documentation, exception message and control of DD compatibility when using UDA backend
+- :merge:`95`: defer loading the default DD definitions
+- :issue:`91`: remove hidden `has_imas` attribute (may break compatibility of applications that used it!)
+
+Bug fixes
+'''''''''
+
+- :merge:`100`: fix incorrect type hints
+- :issue:`89`: properly unpack 0D data when reading an IDS from a netCDF file
+
+
+
 What's new in IMAS-Python 2.1.0
 -------------------------------
 

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/conf.py

@@ -34,6 +34,9 @@ copyright = f"2020-{datetime.datetime.now().year}, ITER Organization"
 author = "ITER Organization"
 src_host = "https://github.com/iterorganization/"
 
+# Warn about missing references
+nitpicky = True
+
 # Parse urls here for convenience, to be re-used
 # ITER docs
 iter_projects = "https://github.com/iterorganization/"

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/identifiers.rst

@@ -14,13 +14,16 @@ enumerated list of options for defining, for example:
 - These may have alternative naming conventions supported through aliases 
   (e.g., "235U" and "U_235" for Uranium 235).
 
-Identifiers are a list of possible valid labels. Each label has up to four
-representations:
+Identifiers are a list of possible valid options. Each option has three representations
+that are stored in an IDS:
 
 1. An index (integer)
 2. A name (short string)
 3. A description (long string)
-4. List of aliases (list of short strings)
+
+.. seealso::
+    `Data Dictionary documentation for identifiers
+    <https://imas-data-dictionary.readthedocs.io/en/latest/identifiers.html>`__
 
 
 Identifiers in IMAS-Python
@@ -32,6 +35,20 @@ constructed on-demand from the loaded Data Dictionary definitions.
 All identifier enums can be accessed through ``imas.identifiers``. A list of
 the available identifiers is stored as ``imas.identifiers.identifiers``.
 
+Each identifier option provides the following attributes:
+
+- ``name``: the name of the option.
+- ``index``: the integer index value of the option.
+- ``description``: a longer string describing the option.
+- ``aliases``: a list of aliases that can be used instead of the name.
+- ``units``: optional information about the units of the quantities that are affected by
+  the identifier option. Take, for example, the `poloidal plan coordinate identifier
+  <https://imas-data-dictionary.readthedocs.io/en/stable/generated/identifier/poloidal_plane_coordinates_identifier.html>`__
+  which affects the units of ``grid/dim1`` and ``grid/dim2``.
+
+.. versionadded:: 2.1.0 ``aliases`` for identifiers.
+.. versionadded:: 2.3.0 ``units`` metadata.
+
 .. code-block:: python
     :caption: Accessing identifiers
 
@@ -47,6 +64,9 @@ the available identifiers is stored as ``imas.identifiers.identifiers``.
     print(csid.total.index)
     print(csid.total.description)
 
+    # Search identifier options by their index value
+    print(csid(1))
+
     # Access identifiers with aliases (when available)
     mid = imas.identifiers.materials_identifier
     print(mid["235U"].name)        # Access by canonical name
@@ -57,12 +77,12 @@ the available identifiers is stored as ``imas.identifiers.identifiers``.
     assert mid["235U"].name is mid.U_235.name
 
     # Item access is also possible
-    print(identifiers["edge_source_identifier"])
+    print(imas.identifiers["edge_source_identifier"])
 
     # You can use imas.util.inspect to list all options
-    imas.util.inspect(identifiers.ggd_identifier)
+    imas.util.inspect(imas.identifiers.ggd_identifier)
     # And also to get more details of a specific option
-    imas.util.inspect(identifiers.ggd_identifier.SN)
+    imas.util.inspect(imas.identifiers.ggd_identifier.SN)
 
     # When an IDS node is an identifier, you can use
     # metadata.identifier_enum to get the identifier
@@ -186,6 +206,7 @@ material_identifier["235U"].
     mat.names[0] = mid.U_235.name  # enum value via alias
     mat.names[0] = mid["U_235"].name  # enum value via alias
 
+
 Compare identifiers
 -------------------
 

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/intro.rst

@@ -86,17 +86,6 @@ get an error message if this is not possible:
 Load and store an IDS to disk with IMAS-Core
 ''''''''''''''''''''''''''''''''''''''''''''
 
-.. note::
-
-    - This functionality requires the IMAS-Core, until this library is openly available
-      on GitHub you may need to fetch it from `git.iter.org <https://git.iter.org/>`_
-      (requires to have an ITER account). Using IMAS-Core also enable slicing methods
-      :py:meth:`~imas.db_entry.DBEntry.get_slice`, 
-      :py:meth:`~imas.db_entry.DBEntry.put_slice` and
-      :py:meth:`~imas.db_entry.DBEntry.get_sample` (with IMAS-Core>=5.4).
-    - If you can't have access to it, you can save IDS to disk with the built-in
-      netCDF backend :ref:`Load and store an IDS to disk with netCDF`
-
 To store an IDS to disk, we need to indicate the following URI to the
 IMAS-Core: ``imas:<backend>?path=<path_to_folder>`` or using the legacy query keys
 ``imas:<backend>?user=<user>;database=<database>;version=<version>;pulse=<pulse>;run=<run>``
@@ -115,11 +104,9 @@ In IMAS-Python you do this as follows:
     >>> # now store the core_profiles IDS we just populated
     >>> dbentry.put(core_profiles)
 
-.. image:: imas_structure.png
-
 To load an IDS from disk, you need to specify the same information as
 when storing the IDS (see above). Once the data entry is opened, you
-can use ``<IDS>.get()`` to load IDS data from disk: 
+can use ``dbentry.get()`` to load IDS data from disk: 
 
 .. code-block:: python
 
@@ -146,7 +133,7 @@ In IMAS-Python you do this as follows:
 
 To load an IDS from disk, you need to specify the same file information as
 when storing the IDS. Once the data entry is opened, you
-can use ``<IDS>.get()`` to load IDS data from disk: 
+can use ``dbentry.get()`` to load IDS data from disk: 
 
 .. code-block:: python
 
@@ -154,3 +141,26 @@ can use ``<IDS>.get()`` to load IDS data from disk:
     >>> dbentry2 = imas.DBEntry("mypulsefile.nc","r")
     >>> core_profiles2 = dbentry2.get("core_profiles")
     >>> print(core_profiles2.ids_properties.comment.value)
+
+
+Data Entry API overview
+'''''''''''''''''''''''
+
+See the documentation of :py:class:`imas.DBEntry <imas.db_entry.DBEntry>` for more
+details on reading and writing IDSs to disk. Useful functions include:
+
+- :py:meth:`~imas.db_entry.DBEntry.put` and :py:meth:`~imas.db_entry.DBEntry.put_slice`
+  to write a full IDS or write append a time slice to existing data.
+- :py:meth:`~imas.db_entry.DBEntry.get`, :py:meth:`~imas.db_entry.DBEntry.get_slice` and
+  :py:meth:`~imas.db_entry.DBEntry.get_sample` to read all time slices, a single time
+  slice, or a sample of time slices from disk. ``get_slice()`` and ``get_sample()`` can
+  also interpolate data to a requested point in time.
+
+  All three ``get()`` methods have a ``lazy`` mode, which will only load data from disk
+  when you need it. This can greatly speed up data access in some scenarios. See
+  :ref:`Lazy loading` for more details.
+- :py:meth:`~imas.db_entry.DBEntry.list_all_occurrences` to query whether there are any
+  occurrences of a certain IDS stored on disk.
+- :py:meth:`~imas.db_entry.DBEntry.list_filled_paths` to query which Data Dictionary
+  paths have data filled inside a specific IDS.
+

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/multi-dd.rst

@@ -290,24 +290,17 @@ you may see the following error:
   Dictionary version of the DBEntry (3.42.0). This is not supported when using the
   UDA backend.
 
-There are three possible workarounds. The first two require passing an additional option
+There are two possible workarounds. The first one requires passing an additional option
 in the IMAS UDA URI: please see the `imas-core documentation
 <https://imas-core.readthedocs.io/en/stable/user_guide/backends_guide.html#query-keys-specific-for-the-uda-backend>`__
-for more details on these URI options.
+for more details on URI options.
 
 1. Use UDA fetch to bypass the cache problem. You can do this by appending ``&fetch=1``
    to the URI when you create the :py:class:`~imas.db_entry.DBEntry`.
 
    Note that this will download the entire IDS files from the remote server, this may
    not be desired if you only want to read a single time slice.
-2. Disable the UDA cache. You can do this by appending ``&cache_mode=none`` to the URI
-   when you create the :py:class:`~imas.db_entry.DBEntry`.
-
-   Note that this may make the ``get()`` (a lot) slower, since a separate request needs
-   to be sent to the remote UDA server for every data variable. However, this may still
-   be the best performing option if you are only interested in a subset of all the data
-   in an IDS (and use :ref:`lazy loading`).
-3. Explicitly provide the data dictionary version when you create the
+2. Explicitly provide the data dictionary version when you create the
    :py:class:`~imas.db_entry.DBEntry`, setting it to match the Data Dictionary version
    of the data you want to load. To obtain the version of the data on the remote server
    from the field `ids_properties.put_version.data_dictionary` via a _lazy_ ``get()``
@@ -316,7 +309,7 @@ for more details on these URI options.
    Note that you may need to call ``imas.convert_ids`` to convert the IDS to your
    desired Data Dictionary version.
 
-All three possible workarounds are shown in the examples below:
+The two possible workarounds are shown in the examples below:
 
 .. md-tab-set::
 
@@ -346,20 +339,7 @@ All three possible workarounds are shown in the examples below:
         with imas.DBEntry(URI, "r") as entry:
             cp = entry.get("core_profiles")
 
-    .. md-tab-item:: 2. Disable the UDA cache
-
-      .. code-block:: python
-
-        import imas
-
-        URI = (
-            "imas://uda.iter.org:56565/uda?backend=hdf5"
-            "&path=/work/imas/shared/imasdb/ITER/3/121013/50&cache_mode=none"
-        )
-        with imas.DBEntry(URI, "r") as entry:
-            cp = entry.get("core_profiles")
-
-    .. md-tab-item:: 3. Explicitly provide the DD version
+    .. md-tab-item:: 2. Explicitly provide the DD version
 
       .. code-block:: python
 

{imas_python-2.2.0 → imas_python-2.3.1}/docs/source/netcdf.rst

@@ -183,3 +183,41 @@ specific paths inside the IDS. The latter variant can also be combined with
     #   profiles_1d.grid.rho_tor
     #   profiles_1d.grid.rho_tor_norm
     #   profiles_1d.grid.psi
+
+
+.. _`Store Xarray Datasets in IMAS-compatible netCDF file`:
+    
+Store Xarray Datasets in IMAS-compatible netCDF file
+''''''''''''''''''''''''''''''''''''''''''''''''''''
+
+.. versionadded:: 2.3.0 :py:meth:`~imas.util.to_xarray` now includes the required
+    metadata to load the IDS from a netCDF file.
+
+The following snippet shows how to store an IMAS Xarray dataset in an IMAS-compatible
+netCDF file. The group name in the netCDF file must correspond to ``<IDS
+Name>/<occurrence>`` (``core_profiles/0`` in the snippet).
+
+.. code-block:: python
+    :caption: Store IMAS Xarray dataset in an IMAS-compatible netCDF file
+
+    import imas.training
+    import netCDF4
+
+    with imas.training.get_training_db_entry() as training_entry:
+        core_profiles = training_entry.get("core_profiles")
+        xrds = imas.util.to_xarray(core_profiles)
+    
+    # Store the xarray dataset in an IMAS-compatible netCDF dataset
+    filename = "data.nc"
+    xrds.to_netcdf(
+        filename,
+        group="core_profiles/0",  # Update to the correct IDS name and occurrence
+        # auto_complex=True,      # Uncomment if the dataset contains complex data
+    )
+    # Set global DD version metadata
+    with netCDF4.Dataset(filename, "a") as ds: 
+        ds.data_dictionary_version = imas.util.get_data_dictionary_version(ids)
+
+    # Test that we can get the IDS from the netCDF file
+    with imas.DBEntry(filename, "r") as entry:
+        ids2 = entry.get("core_profiles")

{imas_python-2.2.0 → imas_python-2.3.1}/imas/_to_xarray.py

@@ -8,7 +8,7 @@ from imas.backends.netcdf.ids_tensorizer import IDSTensorizer
 from imas.ids_data_type import IDSDataType
 
 fillvals = {
-    IDSDataType.INT: -(2**31) + 1,
+    IDSDataType.INT: numpy.int32(-(2**31) + 1),
     IDSDataType.STR: "",
     IDSDataType.FLT: numpy.nan,
     IDSDataType.CPX: numpy.nan * (1 + 1j),
@@ -50,21 +50,28 @@ def to_xarray(ids: IDSToplevel, *paths: str) -> xarray.Dataset:
         var_name = path.replace("/", ".")
         metadata = ids.metadata[path]
         if metadata.data_type in (IDSDataType.STRUCTURE, IDSDataType.STRUCT_ARRAY):
-            continue  # We don't store these in xarray
-
-        dimensions = tensorizer.ncmeta.get_dimensions(path, tensorizer.homogeneous_time)
-        data = tensorizer.tensorize(path, fillvals[metadata.data_type])
-
-        attrs = dict(documentation=metadata.documentation)
-        if metadata.units:
-            attrs["units"] = metadata.units
-        coordinates = tensorizer.filter_coordinates(path)
-        if coordinates:
-            coordinate_names.update(coordinates.split(" "))
-            attrs["coordinates"] = coordinates
+            # Metadata variables for (arrays of) structures
+            if paths and path not in paths:
+                continue
+            dimensions = ()
+            data = b""
+        else:
+            dimensions = tensorizer.get_dimensions(path)
+            data = tensorizer.tensorize(path, fillvals[metadata.data_type])
 
+        attrs = tensorizer.get_attributes(path, fillvals)
+        if "coordinates" in attrs:
+            coordinate_names.update(attrs["coordinates"].split(" "))
         data_vars[var_name] = (dimensions, data, attrs)
 
+        # :shape array for sparse data
+        if path in tensorizer.shapes and metadata.ndim:
+            shape_name = f"{var_name}:shape"
+            dimensions = tensorizer.get_shape_dimensions(path)
+            data = tensorizer.shapes[path]
+            attrs = tensorizer.get_shape_attributes(var_name)
+            data_vars[shape_name] = (dimensions, data, attrs)
+
     # Remove coordinates from data_vars and put in coordinates mapping:
     coordinates = {}
     for coordinate_name in coordinate_names:

imas_python-2.3.1/imas/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '2.3.1'
+__version_tuple__ = version_tuple = (2, 3, 1)
+
+__commit_id__ = commit_id = 'gdc78cc36c'

{imas_python-2.2.0 → imas_python-2.3.1}/imas/assets/ITER_134173_106_equilibrium.ids

@@ -26,8 +26,6 @@ equilibrium/vacuum_toroidal_field/b0
 	dim: 1
 	size: 3 
 -5.2999999999999998e+00 -5.2999999999999998e+00 -5.2999999999999998e+00 
-equilibrium/grids_ggd
-	size: 1
 equilibrium/time_slice
 	size: 3
 equilibrium/time_slice[0]/boundary/outline/r

{imas_python-2.2.0 → imas_python-2.3.1}/imas/assets/equilibrium.ids

@@ -26,8 +26,6 @@ equilibrium/vacuum_toroidal_field/b0
 	dim: 1
 	size: 3 
 -5.2999999999999998e+00 -5.2999999999999998e+00 -5.2999999999999998e+00 
-equilibrium/grids_ggd
-	size: 1
 equilibrium/time_slice
 	size: 3
 equilibrium/time_slice[0]/boundary/outline/r

{imas_python-2.2.0 → imas_python-2.3.1}/imas/backends/db_entry_impl.py

@@ -120,3 +120,11 @@ class DBEntryImpl(ABC):
     @abstractmethod
     def list_all_occurrences(self, ids_name: str) -> List[int]:
         """Implement DBEntry.list_all_occurrences()"""
+
+    @abstractmethod
+    def list_filled_paths(self, ids_name: str, occurrence: int) -> List[str]:
+        """Implement DBEntry.list_filled_paths().
+
+        N.B. DD conversion is handled in DBEntry.list_filled_paths(), this method
+        returns the data paths as stored on-disk.
+        """

{imas_python-2.2.0 → imas_python-2.3.1}/imas/backends/imas_core/al_context.py

@@ -174,6 +174,17 @@ class ALContext:
             return list(occurrences)
         return []
 
+    def list_filled_paths(self, path: str) -> List[str]:
+        """List all filled paths in an IDS.
+
+        Args:
+            path: IDS and occurrence as a string: <IDS>[/<occurrence>]
+        """
+        status, result = ll_interface.list_filled_paths(self.ctx, path)
+        if status != 0:
+            raise LowlevelError(f"list filled paths for {path!r}", status)
+        return result
+
     def close(self):
         """Close this ALContext."""
         ll_interface.end_action(self.ctx)

{imas_python-2.2.0 → imas_python-2.3.1}/imas/backends/imas_core/db_entry_al.py

@@ -364,6 +364,19 @@ class ALDBEntryImpl(DBEntryImpl):
             ) from None
         return occurrence_list
 
+    def list_filled_paths(self, ids_name: str, occurrence: int) -> List[str]:
+        if self._db_ctx is None:
+            raise RuntimeError("Database entry is not open.")
+        ll_path = ids_name
+        if occurrence != 0:
+            ll_path += f"/{occurrence}"
+        paths = self._db_ctx.list_filled_paths(ll_path)
+        if not paths:
+            raise DataEntryException(
+                f"IDS {ids_name!r}, occurrence {occurrence} is empty."
+            )
+        return paths
+
     def _check_uda_warnings(self, lazy: bool) -> None:
         """Various checks / warnings for the UDA backend."""
         cache_mode = self._querydict.get("cache_mode")

{imas_python-2.2.0 → imas_python-2.3.1}/imas/backends/imas_core/imas_interface.py

@@ -166,6 +166,11 @@ class LowlevelInterface:
     ):
         raise self._minimal_version("5.4")
 
+    # New method in AL 5.7
+
+    def list_filled_paths(self, ctx, path):
+        raise self._minimal_version("5.7")
+
 
 # Dummy documentation for interface:
 for funcname in dir(LowlevelInterface):

{imas_python-2.2.0 → imas_python-2.3.1}/imas/backends/imas_core/mdsplus_model.py

@@ -12,7 +12,7 @@ import tempfile
 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