Cleanup: fix incorrect type hints and remove legacy tool

imas/_to_xarray.py

@@ -27,7 +27,7 @@ def to_xarray(ids: IDSToplevel, *paths: str) -> xarray.Dataset:
     # block checks if the paths are valid, and by using "metadata.path_string" we ensure
     # that / are used as separator.
     try:
-        paths = [ids.metadata[path].path_string for path in paths]
+        paths: list[str] = [ids.metadata[path].path_string for path in paths]
     except KeyError as exc:
         raise ValueError(str(exc)) from None
 

imas/backends/imas_core/al_context.py

@@ -115,7 +115,7 @@ def timerange_action(
         tmin: float,
         tmax: float,
         dtime: Optional[numpy.ndarray],
-        interpolation_method: int,
+        interpolation_method: Optional[int],
     ) -> "ALContext":
         """Begin a new timerange action for use in a ``with`` context."""
         ctx = ll_interface.begin_timerange_action(
@@ -163,7 +163,7 @@ def write_data(self, path: str, timebasepath: str, data: Any) -> None:
         """Call ual_write_data with this context."""
         status = ll_interface.write_data(self.ctx, path, timebasepath, data)
         if status != 0:
-            raise LowlevelError(f"write data at {path!r}: {status=}")
+            raise LowlevelError(f"write data at {path!r}", status)
 
     def list_all_occurrences(self, ids_name: str) -> List[int]:
         """List all occurrences of this IDS."""
@@ -359,7 +359,7 @@ def timerange_action(
         tmin: float,
         tmax: float,
         dtime: Optional[numpy.ndarray],
-        interpolation_method: int,
+        interpolation_method: Optional[int],
     ) -> Iterator["LazyALContext"]:
         """Lazily start a lowlevel timerange action, see
         :meth:`ALContext.timerange_action`.

imas/backends/imas_core/db_entry_al.py

@@ -96,7 +96,6 @@ def from_pulse_run(
         options: Any,
         factory: IDSFactory,
     ) -> "ALDBEntryImpl":
-
         # Set defaults
         user_name = user_name or getpass.getuser()
         data_version = data_version or factory.dd_version
@@ -138,7 +137,7 @@ def _setup_backend(cls, backend: str, mode: int, factory: IDSFactory) -> None:
             if idsdef_path is None:
                 # Extract XML from the DD zip and point UDA to it
                 idsdef_path = extract_idsdef(factory.version)
-            os.environ["IDSDEF_PATH"] = idsdef_path
+            os.environ["IDSDEF_PATH"] = str(idsdef_path)
 
         elif backend in ["hdf5", "memory", "ascii", "flexbuffers"]:
             pass  # nothing to set up
@@ -173,7 +172,7 @@ def get(
         destination: IDSToplevel,
         lazy: bool,
         nbc_map: Optional[NBCPathMap],
-    ) -> None:
+    ) -> IDSToplevel:
         if self._db_ctx is None:
             raise RuntimeError("Database entry is not open.")
         if lazy and self.backend == "ascii":
@@ -333,9 +332,12 @@ def delete_data(self, ids_name: str, occurrence: int) -> None:
             ll_path += f"/{occurrence}"
         ids = self._ids_factory.new(ids_name)
         with self._db_ctx.global_action(ll_path, WRITE_OP) as write_ctx:
-            delete_children(ids.metadata, write_ctx, "")
+            delete_children(ids.metadata, write_ctx)
 
     def list_all_occurrences(self, ids_name: str) -> List[int]:
+        if self._db_ctx is None:
+            raise RuntimeError("Database entry is not open.")
+
         try:
             occurrence_list = self._db_ctx.list_all_occurrences(ids_name)
         except LLInterfaceError:

imas/backends/imas_core/mdsplus_model.py

@@ -366,7 +366,7 @@ def jTraverser_jar() -> Path:
     for component in os.environ.get("CLASSPATH", "").split(":"):
         if component.endswith(".jar"):
             if re.search(".*jTraverser.jar", component):
-                return component
+                return Path(component)
         else:  # assume its a directory (strip any '*' suffix)
             search_dirs.append(component.rstrip("*"))
 

imas/backends/imas_core/uda_support.py

@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Union
+from typing import Union, Optional
 from xml.etree import ElementTree as ET
 
 from imas import dd_zip
@@ -10,7 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-def get_dd_version_from_idsdef_xml(path: Union[str, Path]) -> str:
+def get_dd_version_from_idsdef_xml(path: Union[str, Path]) -> Optional[str]:
     """Parse the IDSDef.xml up to the point where the Data Dictionary version is set.
 
     Returns:

imas/backends/netcdf/db_entry_nc.py

@@ -100,7 +100,7 @@ def get(
         destination: IDSToplevel,
         lazy: bool,
         nbc_map: Optional[NBCPathMap],
-    ) -> None:
+    ) -> IDSToplevel:
         # Feature compatibility checks
         if parameters is not None:
             if isinstance(parameters, GetSliceParameters):

imas/backends/netcdf/nc_metadata.py

@@ -1,7 +1,6 @@
 # This file is part of IMAS-Python.
 # You should have received the IMAS-Python LICENSE file with this project.
-"""NetCDF metadata for dimensions and tensorization of IDSs.
-"""
+"""NetCDF metadata for dimensions and tensorization of IDSs."""
 
 from functools import lru_cache
 from typing import Dict, List, Optional, Set, Tuple
@@ -89,7 +88,7 @@ def __init__(self, ids_metadata: IDSMetadata) -> None:
         # Add cache for public API
         self.get_dimensions = lru_cache(maxsize=None)(self.get_dimensions)
 
-    def get_coordinates(self, path: str, homogeneous_time: bool) -> Tuple[str]:
+    def get_coordinates(self, path: str, homogeneous_time: bool) -> Tuple[str, ...]:
         """Get the coordinates (adhering to CF conventions) for a netCDF variable.
 
         Args:
@@ -109,7 +108,7 @@ def get_coordinates(self, path: str, homogeneous_time: bool) -> Tuple[str]:
             for coord in self.coordinates[path]
         )
 
-    def get_dimensions(self, path: str, homogeneous_time: bool) -> Tuple[str]:
+    def get_dimensions(self, path: str, homogeneous_time: bool) -> Tuple[str, ...]:
         """Get the dimensions for a netCDF variable.
 
         Args:

imas/ids_base.py

@@ -1,7 +1,6 @@
 # This file is part of IMAS-Python.
 # You should have received the IMAS-Python LICENSE file with this project.
-"""Base class for all IDS nodes.
-"""
+"""Base class for all IDS nodes."""
 
 import logging
 from typing import TYPE_CHECKING, Optional, Type
@@ -12,6 +11,7 @@
 
 if TYPE_CHECKING:
     from imas.ids_toplevel import IDSToplevel
+    from imas.ids_primitive import IDSInt0D
 
 logger = logging.getLogger(__name__)
 
@@ -35,7 +35,7 @@ class IDSBase:
     """True iff this IDS lazy-loads its data"""
 
     @property
-    def _time_mode(self) -> int:
+    def _time_mode(self) -> "IDSInt0D":
         """Retrieve the time mode from `/ids_properties/homogeneous_time`"""
         return self._parent._time_mode
 

imas/ids_convert.py

@@ -7,7 +7,7 @@
 import logging
 from functools import lru_cache, partial
 from pathlib import Path
-from typing import Callable, Dict, Iterator, List, Optional, Set, Tuple
+from typing import Callable, Dict, Iterator, List, Optional, Set, Tuple, Any
 from xml.etree.ElementTree import Element, ElementTree
 
 import numpy
@@ -70,7 +70,7 @@ def __init__(self) -> None:
         self.ctxpath: Dict[str, str] = {}
         """Map providing the lowlevel context path for renamed elements."""
 
-        self.type_change: Dict[str, Optional[Callable[[IDSBase, IDSBase], None]]] = {}
+        self.type_change: Dict[str, Optional[Callable[[IDSBase, IDSBase], Any]]] = {}
         """Dictionary of paths that had a type change.
 
         Type changes are mapped to None in :py:attr:`path`, this ``dict`` allows to
@@ -1001,9 +1001,7 @@ def _repeat_first_point(node: IDSBase) -> None:
         child.value = numpy.concatenate((child.value, [child.value[0]]))
 
 
-def _remove_last_point_conditional(
-    source_node: IDSStructure, target_node: IDSStructure
-) -> None:
+def _remove_last_point_conditional(source_node: IDSBase, target_node: IDSBase) -> None:
     """Type change method for nbc_description=repeat_children_first_point_conditional*.
 
     This method handles converting from new (DDv4) to old (DDv3).

imas/ids_metadata.py

@@ -1,7 +1,7 @@
 # This file is part of IMAS-Python.
 # You should have received the IMAS-Python LICENSE file with this project.
-"""Core of the IMAS-Python interpreted IDS metadata
-"""
+"""Core of the IMAS-Python interpreted IDS metadata"""
+
 import re
 import types
 from enum import Enum
@@ -77,7 +77,7 @@ def get_toplevel_metadata(structure_xml: Element) -> "IDSMetadata":
         IDSMetadata.__setattr__ = orig_setattr
 
 
-_type_map: Dict[Tuple[IDSDataType, int], Type] = {}
+_type_map: Dict[Tuple[Optional[IDSDataType], int], Type] = {}
 """Map of IDSDataType and ndim to IDSBase implementation class."""
 
 
@@ -205,11 +205,11 @@ def __init__(
         if self._parent is not None:
             self._is_dynamic = self.type.is_dynamic or self._parent._is_dynamic
 
-        self.coordinates: "tuple[IDSCoordinate]"
+        self.coordinates: "tuple[IDSCoordinate, ...]"
         """Tuple of coordinates of this node.
 
         ``coordinates[0]`` is the coordinate of the first dimension, etc."""
-        self.coordinates_same_as: "tuple[IDSCoordinate]"
+        self.coordinates_same_as: "tuple[IDSCoordinate, ...]"
         """Indicates quantities which share the same coordinate in a given dimension,
         but the coordinate is not explicitly stored in the IDS."""
         if self.ndim == 0:
@@ -231,7 +231,7 @@ def __init__(
             self.coordinates_same_as = tuple(coors_same_as)
 
         # Parse alternative coordinates
-        self.alternative_coordinates: "tuple[IDSPath]" = ()
+        self.alternative_coordinates: "tuple[IDSPath, ...]" = ()
         """Quantities that can be used as coordinate instead of this node."""
         if "alternative_coordinate1" in attrib:
             self.alternative_coordinates = tuple(

imas/ids_toplevel.py

@@ -25,6 +25,7 @@
 )
 from imas.ids_metadata import IDSMetadata, IDSType, get_toplevel_metadata
 from imas.ids_structure import IDSStructure
+from imas.ids_primitive import IDSInt0D
 
 if TYPE_CHECKING:
     from imas.db_entry import DBEntry
@@ -61,6 +62,7 @@ class IDSToplevel(IDSStructure):
 
     __doc__ = IDSDoc(__doc__)
     _path = ""  # Path to ourselves without the IDS name and slashes
+    _parent: "IDSFactory"  # In contrast to IDSBase, our parent is the IDSFactory
 
     def __init__(self, parent: "IDSFactory", structure_xml, lazy=False):
         """Save backend_version and backend_xml and build translation layer.
@@ -89,7 +91,7 @@ def _dd_version(self) -> str:
         return self._version
 
     @property
-    def _time_mode(self) -> int:
+    def _time_mode(self) -> IDSInt0D:
         """Retrieve the time mode from `/ids_properties/homogeneous_time`"""
         return self.ids_properties.homogeneous_time