imas-python 0.1.dev1648__tar.gz → 0.1.dev1651__tar.gz

{imas_python-0.1.dev1648/imas_python.egg-info → imas_python-0.1.dev1651}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: imas-python
-Version: 0.1.dev1648
+Version: 0.1.dev1651
 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-0.1.dev1648 → imas_python-0.1.dev1651}/benchmarks/core_profiles.py

@@ -50,7 +50,14 @@ def fill_slices(core_profiles, times):
         profiles_1d.ion.resize(len(ions))
         profiles_1d.neutral.resize(len(ions))
         for i, ion in enumerate(ions):
-            profiles_1d.ion[i].label = profiles_1d.neutral[i].label = ion
+            if hasattr(profiles_1d.ion[i], 'label'):
+                profiles_1d.ion[i].label = ion
+                profiles_1d.neutral[i].label = ion
+            if hasattr(profiles_1d.ion[i], 'name'):
+                profiles_1d.ion[i].name = ion
+                profiles_1d.neutral[i].name = ion
+            
+            # profiles_1d.ion[i].label = profiles_1d.neutral[i].label = ion
             profiles_1d.ion[i].z_ion = 1.0
             profiles_1d.ion[i].neutral_index = profiles_1d.neutral[i].ion_index = i + 1
 

{imas_python-0.1.dev1648 → imas_python-0.1.dev1651}/benchmarks/edge_profiles.py

@@ -46,7 +46,13 @@ def fill_ggd(edge_profiles, times):
         grid.space[i].identifier.index = 1
         grid.space[i].identifier.description = "Description...."
         grid.space[i].geometry_type.index = 0
-    grid.space[0].coordinates_type = np.array([4, 5], dtype=np.int32)
+    grid.space[0].coordinates_type.resize(1)
+    if imas.__version__ >= "4.0.0":
+        grid.space[0].coordinates_type = np.array([4, 5], dtype=np.int32)
+    else:
+        grid.space[0].coordinates_type[0].name = "coordinates type"
+        grid.space[0].coordinates_type[0].index = 0
+        grid.space[0].coordinates_type[0].name = "example coordinates type"
     grid.space[0].objects_per_dimension.resize(3)  # points, lines, surfaces
     points = grid.space[0].objects_per_dimension[0].object
     points.resize(N_POINTS)
@@ -61,7 +67,13 @@ def fill_ggd(edge_profiles, times):
     for i in range(N_SURFACES):
         surfaces[i].nodes = np.random.randint(1, N_LINES + 1, 4, dtype=np.int32)
 
-    grid.space[1].coordinates_type = np.array([6], dtype=np.int32)
+    grid.space[1].coordinates_type.resize(1)
+    if imas.__version__ >= "4.0.0":
+        grid.space[1].coordinates_type = np.array([6], dtype=np.int32)
+    else:
+        grid.space[1].coordinates_type[0].name = "coordinates type"
+        grid.space[1].coordinates_type[0].index = 0
+        grid.space[1].coordinates_type[0].name = "example coordinates type"
     grid.space[1].objects_per_dimension.resize(2)
     obp = grid.space[1].objects_per_dimension[0]
     obp.object.resize(2)

{imas_python-0.1.dev1648 → imas_python-0.1.dev1651}/ci/run_benchmark.sh

@@ -3,14 +3,22 @@
 # Note: this script should be run from the root of the git repository
 
 # Debuggging:
-set -e -o pipefail
+
 echo "Loading modules:" $@
+BENCHMARKS_DIR=$(realpath "$PWD/imas_benchmarks")
+if [[ "$(uname -n)" == *"bamboo"* ]]; then
+    set -e -o pipefail
+    # create 
+    BENCHMARKS_DIR=$(realpath "/mnt/bamboo_deploy/imas/benchmarks/")
+fi
 
 # Set up environment such that module files can be loaded
 source /etc/profile.d/modules.sh
 module purge
 # Modules are supplied as arguments in the CI job:
-module load $@
+# IMAS-AL-Python/5.2.1-intel-2023b-DD-3.41.0 Saxon-HE/12.4-Java-21
+module load IMAS-AL-Core/5.4.3-intel-2023b Saxon-HE/12.4-Java-21
+
 
 # Debuggging:
 echo "Done loading modules"
@@ -32,9 +40,9 @@ pip install virtualenv .[test]
 python -c 'import imas.backends.imas_core.mdsplus_model; print(imas.backends.imas_core.mdsplus_model.mdsplus_model_dir(imas.IDSFactory()))'
 
 # Copy previous results (if any)
-mkdir -p /mnt/bamboo_deploy/imas/benchmarks/results
+mkdir -p "$BENCHMARKS_DIR/results"
 mkdir -p .asv
-cp -rf /mnt/bamboo_deploy/imas/benchmarks/results .asv/
+cp -rf "$BENCHMARKS_DIR/results" .asv/
 
 # Ensure numpy won't do multi-threading
 export OPENBLAS_NUM_THREADS=1
@@ -47,7 +55,7 @@ asv machine --yes
 # Run ASV for the current commit, develop and main
 asv run --skip-existing-successful HEAD^!
 asv run --skip-existing-successful develop^!
-asv run --skip-existing-successful main^!
+# asv run --skip-existing-successful main^!
 
 # Compare results
 if [ `git rev-parse --abbrev-ref HEAD` == develop ]
@@ -61,5 +69,5 @@ fi
 asv publish
 
 # And persistently store them
-cp -rf .asv/{results,html} /mnt/bamboo_deploy/imas/benchmarks/
+cp -rf .asv/{results,html} "$BENCHMARKS_DIR"
 

{imas_python-0.1.dev1648 → imas_python-0.1.dev1651}/imas/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev1648'
-__version_tuple__ = version_tuple = (0, 1, 'dev1648')
+__version__ = version = '0.1.dev1651'
+__version_tuple__ = version_tuple = (0, 1, 'dev1651')

{imas_python-0.1.dev1648 → imas_python-0.1.dev1651}/imas/backends/imas_core/mdsplus_model.py

@@ -13,6 +13,7 @@ import tempfile
 import time
 import uuid
 from pathlib import Path
+from saxonche import PySaxonProcessor
 from subprocess import CalledProcessError, check_output
 from zlib import crc32
 
@@ -22,7 +23,6 @@ except ImportError:  # Python 3.8 support
     from importlib_resources import as_file, files
 
 import imas
-from imas.dd_helpers import get_saxon
 from imas.dd_zip import get_dd_xml, get_dd_xml_crc
 from imas.exception import MDSPlusModelError
 from imas.ids_factory import IDSFactory
@@ -241,35 +241,84 @@ def model_exists(path: Path) -> bool:
     )
 
 
-def create_model_ids_xml(cache_dir_path, fname, version):
-    """Use saxon to compile an ids.xml suitable for creating an mdsplus model."""
+# def create_model_ids_xml(cache_dir_path, fname, version):
+#     """Use saxon to compile an ids.xml suitable for creating an mdsplus model."""
+
+#     try:
+#         # we have to be careful to have the same version of this file as in the access
+#         # layer:
+#         with as_file(files(imas) / "assets" / "IDSDef2MDSpreTree.xsl") as xslfile:
+#             check_output(
+#                 [
+#                     "java",
+#                     "net.sf.saxon.Transform",
+#                     "-s:" + str(fname),
+#                     "-o:" + str(Path(cache_dir_path) / "ids.xml"),
+#                     "DD_GIT_DESCRIBE=" + str(version or fname),
+#                     # if this is expected as git describe it might break
+#                     # if we just pass a filename
+#                     "AL_GIT_DESCRIBE=" + os.environ.get("AL_VERSION", "0.0.0"),
+#                     "-xsl:" + str(xslfile),
+#                 ],
+#                 input=get_dd_xml(version) if version else None,
+#                 env={"CLASSPATH": get_saxon(), "PATH": os.environ.get("PATH", "")},
+#             )
+#     except CalledProcessError as e:
+#         if fname:
+#             logger.error("Error making MDSPlus model IDS.xml for %s", fname)
+#         else:
+#             logger.error("Error making MDSplus model IDS.xml for %s", version)
+#         raise e
+
 
+def create_model_ids_xml(cache_dir_path, fname, version):
+    """Use Saxon/C to compile an ids.xml suitable for creating an MDSplus model."""
     try:
-        # we have to be careful to have the same version of this file as in the access
-        # layer:
-        with as_file(files(imas) / "assets" / "IDSDef2MDSpreTree.xsl") as xslfile:
-            check_output(
-                [
-                    "java",
-                    "net.sf.saxon.Transform",
-                    "-s:" + str(fname),
-                    "-o:" + str(Path(cache_dir_path) / "ids.xml"),
-                    "DD_GIT_DESCRIBE=" + str(version or fname),
-                    # if this is expected as git describe it might break
-                    # if we just pass a filename
-                    "AL_GIT_DESCRIBE=" + os.environ.get("AL_VERSION", "0.0.0"),
-                    "-xsl:" + str(xslfile),
-                ],
-                input=get_dd_xml(version) if version else None,
-                env={"CLASSPATH": get_saxon(), "PATH": os.environ.get("PATH", "")},
-            )
-    except CalledProcessError as e:
+        # Locate the XSL file within the package
+        with as_file(files("imas") / "assets" / "IDSDef2MDSpreTree.xsl") as xslfile:
+            output_file = Path(cache_dir_path) / "ids.xml"
+            
+            # Initialize Saxon/C processor
+            with PySaxonProcessor(license=False) as proc:
+                xslt_processor = proc.new_xslt30_processor()
+
+                # Set the XSLT stylesheet
+                xslt_processor.compile_stylesheet(stylesheet_file=str(xslfile))
+
+                # Prepare the input XML source
+                input_xml = get_dd_xml(version) if version else None
+                if fname:
+                    source_file = str(fname)
+                elif input_xml:
+                    source_file = "-"  # Use standard input for the XML string
+                else:
+                    raise ValueError("Either 'fname' or 'version' must be provided to generate XML.")
+
+                # xdm_ddgit = proc.make_string_value(str(version or fname))
+                # xsltproc.set_parameter("DD_GIT_DESCRIBE", xdm_ddgit)
+                # xdm_algit = proc.make_string_value(os.environ.get("AL_VERSION", "0.0.0"))
+                # xsltproc.set_parameter("AL_GIT_DESCRIBE", xdm_algit)
+                # Transform XML
+                result = xslt_processor.transform_to_file(
+                    source_file=source_file,
+                    output_file=str(output_file),
+                    initial_template_params={
+                        "DD_GIT_DESCRIBE": str(version or fname),
+                        "AL_GIT_DESCRIBE": os.environ.get("AL_VERSION", "0.0.0"),
+                    },
+                )
+
+                if result is False:
+                    logger.error("Transformation failed: Check Saxon/C logs for details.")
+                    raise RuntimeError("Saxon/C XSLT transformation failed.")
+
+    except Exception as e:
         if fname:
-            logger.error("Error making MDSPlus model IDS.xml for %s", fname)
+            logger.error("Error making MDSplus model IDS.xml for %s", fname)
         else:
             logger.error("Error making MDSplus model IDS.xml for %s", version)
         raise e
-
+    
 
 def create_mdsplus_model(cache_dir_path: Path) -> None:
     """Use jtraverser to compile a valid MDS model file."""

{imas_python-0.1.dev1648 → imas_python-0.1.dev1651/imas_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: imas-python
-Version: 0.1.dev1648
+Version: 0.1.dev1651
 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