renamed imaspy to imas

Author: prasad-sawantdesai

.gitignore

@@ -91,21 +91,16 @@ ENV/
 *.swo
 
 # SCM setuptools
-imaspy/version.py
-
-# Saxon symlink or downloaded file
-saxon*.jar
+imas/_version.py
 
 # IMAS DD
 data-dictionary
-access-layer
-containers/arch/imaspy/
+containers/arch/imas/
 containers/arch/data-dictionary/
-containers/arch/access-layer/
-imaspy/assets/IDSDef.zip
+imas/assets/IDSDef.zip
 
 # IDS files
-*.ids
+# *.ids
 
 # ASV folder
 /.asv

MANIFEST.in

@@ -1,6 +1,6 @@
-include imaspy/assets/IDSDef.zip
-include imaspy/assets/IDSDef2MDSpreTree.xsl
-include imaspy/assets/ITER_134173_106_equilibrium.ids
-include imaspy/assets/ITER_134173_106_core_profiles.ids
-include imaspy/assets/equilibrium.ids
-include imaspy/assets/core_profiles.ids
+include imas/assets/IDSDef.zip
+include imas/assets/IDSDef2MDSpreTree.xsl
+include imas/assets/ITER_134173_106_equilibrium.ids
+include imas/assets/ITER_134173_106_core_profiles.ids
+include imas/assets/equilibrium.ids
+include imas/assets/core_profiles.ids

README.md

@@ -1,7 +1,7 @@
-# IMAS-Python
+# imas-python
 
-IMAS-Python is a pure-python library to handle arbitrarily nested data structures.
-It is designed for, but not necessarily bound to, interacting with Interface 
+imas-python is a pure-python library to handle arbitrarily nested data structures.
+imas-python is designed for, but not necessarily bound to, interacting with Interface 
 Data Structures (IDSs) as defined by the Integrated Modelling & Analysis Suite (IMAS) 
 Data Model.
 
@@ -11,7 +11,7 @@ Data Model.
 Install steps are described in the documentation generated from `/docs/source/installing.rst`.
 
 Documentation is autogenerated from the source using [Sphinx](http://sphinx-doc.org/)
-and can be found at the [ITER sharepoint](https://sharepoint.iter.org/departments/POP/CM/IMDesign/Code%20Documentation/IMAS-doc/index.html)
+and can be found at the [readthedocs](https://imas-python.readthedocs.io/en/latest/)
 
 The documentation can be manually generated by installing sphinx and running:
 
@@ -40,7 +40,7 @@ A quick 5 minutes introduction is available in the documentation generated from
 
 ## Legal
 
-IMAS-Python is Copyright 2020-2024 ITER Organization, Copyright 2020-2023 Karel Lucas van de 
+imas-python is Copyright 2020-2024 ITER Organization, Copyright 2020-2023 Karel Lucas van de 
 Plassche <karelvandeplassche@gmail.com>, Copyright 2020-2022 Daan van Vugt <dvanvugt@ignitioncomputing.com>,
 and Copyright 2020 Dutch Institute for Fundamental Energy Research <info@differ.nl>.
 It is licensed under [LGPL 3.0](LICENSE.txt).

asv.conf.json

@@ -4,10 +4,10 @@
     "version": 1,
 
     // The name of the project being benchmarked
-    "project": "imaspy",
+    "project": "imas",
 
     // The project's homepage
-    "project_url": "https://git.iter.org/projects/IMAS/repos/imaspy/browse",
+    "project_url": "https://github.com/iterorganization/imas-python",
 
     // The URL or local path of the source code repository for the
     // project being benchmarked
@@ -53,7 +53,7 @@
     //"install_timeout": 600,
 
     // the base URL to show a commit for the project.
-    "show_commit_url": "https://git.iter.org/projects/IMAS/repos/imaspy/commits/",
+    "show_commit_url": "https://github.com/iterorganization/imas-python/commits/main/",
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.

benchmarks/core_profiles.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import imaspy
+import imas
 
 from .utils import (
     available_backends,
@@ -22,16 +22,16 @@ def fill_slices(core_profiles, times):
     """Fill a time slice of a core_profiles IDS with generated data.
 
     Args:
-        core_profiles: core_profiles IDS (either from IMASPy or AL HLI)
+        core_profiles: core_profiles IDS (either from imas-python or AL HLI)
         times: time values to fill a slice for
     """
     core_profiles.ids_properties.homogeneous_time = 1  # HOMOGENEOUS
-    core_profiles.ids_properties.comment = "Generated for the IMASPy benchmark suite"
+    core_profiles.ids_properties.comment = "Generated for the imas-python benchmark suite"
     core_profiles.ids_properties.creation_date = datetime.date.today().isoformat()
-    core_profiles.code.name = "IMASPy ASV benchmark"
-    core_profiles.code.version = imaspy.__version__
+    core_profiles.code.name = "imas-python ASV benchmark"
+    core_profiles.code.version = imas.__version__
     core_profiles.code.repository = (
-        "https://git.iter.org/projects/IMAS/repos/imaspy/browse"
+        "https://github.com/iterorganization/imas-python"
     )
 
     core_profiles.time = np.array(times)
@@ -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
 
@@ -74,7 +81,7 @@ def setup(self, hli, backend):
 
     def time_get_slice(self, hli, backend):
         for t in TIME:
-            self.dbentry.get_slice("core_profiles", t, imaspy.ids_defs.CLOSEST_INTERP)
+            self.dbentry.get_slice("core_profiles", t, imas.ids_defs.CLOSEST_INTERP)
 
     def teardown(self, hli, backend):
         if hasattr(self, "dbentry"):  # imas + netCDF has no dbentry
@@ -96,8 +103,8 @@ class LazyGet:
     param_names = ["lazy", "backend"]
 
     def setup(self, lazy, backend):
-        self.dbentry = create_dbentry("imaspy", backend)
-        core_profiles = factory["imaspy"].core_profiles()
+        self.dbentry = create_dbentry("imas", backend)
+        core_profiles = factory["imas"].core_profiles()
         fill_slices(core_profiles, TIME)
         self.dbentry.put(core_profiles)
 

benchmarks/edge_profiles.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import imaspy
+import imas
 
 from .utils import available_backends, create_dbentry, factory, hlis
 
@@ -17,18 +17,18 @@ def fill_ggd(edge_profiles, times):
     """Fill nested arrays of structures in grids_ggd and ggd substructures.
 
     Args:
-        edge_profiles: edge_profiles IDS object (either from IMASPy or AL HLI)
+        edge_profiles: edge_profiles IDS object (either from imas-python or AL HLI)
         times: time values to fill
     """
     edge_profiles.ids_properties.homogeneous_time = (
-        imaspy.ids_defs.IDS_TIME_MODE_HETEROGENEOUS
+        imas.ids_defs.IDS_TIME_MODE_HETEROGENEOUS
     )
-    edge_profiles.ids_properties.comment = "Generated for IMASPy benchmark suite"
+    edge_profiles.ids_properties.comment = "Generated for imas-python benchmark suite"
     edge_profiles.ids_properties.creation_date = datetime.date.today().isoformat()
-    edge_profiles.code.name = "IMASPy ASV benchmark"
-    edge_profiles.code.version = imaspy.__version__
+    edge_profiles.code.name = "imas-python ASV benchmark"
+    edge_profiles.code.version = imas.__version__
     edge_profiles.code.repository = (
-        "https://git.iter.org/projects/IMAS/repos/imaspy/browse"
+        "https://github.com/iterorganization/imas-python"
     )
 
     # This GGD grid is not a valid description, but it's a good stress test for the
@@ -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)

benchmarks/technical.py

@@ -1,18 +1,11 @@
-import imaspy
 import imas
 
 
-def timeraw_create_default_imaspy_factory():
+def timeraw_create_default_imas_factory():
     # timeraw to ensure that nothing is cached
     return """
-    import imaspy
-    imaspy.IDSFactory()
-    """
-
-
-def timeraw_import_imaspy():
-    return """
-    import imaspy
+    import imas
+    imas.IDSFactory()
     """
 
 
@@ -38,6 +31,6 @@ def track_imas_versions():
     )
 
 
-def track_imaspy_dd_version():
-    return imaspy.IDSFactory().version
+def track_imas_dd_version():
+    return imas.IDSFactory().version
 """

benchmarks/utils.py

@@ -3,12 +3,8 @@
 import uuid
 from pathlib import Path
 
-import imaspy
-import imaspy.exception
-
-# Don't directly import imas: code analyzers break on the huge code base
-imas = importlib.import_module("imas")
-
+import imas
+import imas.exception
 
 # Backend constants
 HDF5 = "HDF5"
@@ -28,11 +24,11 @@ def backend_exists(backend):
     """Tries to detect if the lowlevel has support for the given backend."""
     uri = create_uri(backend, str(uuid.uuid4()))
     try:
-        entry = imaspy.DBEntry(uri, "r")
+        entry = imas.DBEntry(uri, "r")
     except Exception as exc:
         if "backend is not available" in str(exc):
             return False
-        elif isinstance(exc, (imaspy.exception.ALException, FileNotFoundError)):
+        elif isinstance(exc, (imas.exception.ALException, FileNotFoundError)):
             return True
         return True
     # Highly unlikely, but it could succeed without error
@@ -60,32 +56,27 @@ def backend_exists(backend):
     backend for backend in available_backends if backend not in [ASCII, NETCDF]
 ]
 
-hlis = ["imas", "imaspy"]
+hlis = ["imas"]
 DBEntry = {
     "imas": imas.DBEntry,
-    "imaspy": imaspy.DBEntry,
 }
 factory = {
-    "imas": imas,
-    "imaspy": imaspy.IDSFactory(),
+    "imas": imas.IDSFactory(),
 }
-available_serializers = [imaspy.ids_defs.ASCII_SERIALIZER_PROTOCOL]
+available_serializers = [imas.ids_defs.ASCII_SERIALIZER_PROTOCOL]
 
 
 def create_dbentry(hli, backend):
     if backend == NETCDF:
-        if hli == "imas":
-            # Raising NotImplementedError will skip the benchmarks for this combination
-            raise NotImplementedError("AL-Python HLI doesn't implement netCDF.")
-        if hli == "imaspy":  # check if netcdf backend is available
+        if hli == "imas":  # check if netcdf backend is available
             try:
                 assert (
-                    imaspy.DBEntry._select_implementation("x.nc").__name__
+                    imas.DBEntry._select_implementation("x.nc").__name__
                     == "NCDBEntryImpl"
                 )
             except (AttributeError, AssertionError):
                 raise NotImplementedError(
-                    "This version of IMASPy doesn't implement netCDF."
+                    "This version of imas-python doesn't implement netCDF."
                 ) from None
 
     path = Path.cwd() / f"DB-{hli}-{backend}"

ci/build_dd_zip.sh

@@ -17,4 +17,4 @@ echo "Done loading modules"
 set -x
 
 # Build the DD zip
-python imaspy/dd_helpers.py
+python imas/dd_helpers.py

ci/build_docs_and_dist.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Bamboo CI script to install imaspy and run all tests
+# Bamboo CI script to install imas and run all tests
 # Note: this script should be run from the root of the git repository
 
 # Debuggging:
@@ -27,7 +27,7 @@ pip install --upgrade pip setuptools wheel build
 rm -rf dist
 python -m build .
 
-# Install imaspy and documentation dependencies from the just-built wheel
+# Install imas and documentation dependencies from the just-built wheel
 pip install "`readlink -f dist/*.whl`[docs,netcdf]"
 
 # Debugging: