Rename imaspy to imas

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -1 +1 @@
-imaspy/_version.py export-subst
+.git_archival.txt export-subst

.github/workflows/linting.yml

@@ -0,0 +1,31 @@
+name: imas-python
+
+on: push
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout imas-python sources
+        uses: actions/checkout@v4
+        with:
+          ref: rename-imaspy-to-imas
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install the code linting and formatting tools
+        run: pip install --upgrade 'black >=24,<25' flake8
+
+      - name: Check formatting of code with black
+        run: black --check imas
+
+      - name: Check linting with flake8
+        run: flake8 imas

.github/workflows/publish.yml

@@ -0,0 +1,67 @@
+name: build-wheel-and-publish-test-pypi
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m pip install pip setuptools wheel build
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build .
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish imas-python distribution to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/imas-python
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish imas-python distribution to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/imas-python
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@unstable/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true

.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

.readthedocs.yml

@@ -0,0 +1,23 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow || true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - netcdf
+        - h5py
+
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: false

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
 """