imas-python 1.1.2.dev55__tar.gz → 1.1.2.dev57__tar.gz

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/CONTRIBUTING.md

@@ -1,23 +1,23 @@
 # Contributing guidelines
 
-We welcome any kind of contribution to `imas-python`, 
+We welcome any kind of contribution to `IMAS-Python`, 
 from a simple comment, a question or even a full fledged pull 
 request. 
 Please first make sure you read and follow the 
 [Code of Conduct](CODE_OF_CONDUCT.md).
 
 ## You think you found a bug in the code, or have a question in its use
-1. use the [issue search](https://github.com/iterorganization/imas-python/issues)
+1. use the [issue search](https://github.com/iterorganization/IMAS-Python/issues)
 to check if someone already created a similar issue;
 3. if not, make a **new issue** to describe your problem or question. 
 In the case of a bug suspiscion, please try to give all the relevant 
 information to allow reproducing the error or identifying 
-its root cause (version of the imas-python, OS and relevant 
+its root cause (version of the IMAS-Python, OS and relevant 
 dependencies, snippet of code);
 4. apply relevant labels to the issue.
 
 ## You want to make or ask some change to the code
-1. use the [issue search](https://github.com/iterorganization/imas-python/issues)
+1. use the [issue search](https://github.com/iterorganization/IMAS-Python/issues)
 to check if someone already proposed a similar idea/change;
 3. if not, create a **new issue** to describe what change you would like to see 
 implemented and specify it if you intend to work on it yourself or if some help 

{imas_python-1.1.2.dev55/imas_python.egg-info → imas_python-1.1.2.dev57}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: imas-python
-Version: 1.1.2.dev55
+Version: 1.1.2.dev57
 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
@@ -236,10 +236,10 @@ Requires-Dist: virtualenv; extra == "test"
 Requires-Dist: pint; extra == "test"
 Requires-Dist: xarray; extra == "test"
 
-# imas-python
+# IMAS-Python
 
-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 
+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 
 Data Structures (IDSs) as defined by the Integrated Modelling & Analysis Suite (IMAS) 
 Data Model.
 
@@ -249,7 +249,7 @@ 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 [readthedocs](https://imas-python.readthedocs.io/en/latest/)
+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:
 
@@ -278,7 +278,7 @@ 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 2020-2025 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).

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/README.md

@@ -1,7 +1,7 @@
-# imas-python
+# IMAS-Python
 
-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 
+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 
 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 [readthedocs](https://imas-python.readthedocs.io/en/latest/)
+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 2020-2025 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).

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/asv.conf.json

@@ -7,7 +7,7 @@
     "project": "imas",
 
     // The project's homepage
-    "project_url": "https://github.com/iterorganization/imas-python",
+    "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://github.com/iterorganization/imas-python/commits/main/",
+    "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`.

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/benchmarks/core_profiles.py

@@ -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 imas-python or AL HLI)
+        core_profiles: core_profiles IDS (either from IMAS-Python or AL Python)
         times: time values to fill a slice for
     """
     core_profiles.ids_properties.homogeneous_time = 1  # HOMOGENEOUS
-    core_profiles.ids_properties.comment = "Generated for the imas-python 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 = "imas-python ASV benchmark"
+    core_profiles.code.name = "IMAS-Python ASV benchmark"
     core_profiles.code.version = imas.__version__
     core_profiles.code.repository = (
-        "https://github.com/iterorganization/imas-python"
+        "https://github.com/iterorganization/IMAS-Python"
     )
 
     core_profiles.time = np.array(times)

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/benchmarks/edge_profiles.py

@@ -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 imas-python or AL HLI)
+        edge_profiles: edge_profiles IDS object (either from IMAS-Python or AL Python)
         times: time values to fill
     """
     edge_profiles.ids_properties.homogeneous_time = (
         imas.ids_defs.IDS_TIME_MODE_HETEROGENEOUS
     )
-    edge_profiles.ids_properties.comment = "Generated for imas-python 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 = "imas-python ASV benchmark"
+    edge_profiles.code.name = "IMAS-Python ASV benchmark"
     edge_profiles.code.version = imas.__version__
     edge_profiles.code.repository = (
-        "https://github.com/iterorganization/imas-python"
+        "https://github.com/iterorganization/IMAS-Python"
     )
 
     # This GGD grid is not a valid description, but it's a good stress test for the

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/benchmarks/technical.py

@@ -19,9 +19,10 @@ def timeraw_import_imas():
 # `asv compare` :(
 """
 def track_imas_versions():
-    equilibrium = imas.equilibrium()
-    equilibrium.ids_properties.homogeneous_time = imas.imasdef.IDS_TIME_MODE_INDEPENDENT
-    dbentry = imas.DBEntry(imas.imasdef.MEMORY_BACKEND, "test", 1, 1)
+    ids_factory = imas.IDSFactory()
+    equilibrium = ids_factory.equilibrium()
+    equilibrium.ids_properties.homogeneous_time = imas.ids_defs.IDS_TIME_MODE_INDEPENDENT
+    dbentry = imas.DBEntry(imas.ids_defs.MEMORY_BACKEND, "test", 1, 1)
     dbentry.create()
     dbentry.put(equilibrium)
     equilibrium = dbentry.get("equilibrium")

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/benchmarks/utils.py

@@ -76,7 +76,7 @@ def create_dbentry(hli, backend):
                 )
             except (AttributeError, AssertionError):
                 raise NotImplementedError(
-                    "This version of imas-python doesn't implement netCDF."
+                    "This version of IMAS-Python doesn't implement netCDF."
                 ) from None
 
     path = Path.cwd() / f"DB-{hli}-{backend}"

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/ci/build_docs_and_dist.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Bamboo CI script to install imas and run all tests
+# Bamboo CI script to install imas Python module 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 imas and documentation dependencies from the just-built wheel
+# Install imas Python module and documentation dependencies from the just-built wheel
 pip install "`readlink -f dist/*.whl`[docs,netcdf]"
 
 # Debugging:

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/ci/run_benchmark.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Bamboo CI script to install imas and run all tests
+# Bamboo CI script to install imas Python module and run all tests
 # Note: this script should be run from the root of the git repository
 
 # Debuggging:
@@ -59,7 +59,7 @@ 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 ]
@@ -75,5 +75,5 @@ asv publish
 # And persistently store them
 cp -rf .asv/{results,html} "$BENCHMARKS_DIR"
 
-deactivate
+
 

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/ci/run_pytest.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Bamboo CI script to install imas and run all tests
+# Bamboo CI script to install imas Python module and run all tests
 # Note: this script should be run from the root of the git repository
 
 # Debuggging:
@@ -37,8 +37,10 @@ pip freeze
 # Clean artifacts created by pytest
 rm -f junit.xml
 rm -rf htmlcov
-mkdir -p ~/tmp
-export PYTEST_DEBUG_TEMPROOT=~/tmp
-python -m pytest -n=auto --cov=imas --cov-report=term-missing --cov-report=html --junit-xml=junit.xml -x
 
-deactivate
+# setups local directory to not to full /tmp directory with pytest temporary files
+# mkdir -p ~/tmp
+# export PYTEST_DEBUG_TEMPROOT=~/tmp
+python -m pytest -n=auto --cov=imas --cov-report=term-missing --cov-report=html --junit-xml=junit.xml
+
+

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/conftest.py

@@ -1,5 +1,5 @@
-# This file is part of imas-python.
-# You should have received the imas-python LICENSE file with this project.
+# This file is part of IMAS-Python.
+# You should have received the IMAS-Python LICENSE file with this project.
 #
 # Set up pytest:
 # - Backend parametrization (and corresponding command line options)

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/docs/source/api.rst

@@ -3,11 +3,11 @@
 API reference
 =============
 
-This page provides an auto-generated summary of imas-python's API. For more details
+This page provides an auto-generated summary of IMAS-Python's API. For more details
 and examples, refer to the relevant chapters in the main part of the
 documentation.
 
-imas-python IDS manipulation
+IMAS-Python IDS manipulation
 ----------------------------
 
 .. currentmodule:: imas

{imas_python-1.1.2.dev55 → imas_python-1.1.2.dev57}/docs/source/benchmarking.rst

@@ -1,16 +1,16 @@
-.. _`benchmarking IMAS`:
+.. _`benchmarking IMAS-Python`:
 
-Benchmarking imas-python
+Benchmarking IMAS-Python
 ========================
 
-imas-python integrates with the `airspeed velocity
+IMAS-Python integrates with the `airspeed velocity
 <https://asv.readthedocs.io/en/stable/index.html>`_ ``asv`` package for benchmarking.
 
 
-imas-python benchmarks
+IMAS-Python benchmarks
 ----------------------
 
-imas-python benchmarks are stored in the ``benchmarks`` folder in the git repository. We can
+IMAS-Python benchmarks are stored in the ``benchmarks`` folder in the git repository. We can
 currently distinguish three types of benchmarks:
 
 Technical benchmarks
@@ -19,15 +19,14 @@ Technical benchmarks
     package.
 
 Basic functional benchmarks
-    These are for benchmarking functionality with an equivalent feature in the IMAS
-    Access Layer HLI. In addition to tracking the performance of the imas-python features
-    over time, we can also benchmark the performance against the traditional HLI.
+    These are for benchmarking functionality with an addition to track the performance 
+    of the IMAS-Python features over time.
 
     For example: putting and getting IDSs.
 
-imas-python-specific functional benchmarks
-    These are for benchmarking functionality without an equivalent feature in the IMAS
-    Access Layer HLI. We use these for tracking the imas-python performance over time.
+IMAS-Python-specific functional benchmarks
+    These are for benchmarking core functionalities for checking performance. We use these 
+    for tracking the IMAS-Python core features performance over time.
 
     For example: data conversion between DD versions.
 
@@ -35,7 +34,7 @@ imas-python-specific functional benchmarks
 Running benchmarks (quick)
 --------------------------
 
-When you have an existing imas-python installation, you can run the benchmarks like this:
+When you have an existing IMAS-Python installation, you can run the benchmarks like this:
 
 .. code-block:: console
 
@@ -62,33 +61,31 @@ contains tabular results. Some examples:
 .. code-block:: text
     :caption: Example output for a test parametrized in ``hli``
 
-    [ 58.33%] ··· core_profiles.Generate.time_create_core_profiles          ok
-    [ 58.33%] ··· ======== ============
-                    hli                
-                  -------- ------------
-                    imas    22.9±0.4μs 
-                   imas    408±8μs   
-                  ======== ============
+    [56.25%] ··· core_profiles.Generate.time_create_core_profiles                                                                                  ok
+    [56.25%] ··· ====== =============
+                hli                
+                ------ -------------
+                imas   2.04±0.01μs 
+                ====== =============
 
-Here we see the benchmark ``core_profiles.Generate.time_create_core_profiles`` was
-repeated for multiple values of ``hli``: once for the ``imas`` HLI, and once for the
-``imas`` HLI.
+
+Here we see the benchmark ``core_profiles.Generate.time_create_core_profiles`` for 
+imas-python ``imas-python``.
 
 Some benchmarks are parametrized in multiple dimensions, as in below example. This
 results in a 2D table of results.
 
 .. code-block:: text
-    :caption: Example output for a test parametrized in ``hli`` and ``backend``
-
-    [ 70.83%] ··· core_profiles.Get.time_get                                ok
-    [ 70.83%] ··· ======== ========== ============ =========
-                  --                    backend             
-                  -------- ---------------------------------
-                    hli        13          14          11   
-                  ======== ========== ============ =========
-                    imas    75.1±1ms   70.2±0.5ms   207±2ms 
-                   imas   241±4ms     229±2ms     364±6ms 
-                  ======== ========== ============ =========
+    :caption: Example output for a test parametrized in ``imas-python`` and ``backend``
+
+    [65.62%] ··· core_profiles.Get.time_get     ok
+    [65.62%] ··· ====== ========= ========== ============ ========= ============
+                --                             backend                         
+                ------ --------------------------------------------------------
+                hli      HDF5    MDSplus      memory      ASCII      netCDF   
+                ====== ========= ========== ============ ========= ============
+                imas   172±3ms   86.7±2ms   68.5±0.8ms   291±3ms   14.2±0.7ms 
+                ====== ========= ========== ============ ========= ============
 
 .. note::
     The backends are listed by their numerical IDS:
@@ -103,8 +100,8 @@ Running benchmarks (advanced)
 -----------------------------
 
 Running benchmarks quickly, as explained in the previous section, is great during
-development and for comparing the performance of imas-python against the imas HLI. However,
-``asv`` can also track the performance of benchmarks over various commits of imas-python.
+development and for comparing the performance of IMAS-Python. However,
+``asv`` can also track the performance of benchmarks over various commits of IMAS-Python.
 Unfortunately this is a bit more tricky to set up.
 
 
@@ -112,23 +109,8 @@ Setup advanced benchmarking
 '''''''''''''''''''''''''''
 
 First, some background on how ``asv`` tracks performance: it creates an isolated virtual
-environment (using the ``virtualenv`` package) and installs imas-python for each commit that
-will be benchmarked. However, because the virtual environment is isolated, the ``imas``
-package won't be available. We need to work around it by setting the environment
-variable ``ASV_PYTHONPATH``:
-
-.. code-block:: console
-    :caption: Setting up the ``ASV_PYTHONPATH`` on SDCC
-
-    $ module load IMAS
-    $ export ASV_PYTHONPATH="$PYTHONPATH"
-
-.. caution::
-
-    ``imas`` must not be available on the ``ASV_PYTHONPATH`` to avoid the interfering
-    of two imas modules (one on the ``PYTHONPATH``, and the other installed by ``asv``
-    in the virtual environment).
-
+environment (using the ``virtualenv`` package) and installs IMAS-Python for each commit that
+will be benchmarked. 
 
 Deciding which commits to benchmark
 '''''''''''''''''''''''''''''''''''
@@ -171,7 +153,7 @@ Instead, you can submit a benchmark job to the compute nodes.
     #!/bin/bash
 
     # Set SLURM options:
-    #SBATCH --job-name=imas-python-benchmark
+    #SBATCH --job-name=IMAS-Python-benchmark
     #SBATCH --time=1:00:00
     #SBATCH --partition=gen10_ib
     # Note: for proper benchmarking we need to exclusively reserve a node, even though
@@ -184,19 +166,14 @@ Instead, you can submit a benchmark job to the compute nodes.
 .. code-block:: bash
     :caption: Benchmark run script (``run_benchmarks.sh``)
 
-    # Load IMAS module
+    # Load IMAS-AL-Core module
     module purge
-    module load IMAS
-    # Verify we can run python and import imas
+    module load IMAS-AL-Core
+    module load Python
+
+    # Verify we can run python
     echo "Python version:"
     python --version
-    echo "Import imas:"
-    python -c 'import imas; print(imas)'
-
-    # Set the ASV_PYTHONPATH so we can `import imas` in the benchmarks
-    export ASV_PYTHONPATH="$PYTHONPATH"
-    echo "ASV_PYTHONPATH=$ASV_PYTHONPATH"
-    echo
 
     # Activate the virtual environment which has asv installed
     . venv_imas/bin/activate