Release/2.0.0

.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 +1,34 @@
+name: linting-and-code-formatting
+
+on: 
+  push:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout IMAS-Python sources
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          # until saxonche is available in 3.13
+          # https://saxonica.plan.io/issues/6561
+          python-version: "<3.13"
+
+      - 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 +1,74 @@
+name: build-wheel-and-publish-test-pypi
+
+on:
+  push:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        # until saxonche is available in 3.13
+        # https://saxonica.plan.io/issues/6561
+        python-version: "<3.13"
+    - 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
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-22.04
+    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
+    if: github.ref=='refs/heads/develop'  # only publish to TestPyPI on develop pushes
+    needs:
+    - build
+    runs-on: ubuntu-22.04
+    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

.github/workflows/test_with_pytest.yml

@@ -0,0 +1,51 @@
+name: Test using pytest
+
+on: 
+    push:
+    pull_request:
+      types: [opened, synchronize, reopened]
+
+jobs:
+  test:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]  # Test on multiple Python versions
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+
+        uses: actions/setup-python@v4
+        with:
+          # until saxonche is available in 3.13
+          # https://saxonica.plan.io/issues/6561
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install dependencies
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+          pip install --upgrade pip setuptools wheel
+          pip install .[test]
+
+      - name: Run tests
+        run: |
+          source venv/bin/activate
+          python -m pytest -n=auto --cov=imas --cov-report=term-missing --cov-report=xml:coverage.xml --cov-report=html:htmlcov --junit-xml=junit.xml
+
+      - name: Upload coverage report ${{ matrix.python-version }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report-${{ matrix.python-version }}
+          path: htmlcov
+
+      - name: Upload test report ${{ matrix.python-version }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-report-${{ matrix.python-version }}
+          path: junit.xml

.github/workflows/verify_sphinx_doc.yml

@@ -0,0 +1,53 @@
+name: verify-sphinx-doc-generation
+
+on:
+  push:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout IMAS-Python sources
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          with:
+          # until saxonche is available in 3.13
+          # https://saxonica.plan.io/issues/6561
+          python-version: "<3.13"
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+
+      - name: Set up Python virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install build dependencies
+        run: |
+          pip install --upgrade pip setuptools wheel build
+
+      - name: Build package
+        run: |
+          rm -rf dist
+          python -m build .
+
+      - name: Install package and dependencies
+        run: |
+          pip install "$(readlink -f dist/*.whl)[docs,netcdf]"
+
+      - name: Debug dependencies
+        run: |
+          pip freeze
+
+      - name: Build Sphinx documentation
+        run: |
+          export SPHINXOPTS='-W -n --keep-going'
+          make -C docs clean html

.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

CONTRIBUTING.md

@@ -1,36 +1,36 @@
 # 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. 
+2. 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.
+3. 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 
+2. 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 
 will be needed;
-4. wait until some kind of consensus is reached about your idea being relevant, 
+3. wait until some kind of consensus is reached about your idea being relevant, 
 at which time the issue will be assigned (to you or someone else who can work on 
 this topic);
-5. if you do the development yourself, fork the repository to your own Github 
+4. if you do the development yourself, fork the repository to your own Github 
 profile and create your own feature branch off of the latest develop commit. 
 Make sure to regularly sync your branch with the latest commits from `develop` 
 (find instructions 
 [here](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork));
-6. when your development is ready, create a pull request (find instructions 
+5. when your development is ready, create a pull request (find instructions 
 [here](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork)).
 
 

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

@@ -1,8 +1,8 @@
 # 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 
-Data Structures (IDSs) as defined by the Integrated Modelling & Analysis Suite (IMAS) 
+IMAS-Python (formerly known as IMASPy its for versions < 2) 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 [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:
 
@@ -28,19 +28,25 @@ factory = imas.IDSFactory()
 equilibrium = factory.equilibrium()
 print(equilibrium)
 
-equilibrium.ids_properties.homogeneous_time = imas.ids_defs.IDS_TIME_MODE_HETEROGENEOUS
+equilibrium.ids_properties.homogeneous_time = imas.ids_defs.IDS_TIME_MODE_HOMOGENEOUS
 equilibrium.ids_properties.comment = "testing"
+equilibrium.time = [0.01]
 
-with imas.DBEntry("imas:hdf5?path=./testdb","w") as dbentry:
+with imas.DBEntry("imas:hdf5?path=./testdb", "w") as dbentry:
     dbentry.put(equilibrium)
+
+# or without imas_core dependency
+with imas.DBEntry("./test.nc", "w") as dbentry:
+    dbentry.put(equilibrium)
+
 ```
 
 A quick 5 minutes introduction is available in the documentation generated from `/docs/sources/intro.rst`.
 
 
 ## 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).