Release/2.5

.github/CODEOWNERS

@@ -0,0 +1,8 @@
+# CODEOWNERS: Controls automatic assignment of reviewers for pull requests.
+# -----------------------------------------------------------------------------
+# When a pull request modifies files matching a pattern, the listed code owners will be requested as reviewers.
+# Each line is a file pattern followed by one or more code owners (users or teams) who must review changes to that file.
+# Do not edit unless specifically mandated to do so.
+
+# Global/fallback and technical modifications.
+*   @SimonPinches @olivhoenen @prasad-sawantdesai 

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  # Enable version updates for Github Actions
+  - package-ecosystem: "github-actions"
+    # Look for `/.github/workflows` and `/action.yml` or `.yaml`
+    directory: "/"
+    # Check for updates once a week
+    schedule:
+      interval: "weekly"
+    # Group actions version bumps into a single PR
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
+

.github/workflows/linting.yml

@@ -15,10 +15,10 @@ jobs:
 
     steps:
       - name: Checkout IDStools sources
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           # until saxonche is available in 3.13
           # https://saxonica.plan.io/issues/6561

.github/workflows/publish.yml

@@ -10,11 +10,11 @@ jobs:
     name: Build distribution
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         # until saxonche is available in 3.13
         # https://saxonica.plan.io/issues/6561
@@ -25,7 +25,7 @@ jobs:
     - name: Build a binary wheel and a source tarball
       run: python3 -m build .
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v7
       with:
         name: python-package-distributions
         path: dist/
@@ -43,7 +43,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v8
       with:
         name: python-package-distributions
         path: dist/
@@ -63,7 +63,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v8
       with:
         name: python-package-distributions
         path: dist/

.github/workflows/security.yml

@@ -10,10 +10,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v7
       with:
         python-version: '3.11'
         cache: 'pip'

.github/workflows/test_with_pytest.yml

@@ -17,11 +17,11 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Set up Python ${{ matrix.python-version }}
 
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -40,31 +40,31 @@ jobs:
           TEST_PROFILE: ci
 
       - name: Upload coverage report ${{ matrix.python-version }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-report-${{ matrix.python-version }}
           path: htmlcov
           if-no-files-found: warn
 
       - name: Upload coverage XML ${{ matrix.python-version }}
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-xml-${{ matrix.python-version }}
           path: coverage.xml
           if-no-files-found: warn
 
       - name: Upload test report ${{ matrix.python-version }}
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: test-report-${{ matrix.python-version }}
           path: junit.xml
           if-no-files-found: warn
 
       - name: Upload test output logs ${{ matrix.python-version }}
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: test-output-${{ matrix.python-version }}
           path: test_output.log

.github/workflows/verify_with_sphinx.yml

@@ -14,10 +14,10 @@ jobs:
 
     steps:
       - name: Checkout IDStools sources
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           # until saxonche is available in 3.13
           # https://saxonica.plan.io/issues/6561
@@ -50,7 +50,7 @@ jobs:
 
       - name: Upload Sphinx documentation as artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: sphinx-documentation
           path: docs/build/html/

README.md

@@ -60,11 +60,20 @@ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=IT
 
 ## Requirements
 
-- Python ≥ 3.8
-- IMAS Python Access Layer (`imas-python`)
+- Python ≥ 3.10
+
+### Installed automatically via pip
 - NumPy, Matplotlib, Pandas
 - Rich (for enhanced terminal output)
 
+### Requires separate installation
+- **Tkinter** — usually bundled with Python but may require system packages:
+  - Linux (Debian/Ubuntu): `sudo apt install python3-tk`
+  - Linux (RHEL/CentOS/Rocky): `sudo dnf install python3-tkinter`
+  - Windows: included in the [python.org](https://www.python.org/downloads/) installer ("tcl/tk and IDLE" component, enabled by default)
+  - macOS (python.org installer): included by default
+  - macOS (Homebrew): `brew install python-tk` (or `brew install python-tk@3.x` for a specific version)
+
 ## Documentation
 
 Full documentation is available at the project repository. Each tool includes built-in help:

ci-sdcc/st00-header.sh

@@ -13,7 +13,7 @@ shopt -s expand_aliases
 #print hostname
 hostname -f
 
-IMAS_EXISTS=$(module -r -t list 2>&1 | grep -E "IMAS-AL-Core|IMAS-Core"  | head -n 1) 
+IMAS_EXISTS=$(module -r -t list 2>&1 | grep -E "IMAS-Core"  | head -n 1) 
 if [ -n "$IMAS_EXISTS" ]; then
     echo "> Found already loaded IMAS Module : $IMAS_EXISTS"
     ACCESS_LAYER_VERSION=$(echo "$AL_VERSION" | cut -d '.' -f 1)

ci-sdcc/utils.sh

@@ -19,7 +19,7 @@ getIMASCoreModuleName() {
         DD_VERSION="$3"
     fi
     #Semantic versioning
-    IMASVERSIONSLIST=$(module -t avail IMAS-AL-Core/ 2>&1 | grep -E "^IMAS-AL-Core/$ACCESS_LAYER_VERSION\.[0-9]+\.[0-9]+-$TOOLCHAIN_VERSION")
+    IMASVERSIONSLIST=$(module -t avail IMAS-Core/ 2>&1 | grep -E "^IMAS-Core/$ACCESS_LAYER_VERSION\.[0-9]+\.[0-9]+-$TOOLCHAIN_VERSION")
 
     if [[ $TOOLCHAIN_VERSION == *"intel"* ]]; then
         CORE_MODULE_VERSION=$(echo "$IMASVERSIONSLIST" | grep "intel" | sort -rV | head -n 1)

docs/source/cheatsheet.rst

@@ -73,7 +73,7 @@ This cheat sheet provides quick reference of commonly used commands in IDStools.
 |                            |                                                                                                                              |
 |                            |    $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134173;run=2326;database=TEST;version=3"                          |
 |                            |    -md "imas:mdsplus?user=public;pulse=111001;run=103;database=ITER_MD;version=3#pf_active"                                  |
-|                            |    "imas:hdf5?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall" --rho                                          |
+|                            |    "imas:hdf5?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall" --phi                                          |
 |                            |                                                                                                                              |
 +----------------------------+------------------------------------------------------------------------------------------------------------------------------+
 | *plotequicomp*             | Shows plasma equilibrium and quantities related with it                                                                      |

docs/source/idsprint.rst

@@ -183,16 +183,18 @@ It can also save generated figures to a specified directory or the default locat
 
       $ idsprint --uri "imas:mdsplus?user=public;pulse=122481;run=1;database=ITER;version=3#edge_profiles/ggd[:]/electrons/density[1].values" -p
 
-      $ idsprint --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3#core_profiles/profiles_1d(:)/electrons/temperature" -p
+   $ idsprint --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3#core_profiles/profiles_1d(:)/electrons/temperature" -p
 
-   .. image:: _static/images/idsprint_1.png
-      :alt: image not found
-      :align: center
+   $ idsprint --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3#summary/time"
 
-   .. image:: _static/images/idsprint_2.png
-      :alt: image not found
-      :align: center
+.. image:: _static/images/idsprint_1.png
+   :alt: image not found
+   :align: center
 
-   .. image:: _static/images/idsprint_3.png
-      :alt: image not found
-      :align: center
+.. image:: _static/images/idsprint_2.png
+   :alt: image not found
+   :align: center
+
+.. image:: _static/images/idsprint_3.png
+   :alt: image not found
+   :align: center

docs/source/jupyter.rst

@@ -0,0 +1,51 @@
+#######################
+ Jupyter notebook usage
+#######################
+
+IDStools command-line tools can also be used directly from Jupyter notebooks.
+Import ``idstools`` once in the notebook kernel to register the IDStools
+commands as IPython line magics:
+
+.. code-block:: python
+
+   import idstools
+
+After that, commands such as ``idsprint`` and ``plotequilibrium`` can be
+called with ``%``:
+
+.. code-block:: python
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p
+
+.. code-block:: python
+
+   %plotequilibrium -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5"
+
+
+******************************
+ Interactive Matplotlib plots
+******************************
+
+For interactive Matplotlib figures in Jupyter, use the ``ipympl`` backend. If
+``ipympl`` is installed in the same Python environment as IDStools, the backend
+can be selected with Matplotlib's notebook magic before plotting:
+
+.. code-block:: python
+
+   %matplotlib widget
+   import idstools
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p
+
+Alternatively, the backend can be selected through the IDStools ``--rc``
+option before Matplotlib has been imported in the current kernel:
+
+.. code-block:: python
+
+   import idstools
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p --rc "backend='module://ipympl.backend_nbagg'"
+
+.. code-block:: python
+
+   %plotequilibrium -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5" --rc "backend='module://ipympl.backend_nbagg'"

docs/source/plotequilibrium.rst

@@ -3,9 +3,17 @@
 #################
 
 *plotequilibrium* script shows plasma equilibrium. Optionally it also
-shows pf coils position and toroidal flux.
+shows PF coil positions and a toroidal-flux contour overlay.
 `refer data dictionary <https://imas-data-dictionary.readthedocs.io/en/latest/>`_.
 
+``--phi`` overlays contours of the toroidal magnetic flux Φ(R,Z) [Wb] read directly from
+``equilibrium/time_slice/profiles_2d/phi``:
+
+.. math::
+
+   \Phi(R,Z) \quad [\mathrm{Wb}]
+
+
 ************************
  Syntax plotequilibrium
 ************************
@@ -19,10 +27,11 @@ shows pf coils position and toroidal flux.
 
    .. code-block:: bash
 
-        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3" --rho -md pf_active wall --plots
-        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3" --rho -md "imas:mdsplus?user=public;pulse=111001;run=103;database=ITER_MD;version=3#pf_active" "imas:mdsplus?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall"
-        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134173;run=2326;database=TEST;version=3" --rho --md "imas:mdsplus?user=public;pulse=111001;run=103;database=ITER_MD;version=3#pf_active" "imas:hdf5?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall"
-
+        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3" --phi -md pf_active wall --profiles
+        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134174;run=117;database=ITER;version=3" --phi -md "imas:mdsplus?user=public;pulse=111001;run=103;database=ITER_MD;version=3#pf_active" "imas:mdsplus?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall"
+        $ plotequilibrium --uri "imas:mdsplus?user=public;pulse=134173;run=2326;database=TEST;version=3" --phi --md "imas:mdsplus?user=public;pulse=111001;run=103;database=ITER_MD;version=3#pf_active" "imas:hdf5?user=public;pulse=116000;run=4;database=ITER_MD;version=3#wall"
+        $ plotequilibrium --uri "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5" --md "imas:hdf5?path=/work/imas/shared/imasdb/ITER_MD/3/116000/5#wall" --profiles --no-provenance
+
    .. image:: _static/images/plotequilibrium.png
       :alt: image not found
       :align: center
@@ -33,4 +42,4 @@ shows pf coils position and toroidal flux.
 
    .. image:: _static/images/plotequilibrium3.png
       :alt: image not found
-      :align: center
+      :align: center

docs/source/tools.rst

@@ -12,3 +12,4 @@ Following are the different command line tools available in the
    ids_manipulation_tools
    database_tools
    scenariodb_tools
+   jupyter

idstools/compute/core_sources.py

@@ -365,8 +365,8 @@ def get_single_and_total_electrons_ions_waveforms(self, time_slice):
         # single_power_waveform = dict()  # waveform
         # single_particles_waveform = dict()  # waveform
         time_length = len(self.ids.time)
-        total_power_waveform = np.zeros(time_length)
-        total_particles_waveform = np.zeros(time_length)
+        total_ion_power_waveform = np.zeros(time_length)
+        total_ion_particles_waveform = np.zeros(time_length)
         single_power_waveform = {}
         single_particles_waveform = {}
         dict_single_and_total_electrons_waveforms = self.get_single_and_total_electrons_waveforms(time_slice)
@@ -398,16 +398,14 @@ def get_single_and_total_electrons_ions_waveforms(self, time_slice):
                     if total_ion_power < 0:
                         total_ion_power = 0.0
 
-                    total_power_waveform[time_index] = (
-                        total_electron_power_waveform[time_index] + electrons_power + total_ion_power
-                    )
-                    total_particles_waveform[time_index] = (
-                        total_electron_particles_waveform[time_index] + electrons_particles
-                    ) + total_ion_particles
+                    total_ion_power_waveform[time_index] += total_ion_power
+                    total_ion_particles_waveform[time_index] += total_ion_particles
                     single_power_waveform[source_index].append(electrons_power + total_ion_power)
                     single_particles_waveform[source_index].append(electrons_particles + total_ion_particles)
                 single_power_waveform[source_index] = np.array(single_power_waveform[source_index])
                 single_particles_waveform[source_index] = np.array(single_particles_waveform[source_index])
+        total_power_waveform = total_electron_power_waveform + total_ion_power_waveform
+        total_particles_waveform = total_electron_particles_waveform + total_ion_particles_waveform
         return {
             "total_power_waveform": total_power_waveform,
             "total_particles_waveform": total_particles_waveform,