Write xarray data back to xarray

.github/workflows/test.yaml

@@ -27,6 +27,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -86,6 +88,7 @@ jobs:
   coverage:
     name: Coverage
     needs: test
+    if: github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tests/hdf5"]
+	path = tests/hdf5
+	url = https://github.com/duqtools/hdf5_testdata

docs/plotting_example.md → docs/examples.md

@@ -1,4 +1,18 @@
-## Plotting example
+# Examples
+
+## Modify data
+
+Below is an example of how to use **imas2xarray** to data in-place.
+
+Note that **Imas2xarray** can only update data in-place, i.e. the new data must have the same shape as the existing data.
+
+```python
+{!../scripts/modify_data.py!}
+```
+
+[Source code](https://github.com/duqtools/imas2xarray/tree/main/scripts/modify_data.py)
+
+## Plotting single dataset
 
 Below is an example of how to use **imas2xarray** to plot data with [matplotlib](https://matplotlib.org/).
 
@@ -8,6 +22,8 @@ Below is an example of how to use **imas2xarray** to plot data with [matplotlib]
 
 [Source code](https://github.com/duqtools/imas2xarray/tree/main/scripts/plot_with_matplotlib.py)
 
+## Plotting multiple datasets
+
 The code below shows how to make a plot with [matplotlib](https://matplotlib.org/) for multiple datasets.
 
 For a more advanced example of how to concatenate data, check out the [example notebooks](../notebooks/xarray).

mkdocs.yml

@@ -7,7 +7,7 @@ nav:
   - Home: index.md
   - Variables: variables.md
   - Python API: api/index.md
-  - Plotting example: plotting_example.md
+  - Examples: examples.md
   - Notebook - Variables: notebooks/xarray.ipynb
   - Notebook - 2D data: notebooks/xarray-2D.ipynb
   - Notebook - Ions: notebooks/xarray-ions.ipynb
@@ -17,7 +17,6 @@ nav:
   - 🔗 Issues: https://github.com/duqtools/imas2xarray/issues
   - 🔗 Duqtools: https://duqtools.readthedocs.io
 
-
 theme:
   name: material
   primary: blue

scripts/modify_data.py

@@ -0,0 +1,20 @@
+from imas2xarray import to_imas, to_xarray
+
+variables = ('rho_tor_norm', 'time', 't_e')
+ids = 'core_profiles'
+
+dataset = to_xarray(
+    '/pfs/work/g2aho/public/imasdb/test/3/92436/1/',
+    ids=ids,
+    variables=variables,
+)
+
+print(dataset['t_e'])
+dataset['t_e'] += 1
+
+to_imas(
+    '/pfs/work/g2aho/public/imasdb/test/3/92436/1/',
+    dataset=dataset,
+    ids=ids,
+    variables=variables,
+)

src/imas2xarray/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from ._io import H5Handle, to_xarray
+from ._io import H5Handle, to_imas, to_xarray
 from ._lookup import VariableConfigLoader, var_lookup
 from ._models import IDSPath, VariableConfigModel
 from ._models import IDSVariableModel as Variable
@@ -30,6 +30,7 @@
     'standardize_grid',
     'standardize_grid_and_time',
     'to_xarray',
+    'to_imas',
     'var_lookup',
     'VariableConfigLoader',
     'VariableConfigModel',