Merge pull request #184 from NeuroML/development

Minor update hdf5 page

.github/workflows/prs.yaml

@@ -16,9 +16,10 @@ jobs:
       with:
         python-version: 3.9
     - name: Set up JDK 11 for jNeuroML etc
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 11
+        distribution: 'temurin'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/publish.yml

@@ -16,9 +16,10 @@ jobs:
       with:
         python-version: 3.9
     - name: Set up JDK 11 for jNeuroML etc
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 11
+        distribution: 'temurin'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

source/Userdocs/HDF5.md

@@ -2,11 +2,12 @@
 # HDF5 support
 
 The XML serializations of large NeuroML models can be prohibitive to store.
-For such cases, NeuroML also includes support for saving models in the binary [HDF5](https://www.hdfgroup.org/solutions/hdf5) format via the [NeuroMLhdf5Writer in libNeuroML](https://libneuroml.readthedocs.io/en/stable/userdocs/writers.html#neuroml.writers.NeuroMLHdf5Writer).
+For such cases, NeuroML also includes support for saving models in the binary [HDF5](https://www.hdfgroup.org/solutions/hdf5) format via the [NeuroMLHdf5Writer in libNeuroML](https://libneuroml.readthedocs.io/en/stable/userdocs/writers.html#neuroml.writers.NeuroMLHdf5Writer). The same format can be exported also from the Java API ([example](https://github.com/NeuroML/org.neuroml.model/blob/master/src/test/java/org/neuroml/model/test/HDF5Test.java)).
+
 The format of the export is documented below:
 
 
-- {ref}`Network <schema:network>` is exported as a `network` group with `id`, `notes`, and the `temperature` (optional) stored as attributes.
+- {ref}`Network <schema:network>` is exported as a `network` HDF5 group with `id`, `notes`, and the `temperature` (optional) stored as attributes.
 - {ref}`Population <schema:population>` is exported as a group with id `population_<id of the population>` with `id`, `component`, `size`, `type`, and `property` tags stored as attributes.
   - If the population is a {ref}`population list <schema:populationlist>` that includes {ref}`instances <schema:instance>` of cells, the locations of cells (x, y, z), these are stored in a 3 column table ("chunked array") with a row per instance.
 
@@ -18,6 +19,6 @@ The format of the export is documented below:
 - {ref}`InputList <schema:inputlist>` is exported similar to Projection with the {ref}`Input <schema:input>`, and {ref}`InputW <schema:inputw>` entries stored in tables.
 
 
-The source code of these export functions can be seen [here in the libNeuroML repository](https://github.com/NeuralEnsemble/libNeuroML/blob/2d8112178d8d82b07a20f8395ec22a23a6323a6c/neuroml/nml/helper_methods.py#L2548).
+For more details, the source code of these export functions can be seen [here in the libNeuroML repository](https://github.com/NeuralEnsemble/libNeuroML/blob/2d8112178d8d82b07a20f8395ec22a23a6323a6c/neuroml/nml/helper_methods.py#L2548) and [here in org.neuroml.model](https://github.com/NeuroML/org.neuroml.model/blob/master/src/main/java/org/neuroml/model/util/hdf5/NeuroMLHDF5Writer.java).
 
-HDF5 NeuroML files can also be passed to `jnml` like `XML` files.
+HDF5 NeuroML files can be read and processed by `jnml` and `pynml` in the same way as XML files (see [here](https://github.com/OpenSourceBrain/OpenCortex/tree/master/examples/HDF5) for LEMS Simulation file examples which reference HDF5 NeuroML models).