From 1767daf31da3d65dc5c1206119c979d9b0205a82 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 21 Nov 2023 10:32:35 +0000 Subject: [PATCH 1/2] Update GHA versions --- .github/workflows/prs.yaml | 3 ++- .github/workflows/publish.yml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/prs.yaml b/.github/workflows/prs.yaml index 6e4cb1ad..ed45723c 100644 --- a/.github/workflows/prs.yaml +++ b/.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 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 778fba09..170bb910 100644 --- a/.github/workflows/publish.yml +++ b/.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 From 350cf1d4661027ebc581912e7d051b4dd6b84293 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 5 Dec 2023 12:18:42 +0000 Subject: [PATCH 2/2] Minor update hdf5 page --- source/Userdocs/HDF5.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/source/Userdocs/HDF5.md b/source/Userdocs/HDF5.md index b95e2f1a..894585b5 100644 --- a/source/Userdocs/HDF5.md +++ b/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 ` is exported as a `network` group with `id`, `notes`, and the `temperature` (optional) stored as attributes. +- {ref}`Network ` is exported as a `network` HDF5 group with `id`, `notes`, and the `temperature` (optional) stored as attributes. - {ref}`Population ` is exported as a group with id `population_` with `id`, `component`, `size`, `type`, and `property` tags stored as attributes. - If the population is a {ref}`population list ` that includes {ref}`instances ` 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 ` is exported similar to Projection with the {ref}`Input `, and {ref}`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).