Feature/sina/hdf5 output support #1480

doutriaux1 · 2024-12-20T00:09:23Z

Summary

This PR is a feature
It does the following (modify list as needed):
- Adds the capacity to output sina files as hdf5 and opens the door for more formats in the future

cyrush · 2024-12-20T00:13:08Z

src/axom/sina/core/Document.cpp

-      message << "The '" << RELATIONSHIPS_KEY
-              << "' element of a document must be an array";
-      throw std::invalid_argument(message.str());
+        conduit::Node relationship_nodes = asNode[RELATIONSHIPS_KEY];


this should be a ref to avoid a copy

Removed as many copies as I could, this one underwent additional changes

cyrush · 2024-12-20T00:19:56Z

src/axom/sina/core/Document.cpp

+        conduit::Node modifiedRelationshipsNode;
+
+        removeSlashes(relationshipNode, modifiedRelationshipsNode);
+        relationshipsNode.append() = modifiedRelationshipsNode;


you could pass ref to append result into removeSlashes to avoid one extra copy.

Copy removed

are the changes pushed? I see:

removeSlashes(relationshipNode, modifiedRelationshipsNode); relationshipsNode.append() = modifiedRelationshipsNode;

however, I expect something like:

removeSlashes(relationshipNode, relationshipsNode.append());

@cyrush @gwaegner cannot push. I just pushed the changes.

cyrush · 2024-12-20T01:22:34Z

src/spack

was this sub module add intended?

Submodule removed

Looks like the PR is trying to make unintended changes to submodules (blt, data, radiuss-spack-configs)

Submodule changes came from develop merges, double checked for intentionality

bgunnar5

Left some suggestions for you. Also wondering if the fortran changes are tested?

src/axom/sina/core/Document.cpp

src/axom/sina/core/Document.hpp

src/axom/sina/docs/sphinx/tutorial.rst

src/axom/sina/examples/sina_tutorial.cpp

…tion

doutriaux1 · 2025-01-26T16:40:50Z

@gwaegner please take a look at the failures

bmhan12

The updated ReadTheDocs documentation for this PR can be previewed here: https://axom.readthedocs.io/en/feature-sina-hdf5_output_support/axom/sina/docs/sphinx/index.html

src/axom/sina/core/Document.hpp

white238 · 2025-04-02T16:33:07Z

src/axom/sina/core/Document.cpp

+      conduit::Node &newChild = restoredNode.add_child(restoredKey);
+
+      // Leaves empty keys empty but continues recursive call if its a list
+      if(it.node().dtype().is_string() || it.node().dtype().is_number() ||


This could be more readable and possibly more efficent if you stored the type then checked instead of calling the same function again and again.

Something like:

auto dtype = it.node().dtype(); if (dtype.is_string() || dtype.is_number() || dtype.is_object()) { newChild.set(it.node()); } else if(dtype.is_list()) { restoreSlashes(it.node(), newChild); // Handle nested lists }

it.node().dtype() stored as an auto data_type that is now referenced instead of additional calls.

white238 · 2025-04-02T16:37:26Z

src/axom/sina/core/Document.cpp

 }

 }  // namespace sina
-}  // namespace axom
+}  // namespace axom


Suggested change

} // namespace axom

} // namespace axom

Implemented.

white238 · 2025-04-02T16:38:47Z

src/axom/sina/docs/sphinx/documents.rst

+
+In addition to assembling ``Document`` instances from existing JSON files, it
+is possible to generate ``Document`` objects from existing HDF5 files using
+conduit.


Suggested change

conduit.

Conduit.

white238 · 2025-04-02T16:42:57Z

src/axom/sina/docs/sphinx/hdf5_vs_json.rst

@@ -0,0 +1,55 @@
+.. ## Copyright (c) 2017-2025, Lawrence Livermore National Security, LLC and


As far as I can tell this is not showing up in the Sphinx documentation. Also the "Records" page is a bad link.

It is probably because of line 6 needing to be unique and also it needs to be added to the toctree probably here:

axom/src/axom/sina/docs/sphinx/core_concepts.rst

Line 24 in bdab620

records

HDF5_vs_JSON nested in the Documents page as a new toctree, broken links on the Documents page are fixed.

white238 · 2025-04-02T16:50:11Z

src/axom/sina/docs/sphinx/tutorial.rst

+Once you have a document, it is easy to save it to a file. To save to a JSON, we
+run the saveDocument() with the optional argument Protocol set to JSON or set as
+nothing. Alternatively if you wish to save the document to an HDF5 file: Configure 
+axom for HDF5 support then you can set saveDocument()'s optional Protocol parameter 


There is a lot of code in these paragraphs that is not formatted. A lot of it is pre-existing but should be fixed at some point. I would be fine if it happened after this PR.

I can look into adjusting this one for my Append MR, it will just need this one merged first.

src/axom/sina/examples/CMakeLists.txt

src/axom/sina/interface/sina_fortran_interface.f.in

src/axom/sina/tests/config.py.in

src/axom/sina/tests/sina_Document.cpp

src/axom/sina/tests/test_fortran_integration.py

white238 · 2025-04-02T16:56:30Z

Some minor changes on my end then it is fine to be merged. The reason for wanting a newline at the end of a file is because it can lead to obscure issues that are very hard to track down.

white238

Fix docs and minor tweaks

…into sina_hdf5_implementation

white238 · 2025-04-07T22:10:29Z

/style

doutriaux1 and others added 6 commits December 18, 2024 16:19

created a clean new branch from Gabriel's work to push to github repo

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Comments Implemented

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More Comments

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Fix?

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Fix??

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Final Fix

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doutriaux1 requested review from white238, cyrush, kennyweiss, rhornung67, bgunnar5 and HaluskaR December 20, 2024 00:09

cyrush reviewed Dec 20, 2024

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Axom Changes

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bgunnar5 reviewed Dec 21, 2024

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gwaegner and others added 7 commits January 8, 2025 14:55

Brian's Changes, Wait to hear back on createFromNode

c5c0cb4

Merge branch 'develop' into sina_hdf5_implementation

8dd8a84

Create From Node Changes

8e6afc1

Forgot to delete some leftover comments

247591f

Small fix

703dbd1

Merge remote-tracking branch 'llnl/develop' into sina_hdf5_implementa…

e1d7631

…tion

merged github's develop in

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Pipeline Fix

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kennyweiss requested a review from bmhan12 January 27, 2025 22:19

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gwaegner added 2 commits January 28, 2025 09:26

Clang Format

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More ClangFormat

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gwaegner added 10 commits April 2, 2025 10:07

Everything except the big doc changes

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Attempted Docs fix?

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Merge remote-tracking branch 'llnl/feature/sina/hdf5_output_support' …

d7f25de

…into sina_hdf5_implementation

Doc Fixes

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Another Attempted Docs fix

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Last Doc update?

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Missed a Whitespace

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Merge branch 'develop' into feature/sina/hdf5_output_support

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gwaegner requested a review from white238 April 3, 2025 18:36

white238 approved these changes Apr 4, 2025

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rhornung67 approved these changes Apr 7, 2025

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Merge branch 'develop' into feature/sina/hdf5_output_support

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Apply style updates

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kennyweiss merged commit 5e0c4b4 into develop Apr 8, 2025
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kennyweiss deleted the feature/sina/hdf5_output_support branch April 8, 2025 01:18

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Feature/sina/hdf5 output support #1480

Feature/sina/hdf5 output support #1480

doutriaux1 commented Dec 20, 2024

cyrush Dec 20, 2024

gwaegner Jan 24, 2025

cyrush Dec 20, 2024

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white238 commented Apr 7, 2025

		@@ -0,0 +1,55 @@
		.. ## Copyright (c) 2017-2025, Lawrence Livermore National Security, LLC and

Feature/sina/hdf5 output support #1480

Feature/sina/hdf5 output support #1480

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doutriaux1 commented Dec 20, 2024

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