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"The above may not be 100% right. But, definitely, there's no need to regenerate images for `.puml` files that aren't changed, and probably this shouldn't put the images into the repo, but rather into the orphan documentation branch."
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https://github.com/UWB-Biocomputing/Graphitti/blob/868a36980ce72c982c754ebbbc76879d2acc28d6/.github/workflows/plantUML.yml#L29-L30
It appears that `awk` is being used to ensure that only actual file names are produced by the `find`, but that is something that can be done with the appropriate argument to `find`. | null | {
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Also will likely need to add something like "All911EdgesDeviceFuncs.h" and "All911EdgesDeviceFuncs_d.cpp" files. | null | {
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Closes #720
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This pull request addresses an issue caused by merge conflicts in the `Xml911Recorder` class. Removed the definitions of the functions `initDefaultValues()`, `initValues()`, and `getValues()` from `Xml911Recorder.cpp`, which had no corresponding declarations in `Xml911Recorder.h`.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
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"Actually, I would say that we need to eliminate the `Xml911Recorder` class and instead just have the 911 classes register their variables with the `Recorder` interface so that they can be output in either XML or HDF5."
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"Ready for manual testing. @KamathScience will do GPU test and a long Growth simulation. @nyeshlur will look into what's up with the bad PlantUML conversion. @stiber will look into the tests.yml."
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Closes #
<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
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"While \"epoch duration\" is written above, I believe what is meant is \"number of epochs\". We generally don't change the epoch duration for growth simulations — we keep it at 100, because it influences the relative rates between neuron activity and outgrowth.",
"Ack, updated the description"
] | 2024-10-28T23:38:33 | 2024-12-18T00:14:13 | null | COLLABORATOR | null | {
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For instance, `test-small-connected-long.xml` previously had the number of epochs set at 10, while connections were scheduled to form at epoch 95. This discrepancy led to incorrect simulation behavior.
Task:
1. For each connected configuration file identify the earliest epoch at which a new connection is scheduled to form; and modify the number of epochs to accommodate this earliest connection formation.
Note: test-small-connected-long.xml has already been updated to an epoch duration of 100.
2. Ensure that regression and unit tests are updated to reflect the changes in connected configuration files.
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} | null | This should include:
- Model file named "test-large-911.xml"
- Input file named "test-large-911.xml"
Requirements for the dataset:
- Should take roughly 2 hours to run with the current CPU implementation. This should be long enough to easily see improvements from GPU implementation.
Model generation tool: https://github.com/UWB-Biocomputing/Graphitti/blob/development/Tools/Graph%20Generation
Input generation tool: https://github.com/UWB-Biocomputing/Graphitti/blob/master/Tools/InputGeneration | null | {
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"I suggest breaking into 3 parts: unit tests, CPU tests, GPU tests. I agree that unit tests can just be for CPU right now.\r\n\r\nShould also set up the actions so they only run if applicable files change. No sense in running any of these, for example, if someone modifies documentation.",
"Given that we can use l... | 2024-10-14T05:59:46 | 2025-01-23T02:09:03 | null | CONTRIBUTOR | null | {
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} | null | With the move to the UW Enterprise account, we should have access to GitHub's larger runners which include extra resources such as GPU-powered runners. This should allow us to implement tests that run on a GPU resource using GitHub Actions. I am proposing the following items to better separate the CPU- and GPU-based testing actions:
- Some of the lines of the test.yml look like they should be shared between CPU and GPU actions. Thus, we should refactor test.yml into a TestBase.yml and a CPUTest.yml.
- The "run unit tests" in the test.yml is likely just CPU tests (should be confirmed if it's not obvious) so the ./tests should be renamed to ./cpu_tests
- This will require documentation updates in areas such as the Quick Sanity Test page that reference ./tests.
- Implement a GPUTest.yml file with a simple GPU unit test and hook up to the GPU-powered runner.
- Implementing the GPU unit test will require adding an if(ENABLE_CUDA) block to the TESTS EXECUTABLE section of the CMakeLists.txt file.
- We may be able to reuse the CPU pattern with GoogleTest to build the GPU unit tests at this stage. | null | {
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"Also, the link to the contributing guide at the bottom of the page is broken.",
"Actually, we are going to go away from cherry picking. So, this is useful information, but just from the point of view of documenting why we are going with the approach we will be using (per-user development branches).",
"Supersed... | 2024-10-09T21:49:22 | 2025-01-22T17:45:51 | 2025-01-22T17:45:49 | CONTRIBUTOR | null | {
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Closes #710
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Add Vanessa Arndorfer to the Contributors.md file as part of the lab onboarding process
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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"Closed by PR #711"
] | 2024-10-09T05:16:58 | 2024-10-11T14:53:35 | 2024-10-11T14:53:35 | CONTRIBUTOR | null | {
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As a part of the onboarding task add Vanessa Arndorfer to the Contributors list of Graphitti.
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"This was a bit of a mistake"
] | 2024-10-05T16:45:34 | 2024-10-29T00:46:12 | 2024-10-29T00:46:12 | CONTRIBUTOR | null | {
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#### Description
It may be the case that we can release everything sitting in development into this release. This PR is set to prepare us for that possibility.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [ ] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
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"Not going to do this"
] | 2024-10-04T19:56:50 | 2024-10-29T00:46:34 | 2024-10-29T00:46:34 | CONTRIBUTOR | null | {
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Closes #706
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Removed the versioning logic from individual base classes - `AllEdges`, `Layout`, `AllVertices`, `Connections`; into the `Model` class. This change simplifies the versioning structure by maintaining version info only in the `Model` class, which is the starting point of the serialization and deserialization.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
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#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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"Also, the linked GitHub pages file has an old example data file in it."
] | 2024-09-25T00:28:04 | 2024-12-20T21:39:30 | 2024-12-20T21:39:30 | CONTRIBUTOR | null | {
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In the above documentation, the hyperlink isn't formatted right and the data file example must be from an early version of the code. | {
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"Can’t the full length simulation results just be cached? Or is that too much like a recession test?",
"> Can’t the full length simulation results just be cached? Or is that too much like a recession test?\r\n\r\nIt is possible, the cached result will need to be updated if any member variable is changed. Shall I ... | 2024-09-16T17:38:18 | 2024-12-17T21:54:20 | 2024-12-17T21:54:16 | COLLABORATOR | null | {
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Closes #703
Closes #598
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR introduces three test files to validate the correctness of the serialization process:
1. `SerializeFullFileTest.cpp`: Runs a full simulation (e.g., 10 epochs) and saves the serialized output.
2. `SerializationFirstHalfTest.cpp`: Runs the first half of the simulation (e.g., 5 epochs) and saves the serialized output.
3. `SerializationSecondHalfTest.cpp`: Runs the second half of the simulation (e.g., 5 epochs), using the serialized output from the first half, and compares it with the full simulation's serialized output.
4. Implemented a bash script (`run_serial_test.sh`) to automate the testing process.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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Closes #697
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR includes several updates for serialization cleanup and improvements to the `Serializer` class:
1. Removed code previously used to create synapses from synapse weights saved in the serialization file: `Connections::createSynapsesFromWeights`. This is no longer needed as we serialize all values including synapses.
2. Updated comments and functions in the `Serializer` class for better clarity.
3. Removed unused variables: `totalNeurons_` and `numCallerVertices_`.
4. Removed unused functions: `Simulator::copyGPUSynapseToCPU` and `Simulator::copyCPUSynapseToGPU`. These functions are moved into Model class.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
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} | null | #569 CPU-based Neuron serialization operates as expected. We verified this by comparing two simulation approaches:
1. Running the entire configuration file in a single simulation (e.g., 10 epochs).
2. Running the same configuration in two stages:
Stage 1: Simulating and serializing the first half of the configuration (e.g., 5 epochs).
Stage 2: Deserializing the saved state from Stage 1 and completing the simulation with the second half (e.g., 5 epochs).
The final result file from both the full simulation and Stage 1 & Stage 2 are identical, confirming the correctness of the serialization process.
However, for GPU-based simulations, while serialization is functional, the output result file from a full simulation and two half simulations differ. This discrepancy arises because the GPU’s random noise array is not serialized. To resolve this, we need to implement a method to manually copy the GPU state into temporary storage during serialization and restore it during deserialization. | null | {
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Updated the PR template to reflect the correct GPU Test. | {
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Closes #694
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR addresses the issue of renaming variables in the serialize function across multiple classes to improve code clarity and consistency. This PR also adds serialize function to Model class.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x] Tested for GPU (test-medium-connected.xml)
- [x] Tested for GPU (test-long-connected.xml)
<!--
Please assign the PR to yourself and add the appropriate label.
Please add the reviewer after all the actions are passed successfully.
Thank you for your contribution!
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Closes #692
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR refactors the spike history variable registration function, moving it from the `AllSpikingNeurons` class to the `AllVertices` class. Additionally, the function name has been changed from `registerSpikeHistoryVariables` to `registerHistoryVariables` to make it more generic and less Neuron-specific. This change allows the function to be accessible from the Core module, particularly after the deserialization process.
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#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x] Tested for GPU (test-medium-connected.xml)
- [x] Tested for GPU (test-long-connected.xml)
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"And it should probably be renamed to something like `registerHistoryVariables()`"
] | 2024-08-21T21:57:00 | 2024-09-09T18:21:20 | 2024-09-09T18:21:20 | COLLABORATOR | null | {
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Closes #358
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Improved regression testing coverage by adding good output files for GPU neuron model. The existing good output files were for the CPU neuron model so these were moved into an appropriately labeled "Cpu" folder in Testing/RegressionTesting/GoodOutput. This structure allows for regression testing of both the CPU and GPU neuron models.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [X] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [X] Tested for GPU (test-medium-connected.xml)
- [X] Tested for GPU (test-large-long.xml)
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"I think this is my last pull request, right? I remember the last time we talked about I don't need to Refactor the code since I don't have enough time."
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#### Description
I Implement Hdf5Recorder::registerVariable() for vector of RecordableBase, the code inside is the same, but I can't remove it because for the singleVariableInfo , the code inside is different, and inside the registerVariable we gonna use this class. And I also remove some functions that we don't need like initdefaultvalue, initvalue, and getvalue. And after that I updated the documentation.
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#### Description
As a part of the onboarding task add Zaina Shaikh to the Contributors list of Graphitti.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [ ] Tested for GPU (test-medium-connected.xml)
- [ ] Tested for GPU (test-long-connected.xml)
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#### Description
Add implemented code for synthetic graph generation and visualization in the Graphitti tools folder. Include documentation for both the graph generation and visualization processes. This is for Summer 2024 Undergraduate Research.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x] Tested for GPU (test-medium-connected.xml)
- [x] Tested for GPU (test-long-connected.xml)
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#### Description
Add implemented code for synthetic graph generation and visualization in the Graphitti tools folder. Include documentation for both the graph generation and visualization processes. This is for Summer 2024 Undergraduate Research.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ x] Added Documentation
- [x ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x ] Tested for GPU (test-medium-connected.xml)
- [x ] Tested for GPU (test-long-connected.xml)
<!--
Please assign the PR to yourself and add the appropriate label.
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Description
Add implemented code for synthetic graph generation and visualization in the Graphitti tools folder.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x ] Added Documentation
- [x ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x ] Tested for GPU (test-medium-connected.xml)
- [x ] Tested for GPU (test-long-connected.xml)
<!--
Please assign the PR to yourself and add the appropriate label.
Please add the reviewer after all the actions are passed successfully.
Thank you for your contribution!
-->
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#### Description
Implement compileHistories() for UpdatedType:: DYNAMIC for Hdf5 Recorder, inside the compileHistories(), in order to allow us to create HDF5 files that hold data that is generated incrementally during the simulation and saved after each simulation epoch, we need to extend the size of the dataset, so I change a way to create a dataset by using chunk, and then using the hyperslab to the extended portion of the dataset, but don't forget to call startNewEpoch at the beginning of each simulation epoch to prepare for recording new events.
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<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [ ] Tested for GPU (test-medium-connected.xml)
- [ ] Tested for GPU (test-long-connected.xml)
<!--
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"Note that I changed the PR name to match our naming conventions."
] | 2024-07-24T21:02:37 | 2024-07-31T03:20:04 | 2024-07-31T03:15:40 | CONTRIBUTOR | null | {
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Closes #674
<!-- Please provide a brief overview of the changes implemented -->
#### Description Add Jasleen Kaur Saini to the Contributor List
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [x] Tested for GPU (test-medium-connected.xml)
- [x] Tested for GPU (test-long-connected.xml)
<!--
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Please add the reviewer after all the actions are passed successfully.
Thank you for your contribution!
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"Discussed with @stiber and decided to not make this change. Instead, we'll open a new issue to add documentation to indicate that no output means that there were no recordable events for that element."
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#### Description
This time I implemented the saveSimData function to replace Hdf5Recorder::initDataset() for UpdatedType::CONSTANT, which is responsible for saving simulation data into HDF5 datasets. I decide to use two different function for different UpdatedType to save and store data. Because after I see the XML recorder, I think saveSimData is more matches the initDataset() for UpdatedType::CONSTANT, I think for our new hdf5 recorder we don't have to have the initDataset(), and also for the latter task initDataset() for UpdatedType:: DYNAMIC we can use compileHistories() to responsible instead, if we really need to use initDataset() we can both find some way to call compileHistories() and saveSimData() in initDataset() after I implementer both function. And also this time create a helper function- captureData, to ensure that the dataset exists and that data can be written to it. | {
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"Ok, I just deleted that line and made a commit, right now just need to wait the unit and regression tests to pass, that gonna take some time"
] | 2024-07-12T05:34:24 | 2024-07-16T21:41:12 | 2024-07-16T21:39:04 | CONTRIBUTOR | null | {
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#### Description
I implement the rigisterVariable function for Hdf5 Recorder, in order to make it more efficient, I implement the singleVariableInfo class in hdf5Recorder.h, inside I add some variables like hdf5Datatype_ and hdf5DataSet_, and I also make function convertType() to help convert the data type of the variable to HDF5 data type, and also create a createDynamicDataset function for future use.
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/677 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/677/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/677/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/677/events | https://github.com/UWB-Biocomputing/Graphitti/pull/677 | 2,394,731,847 | PR_kwDOEEdqD850paWg | 677 | [ISSUE 675] Added frontier delta computation back into ConnGrowth | {
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#### Description
This adds back the frontier delta computation into the `ConnGrowth` class. The previous removal of this computation caused the simulation results to deviate from the good known results, for long simulations. For example, 46 epochs or more for the `test-medium-connected-long.xml` simulation.
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
#### Testing (Mandatory for all changes)
- [ ] Tested for GPU (test-medium-connected.xml)
- [ ] Tested for GPU (test-long-connected.xml)
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"Fixed with Recorder redesign."
] | 2024-07-07T09:27:36 | 2025-01-22T17:48:00 | 2025-01-22T17:47:59 | CONTRIBUTOR | null | {
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} | null | See v0.9; the code got dropped after that for some reason. See lines 151-183, 191-201, 232-239, 259-305 (and maybe other places) in `Hdf5Recorder.cpp`, plus likely in the `.h` file. | {
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"Fixed this issue in `release-v0.9.3`, as part of #639, and will add a hot-fix to the `development` branch.",
"This got merged back into development at some point."
] | 2024-07-07T09:19:08 | 2025-01-22T17:47:29 | 2025-01-22T17:47:28 | CONTRIBUTOR | null | {
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Add this as sort of like a hotfix to both branch release-v0.9.3 and to development. However, in the release-v0.9.3 branch, the `CompleteMatrix` objects are allocated dynamically, while for development the code reflects that there is no need to dynamically allocate these objects. Probably need to add this back in as two separate fixes with the two different styles.
This may fix the broken master branch. | {
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<!-- Please provide a brief overview of the changes implemented -->
#### Description
I implemented the init() and term() for Hdf5Recorder, but for there are still some problems with the init(), I can't fix it for now
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#### Description
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Closes #654
<!-- Please provide a brief overview of the changes implemented -->
#### Description
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Closes #654
<!-- Please provide a brief overview of the changes implemented -->
#### Description
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Closes #547
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Onboarding task: Cleanup unused function parameters
Fixes issue #547 (well, tries to, as of now. Although due to the nature of the problem, this could be a periodically recurring issue)
Status: Tiny, Small & Medium tests have been run and have passed
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Please check the boxes after testing -->
#### Testing (Mandatory for all changes)
- [ ] Tested for GPU (test-medium-connected.xml)
- [ ] Tested for GPU (test-long-connected.xml)
<!--
Please assign the PR to yourself and add the appropriate label.
Please add the reviewer after all the actions are passed successfully.
Thank you for your contribution!
-->
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"Just noticed: this is the pull request of the beast! 😀"
] | 2024-06-05T00:44:06 | 2024-10-07T16:08:43 | 2024-10-07T16:08:39 | COLLABORATOR | null | {
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Closes #581
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This pull request introduces documentation detailing the process of adding serialization to both future and existing classes within the project.
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#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
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#### Testing (Mandatory for all changes)
- [x] Tested for GPU (test-medium-connected.xml)
- [x] Tested for GPU (test-long-connected.xml)
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} | null | So, Prof. Stiber has been thinking of the part of the `EventBuffer` interface that looks like a vector and accesses the events from the most recent epoch as the `Recorder` interface. However, that's not true; it's also used by `ConnGrowth`. We should update comments in `EventBuffer`, and any documentation, so that we call it something different, like the "last epoch" interface.
https://github.com/UWB-Biocomputing/Graphitti/blob/d05d3504ec3a911a989ba11cf03da7893eb1096b/Simulator/Connections/Neuro/ConnGrowth.cpp#L143-L148 | null | {
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This PR adds a PR template for Graphitti | {
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"From conversation with Marina, it does seem that spikes are getting recorded and are visible to the Recorder and ConnGrowth, but the number of spikes is off. So, if a neuron is not producing any spikes, no spikes are seen in the epoch. OTOH, if the neuron does produce spikes, it seems that the count it off.",
"R... | 2024-05-31T19:18:23 | 2025-01-25T18:57:18 | 2025-01-25T18:57:17 | CONTRIBUTOR | null | {
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} | null | In `release-v0.9.3`, it appears that the eventbuffers are empty and so no events get recorded. So, is this just the recorder side of the interface, or are the eventbuffers completely broken and don't work in the simulation side either? One way to tell would be to look at (could plot in Matlab) the radii history; if they grow linearly throughout a 600 epoch simulation, then the buffers are broken on both sides. OTOH, if they become stationary, like the results in Kawasaki-stiber14, then it would seem that the buffers are only broken from the Record interface side.
https://github.com/UWB-Biocomputing/Graphitti/blob/d05d3504ec3a911a989ba11cf03da7893eb1096b/Simulator/Recorders/Hdf5Recorder.cpp#L237 | {
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"Dropping this as not responsive to issue."
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Documentation now included GraphML details, as well as a README for the GraphML python script. | {
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"issue resolved by #683 "
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"issue resolved by #679"
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"issue resolved by #678 "
] | 2024-05-28T23:08:27 | 2024-11-13T20:07:13 | 2024-11-13T20:07:13 | CONTRIBUTOR | null | {
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"We need to make sure that all variables are registered before initDataset() is called. Need to check that init() gets called after.",
"issue is closed by #672 "
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"this issue is resolved by #670 "
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"@rimjhimsudhesh you need to merge your branch into `development` branch and not `master`."
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"The stand alone NLEdit, in Java, exists somewhere in the workbench repo."
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} | null | We actually have an algorithm to create the pattern of neuron types from the grid size, which is embedded in the Workbench neuron layout editor code (NLEdit). This would allow the tool to just take in something like the grid size and compute all of the other stuff. I think the inputs would need to be sub-block dimensions and the number of horizontal and vertical repetitions of the sub-block to create the grid. This should be clarified by the Workbench code.
I have no doubt that this algorithm needs to be better documented. | null | {
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"I am sure that to implement this, the `GraphManager` must be a template class. Inheritance in the structs alone might not be enough."
] | 2024-05-15T18:32:37 | 2025-03-14T22:06:01 | 2025-03-14T22:06:01 | CONTRIBUTOR | null | {
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"> I believe that my review of #649 covers these changes.\r\n\r\nThe changes in #649 should overwrite this branch."
] | 2024-05-13T17:34:51 | 2024-06-05T18:33:12 | 2024-06-05T18:31:43 | CONTRIBUTOR | null | {
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There is now no longer a need for the inhibitory list xml files for the Regression Testing (soon to be applied to all other config files).
Note: This branch was pulled from the branch labeled issue 371, which is why it has extra changes. | {
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"This looks good. There are just some empty lines and 4-space indentations that clang-format complains about in the C++ code and one small suggestion for the Python script.",
"I have one question about the purpose of the Python script. Is it meant to be a tool for generating the neural network graph, with x and ... | 2024-05-11T16:58:48 | 2024-05-31T19:27:41 | 2024-05-31T19:26:22 | CONTRIBUTOR | null | {
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As a part of the onboarding task add Rimjhim Sudhesh to the Contributors list of Graphitti.
#### Files
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"Here are some files to use for testing:\r\n\r\n1. Reference outputs: [GPU-Regression-Test-GoodOutput.zip](https://github.com/user-attachments/files/15906433/GPU-Regression-Test-GoodOutput.zip)\r\n2. Full config file: [edited_full_tR_1.0--fE_0.98_10000.xml.zip](https://github.com/user-attachments/files/15906436/edi... | 2024-05-09T19:38:21 | 2024-07-30T22:03:25 | 2024-07-30T22:03:19 | CONTRIBUTOR | null | {
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Since Google Test acts up when we test for an exit. We will keep factory returning nullptr, but each class that uses the factory will check for nullptr, and will exit the program if that is the case. | {
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"Currently 4 of the Graph Manager's tests fail. This is because of the Parameter Manager's dependency that is outlined in issue #634 . These tests will pass once that issue has been fixed.",
"We indent to 3 spaces in our code base. I recommend adjusting the indentation spaces in your IDE or our clang-format check... | 2024-05-02T21:03:41 | 2024-05-30T23:01:36 | 2024-05-29T19:58:08 | CONTRIBUTOR | null | {
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Removed GraphManager's dependence on ParameterManager in readGraph(). Now ParameterManager is only used when graphFilePath_ has not been defined yet. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/634 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/634/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/634/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/634/events | https://github.com/UWB-Biocomputing/Graphitti/issues/634 | 2,269,525,271 | I_kwDOEEdqD86HRjUX | 634 | Modify the `GraphManager` class so unit tests can be written without needing a `ParameterManager` object | {
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"Fixed by #635 "
] | 2024-04-29T17:01:06 | 2024-06-03T07:28:21 | 2024-06-03T07:28:20 | CONTRIBUTOR | null | {
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} | null | Currently, the `GraphManager` class needs a `ParameterManager` object to get the path to the `graphML` file from a configuration file. It contains a method to set the path to the `graphML` file however, that is overwritten in the `readGraph` method. In the `readGraph` method we need to check if that path has already been set and only retrieve it from the `ParameterManager` if it hasn't.
This will allow us to write Unit Tests for the `GraphManager` independently from the `ParameterManager` class and without configuration files. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/633 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/633/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/633/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/633/events | https://github.com/UWB-Biocomputing/Graphitti/pull/633 | 2,266,361,716 | PR_kwDOEEdqD85t37ro | 633 | function parameters cleanup and suggestions for modularization | {
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Fixes issue #547 (well, tries to, as of now. Although due to the nature of the problem, this could be a periodically recurring issue)
Status: Tiny, Small & Medium tests have been run and have passed
 | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/632 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/632/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/632/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/632/events | https://github.com/UWB-Biocomputing/Graphitti/issues/632 | 2,259,242,835 | I_kwDOEEdqD86GqU9T | 632 | Create Unit Tests for Graph Manager | {
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"> Could you move the \"How the Redesigned Recorder Works (Q1 2024)\" section of `RecorderNotes.md` near the top of the file, with the legacy documentation below it?\r\n\r\nSure, I have updated the page"
] | 2024-04-22T21:35:56 | 2024-04-26T14:41:23 | 2024-04-26T14:41:18 | CONTRIBUTOR | null | {
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After completing the redesigned XmlRecorder implementation, three files need to be updated for documentation:
1. Add a sequential diagram for the Recorder workflow (including the XmlRecorder and HDF5Recorder.
2. Include a Recorder Class Diagram.
3. Update the GitHub Page with Recorder Notes (Section 4.6). I formatted the previous Recorder notes and added the redesigned XmlRecorder notes.
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There are two small issues that are addressed in the XmlRecorder class
1. Remove the "> 0" condition.
[Link to the code](https://github.com/UWB-Biocomputing/Graphitti/blob/93197dc18cf8bcf213af8b47293774a2ab28e439/Simulator/Recorders/XmlRecorder.h#L168-L170)
2. Replace "double" with "bool".
[Link to the code](https://github.com/UWB-Biocomputing/Graphitti/blob/93197dc18cf8bcf213af8b47293774a2ab28e439/Simulator/Recorders/XmlRecorder.cpp#L129-L130) | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/629 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/629/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/629/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/629/events | https://github.com/UWB-Biocomputing/Graphitti/issues/629 | 2,257,272,040 | I_kwDOEEdqD86Gizzo | 629 | Correct Two Minor Errors in the Redesigned XmlRecorder Class | {
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} | null | There are two issues that need addressing in the XmlRecorder class:
1. Remove the "> 0" condition in the reserve method.
[Link to the code](https://github.com/UWB-Biocomputing/Graphitti/blob/93197dc18cf8bcf213af8b47293774a2ab28e439/Simulator/Recorders/XmlRecorder.h#L168-L170)
2. Replace "double" with "bool".
[Link to the code](https://github.com/UWB-Biocomputing/Graphitti/blob/93197dc18cf8bcf213af8b47293774a2ab28e439/Simulator/Recorders/XmlRecorder.cpp#L129-L130 )
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```
<!-- Insert the issue number and appropriate closing keyword. If using another keyword, change the default 'Closes' keyword -->
Closes #
#### Description
<!-- Please provide a brief overview of the changes implemented -->
#### Checklist (Mandatory for new features)
<!-- Please check the boxes as applicable -->
- [ ] Added Documentation
- [ ] Added Unit Tests
#### Testing (Mandatory)
<!-- Please check the boxes after testing -->
- [ ] Tested for GPU (test-medium-connected.xml)
- [ ] Tested for GPU (test-long-connected.xml)
<!--
Please assign the PR to yourself and add the appropriate label.
Please add the reviewer after all the actions are passed successfully.
Thank you for your contribution!
-->
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"type": "User",
"user_view_type": "public",
"site_admin": false
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} | [
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"url": "https://api.github.com/users/Hsu0227",
"html_url": "https://github.com/Hsu0227",
"followers_url": "https://api.github.co... | null | [] | 2024-04-03T02:38:50 | 2024-04-04T18:14:10 | 2024-04-04T18:14:00 | CONTRIBUTOR | null | {
"total": 0,
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} | null | Closes #626
This PR adds <Chenghao Hsu> to the Contributors.txt file.
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"repos_url": "https://api.github.com/users/Hsu0227/repos",
"events_url": "https://api.github.com/users/Hsu0227/events{/privacy}",
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"type": "User",
"user_view_type": "public",
"site_admin": false
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"merged_at": "2024-04-04T18:14:00"
} | true |
https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/626 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/626/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/626/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/626/events | https://github.com/UWB-Biocomputing/Graphitti/issues/626 | 2,221,543,643 | I_kwDOEEdqD86EahDb | 626 | Add <Chenghao_Hsu> to Contributor List. | {
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"avatar_url": "https://avatars.githubusercontent.com/u/114702110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Hsu0227",
"html_url": "https://github.com/Hsu0227",
"followers_url": "https://api.github.com/users/Hsu0227/followers",
"following_url": "https://api.github.com/users/Hsu0227/following{/other_user}",
"gists_url": "https://api.github.com/users/Hsu0227/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Hsu0227/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Hsu0227/subscriptions",
"organizations_url": "https://api.github.com/users/Hsu0227/orgs",
"repos_url": "https://api.github.com/users/Hsu0227/repos",
"events_url": "https://api.github.com/users/Hsu0227/events{/privacy}",
"received_events_url": "https://api.github.com/users/Hsu0227/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
} | [
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"node_id": "MDU6TGFiZWwyMTQ0NDIzMTUy",
"url": "https://api.github.com/repos/UWB-Biocomputing/Graphitti/labels/documentation",
"name": "documentation",
"color": "0075ca",
"default": true,
"description": "Improvements or additions to documentation"
}
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"subscriptions_url": "https://api.github.com/users/Hsu0227/subscriptions",
"organizations_url": "https://api.github.com/users/Hsu0227/orgs",
"repos_url": "https://api.github.com/users/Hsu0227/repos",
"events_url": "https://api.github.com/users/Hsu0227/events{/privacy}",
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"type": "User",
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"node_id": "U_kgDOBtY3Hg",
"avatar_url": "https://avatars.githubusercontent.com/u/114702110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Hsu0227",
"html_url": "https://github.com/Hsu0227",
"followers_url": "https://api.github.co... | null | [] | 2024-04-02T22:08:41 | 2024-04-04T18:15:31 | 2024-04-04T18:15:31 | CONTRIBUTOR | null | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | null | #### Description
As a part of the onboarding task add <Chenghao_Hsu> to the Contributors list of Graphitti.
#### Files
Contributors.txt | {
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"id": 114702110,
"node_id": "U_kgDOBtY3Hg",
"avatar_url": "https://avatars.githubusercontent.com/u/114702110?v=4",
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"url": "https://api.github.com/users/Hsu0227",
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"organizations_url": "https://api.github.com/users/Hsu0227/orgs",
"repos_url": "https://api.github.com/users/Hsu0227/repos",
"events_url": "https://api.github.com/users/Hsu0227/events{/privacy}",
"received_events_url": "https://api.github.com/users/Hsu0227/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/625 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/625/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/625/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/625/events | https://github.com/UWB-Biocomputing/Graphitti/issues/625 | 2,220,940,706 | I_kwDOEEdqD86EYN2i | 625 | Add STDP regression tests | {
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"color": "C3C92B",
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"user_view_type": "public",
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"html_url": "https://github.com/marinarosenwald",
"followers_url"... | null | [] | 2024-04-02T16:28:18 | 2024-04-02T17:16:05 | null | CONTRIBUTOR | null | {
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