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1. Copy and Move operations
2. Smart Pointers
3. Aliases
4. Inputs and Outputs
This is a fix for issue #399 and extension of PR [#400](https://github.com/UWB-Biocomputing/Graphitti/pull/400) | {
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"Will it be OK to let the eventual merge of the development branch into master fix it there, or is this something that needs to be resolved in master before July?",
"> Will it be OK to let the eventual merge of the development branch into master fix it there, or is this something that needs to be resolved in mast... | 2023-03-03T21:16:48 | 2023-05-15T05:45:52 | 2023-05-15T05:45:47 | CONTRIBUTOR | null | {
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Upgrades GitHub checkout action v2 to v3, because actions that use Node.js 12 are being deprecated. | {
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"Thanks for finding this bug. I saw that empty space in the empty line. Do I need to update the file and push it to GitHub?",
"These two regression testing files were updated."
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Testing/RegressionTesting/GoodOutput/test-small-out.xml: Line 14
Testing/RegressionTesting/GoodOutput/test-small-connected-long-out.xml: Line 30
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In our case, we need to upgrad... | {
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"I have looked over the code and everything I checked in test files and code have default cases which return ETYPE_UNDEF which is similiar to issue #409 "
] | 2023-02-26T22:10:29 | 2023-07-20T20:39:34 | 2023-07-20T20:39:34 | COLLABORATOR | null | {
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See also issue #409 and #404 | {
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"Closing this issue as it's no more relevant. "
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Closes #24
Closes #76
Closes #129
Closes #237
Closes #372
This PR addresses multiple issues as they are mostly interrelated. Some of the changes addressed in the PR are as follows :
1. C++ version has been updated to C++17 in the CMake file
2. Dynamically allocated arrays are changed to vector... | {
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Fixes #401
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Added documentation for const and constexpr.
Fixed the existing coding style. | {
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} | null | Graphitti is primarily written in C++98 and as a part of upgrading the codebase to modern C++ (C++11, C++14, and C++17), new features will be adopted. These features must be recorded and documented in the `codingConvention.md` and `cppStyleGuide.md` files.
Features that must be added :
1. const and constexpr | {
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"> Since you raise the issue of C++17, consult with @KamathScience on her future plans for presenting language features and when the feels that she would be ready to facilitate a discussion of which C++ version we should target. My guess is that it will be C++17, but let's make sure we have heard about the key feat... | 2023-01-31T05:22:31 | 2023-02-20T06:27:50 | 2023-02-19T08:00:38 | CONTRIBUTOR | null | {
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In the current implementation, the `get()` method returns a default constructed object when called on an empty buffer. If we decide that it's worth it, we could move our target standard to C++1... | {
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"This is an important point for GPU compatibility: as currently designed, such CPU-side data structures should _never_ be resized, so this is actually a desirable behavior. If there is a reason for needing such a thing, then we need to talk about mid-level architectural decisions. In particular, being able to chang... | 2023-01-31T02:53:32 | 2023-06-23T19:08:12 | null | CONTRIBUTOR | null | {
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"PR#492 is deleted because it contains unwanted commits."
] | 2023-01-20T19:02:35 | 2023-08-03T06:29:05 | 2023-08-03T06:29:05 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/84d9f6ee28264e2a50ba211ec5efd2a30be6b7d2/Simulator/Vertices/EventBuffer.h#L66 | {
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- The InputManager class implementation
- Unit tests for the InputManager class
- InputManager and GraphManager documentation
- A Python script for generating an XML file from a CSV formatted 911 call log
- Improvements to the Python script that generated the GraphML file | {
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"Serialization currently only includes version numbers for base classes, as a reminder/example. Could be extended to all classes, if desired, when this issue is addressed."
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CEREAL_CLASS_VERSION is a macro defined in the Cereal library which is used to specify the version of a class when serializing and deserializing data.
When serializing an instance of a class, the version number specified with CEREAL_CLASS_VERSION will be stored in the serialized data. This version ... | null | {
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This PR adds CEREAL_CLASS_VERSION macro on AllEdges and ConnGrowth class.
In addition, we also extend the serialization unit test to confirm that the output XML file contains the expected class version. | {
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1.2.2: "Download a release" hyperlink does nothing as we are already where the link is supposed to direct you to
I added a release page link
1.2.2: "Fork and Clone Graphitti" doesn't take you to a different page
I added a link pointing to the section header
1.2.2.1: Says there are no releases, but on... | {
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This PR modifies the below 3 Plant UML diagram script to change the reference of Driver to Core where required.
1. graphitti.puml
2. simulatorSimulate.puml
3. topLevelFlow.puml
In addition to the PlantUML script, the PR updates the helper comments in the code that refer to Driver.cpp. | {
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In the [PR-382](https://github.com/UWB-Biocomputing/Graphitti/pull/382), we refactored the main class (Driver.cpp) into Graphitti_Main.cpp, Core.h, Core.cpp, Serializer.h, Serializer.cpp to improve the testability of Serialization and Deserialization.
However, 20 places refer/mention the old class... | {
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section 2
Create a PlantUML class diagram that is like the hand-draw block diagram | {
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CEREAL_CLASS_VERSION is a macro defined in the Cereal library which is used to specify the version of a class when serializing and deserializing data. When serializing an instance of a class, the version number specified with CEREAL_CLASS_VERSION will be stored in the serialized data. This version numb... | {
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An option would be ... | null | {
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- Within the action, and assuming all other tests pass, do a git merge into master just locally within that VM.
- Run all tests
Since this is just local to the VM, the merge has no effect on the repo | null | {
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The code change also improves the size validation checks of deserialized data by adding size variables for each vector... | {
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"all comments on PR #380 are addressed in this Pull Request along with Fixes to Code Style Errors"
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"Addressed all code style errors in #381.\r\n"
] | 2022-11-18T18:08:33 | 2022-11-23T20:16:23 | 2022-11-22T20:03:22 | CONTRIBUTOR | null | {
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It addresses most of what is needed for issue #369. Not all the parameters needed for a fully functional 911 implementation are there yet... | {
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"And to follow up, if we give each of the numbered items in the startup sequence a separate operation in the manager, then we can \"script\" the startup (and shutdown, which we haven't addressed) entirely using OperationManager, with top-level abstract classes registering appropriate methods. This will mean that, i... | 2022-11-08T05:51:21 | 2024-01-30T19:10:11 | 2024-01-30T19:10:11 | CONTRIBUTOR | null | {
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- We must figure out where and when input and graph parameters must be loaded.
- We need to figure out if we can leverage the OperationsManager for some initialization steps that don't n... | {
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Currently command line options for stimulusfile (-s), deserializefile(-r) and serializefile(-w) does not closely match their description. This can be hard for a user to remember or lead to confusion.
```
dkamath@otachi:~/Graphitti/build$ ./cgraphitti -help
[TRACE][2022-11-02 17:25:37] Instantiati... | {
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This link is broken: http://depts.washington.edu/cssuwb/wiki/computing_resources#raijuuwbedu
Can someone update the link with info on these hardware? | null | {
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} | null | Currently, the neurons' spike history is reset at the end of the Recorder `compileHistories()` in CPU code. Then, the equivalent GPU structure is updated by copying the values over using `cudaMemcpy`. This is confusing.
Perhaps, the resetting of spike history in GPU code should be done in a CUDA kernel call. The log... | null | {
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"This connects to one of the remaining \"most confusing\" parts of the simulator."
] | 2022-10-27T06:14:25 | 2023-04-10T17:18:06 | 2023-04-10T17:18:05 | CONTRIBUTOR | null | {
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- `vertexType *rgNeuronTypeMap_`, and
- `bool *rgEndogenouslyActiveNeuronMap_`
There are getters for these but they are not called anywhere. They should be removed if not needed.
Besides, the class has a pointer (`pSummatio... | {
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With this, we will also merge several config files (for vertex types) into one.
Tied to Workbench issue: https:... | {
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"I am using XML as the format for the input files. At the moment it holds a `data` element that contains a list of `event` items each representing an event that occurs at a given vertex. In the case of 911 calls, they have the following attributes:\r\n- vertex_id\r\n- time (time of occurrence)\r\n- duration\r\n- x\... | 2022-10-18T17:54:59 | 2023-02-25T16:00:54 | 2023-02-25T16:00:54 | CONTRIBUTOR | null | {
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"Also add at least a `TestOutput` subdirectory, and entries in `.gitignore` to not track `.xml` and `.h5` files there."
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The subfolder `Core` under Testing has unit tests from all the components of the simulator, not just the Core. Hence the name should be replaced with `UnitTesting`. This name will also be consistent with the names of other sub-folders in Testing like `RegressionTesting`. Finally, it is important to re... | {
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Tested and verified and Output compared with v0.9 branch | {
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"2. Garbage collection in Vector allocation ",
"Appears to be obsolete."
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1. Replace shared_ptrs with make_shared while instantiating the Objects
[reference: 15.2.1: https://learning.oreilly.com/library/view/a-tour-of/9780136823575/ch15.xhtml#sec15_2_1 ]
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"I have completed the following this.\r\n1. Renaming `copyNeuronHostToDevice()` to `copyToDevice()`\r\n2. Renaming `copyNeuronDeviceToHost()` to `copyFromDevice()`\r\n3. This change has been cascaded from top level neuron class to all its sub classes "
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Note that, for subclasses, at each level in the hierarchy, should copy the corresponding *new* elements of the device properties `struct`. So, it should call the superclass copy method first.
Also, all of these methods should take a single argument that is a devi... | {
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The python script to turn GIS data into a graph representation was not working on Linux because of capitalization inconsistencies with the file names, this fixes that. I also removed the spaces from the names of files and directories.
In addition, I added a `.graphml` format output. The reasoning is ... | {
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I've also edited the docs/index.md file to include the new documentation. | {
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These classes sho... | {
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2. Serialized config file test-large-very-long.xml using GPU (8 hours)
3. Edited config file full-100x100-cpu-stdp.xml to use with the above serialized file
4. Collected CPU output using command (./cgraphitti -c ../configfiles/full-100x100-cpu-stdp.xml -r Output/Results/GPUSERIAL_test_large_very_... | {
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"Hi Professor @stiber , we can merge this branch now. Tested all clang-format changes on CPU and GPU Outputs ,no change in any output or time of running input config files. I will now check the time change during compilation. "
] | 2022-07-11T18:03:18 | 2022-07-15T22:14:14 | 2022-07-15T22:13:37 | CONTRIBUTOR | null | {
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" https://docs.google.com/spreadsheets/d/1WW1iFUQ-m6wms38ipnbmw4X_CgMmMdAKxw0CbkBFYcs/edit?usp=sharing " | {
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"Thoughts on work to close this out:\r\n1. Add 'GoodOutput/CPU' and 'GoodOutput/GPU' directories to 'Testing/RegressionTesting/'.\r\n2. Move current xml files into 'GoodOutput/CPU'.\r\n3. Change all instances of 'GoodOutput' to 'GoodOutput/Cpu' in .github/workflows/tests.yml.\r\n4. Add a variable to 'Testing/RunTes... | 2022-07-08T23:59:22 | 2024-08-28T19:50:23 | 2024-08-28T19:50:23 | CONTRIBUTOR | null | {
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"CONTRIBUTING.md looks good. \r\n\r\nIn near future we can add link to Google unit tests documentation Link and GPU tests script location in this. "
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"completed the following things.\r\n1. multiple methods were present to accomplish the copy to or from Device. Clubbed them into one.\r\n2. completed the the renaming of copy methods to to avoid confusion "
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"The event buffer data structure to capture neuron spike has been extended to GPU side. We are only writing CPU side code to copy to-from the GPU side that translates between the CPU and GPU data structure reorganization"
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"I think these can be a set of small things that you could work on to familiarize yourself with our software development processes. Read our contributing guide and then touch bases with me on this."
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} | null | 1.2.2: "Download a release" hyperlink does nothing as we are already where the link is supposed to direct you to
1.2.2: "Fork and Clone Graphitti" doesn't take you to a different page
1.2.2.1: Says there are no releases, but on BrainGrid GitHub page there are 5 releases
1.2.3: Where is CMakeLists.txt located?
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"Can we merge this?",
"Sorry for the slow response time..."
] | 2022-06-10T00:02:52 | 2022-09-28T17:03:51 | 2022-09-28T17:03:43 | CONTRIBUTOR | null | {
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I did some cleaned up of the various factory classes. If nothing else, this should improve readability.
Summary:
- Switched to using `find`, instead of looping over the `createFunctions` map.
- Changed `noiseRNG` from a naked pointer to a `shared_ptr`.
- Removed not needed class member pointer t... | {
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"I think we need to schedule an \"architecture day\" (or, maybe \"architecture cleanup day\") for mid-summer 2022. The Graphitti architecture, at the top level, is greatly improved from BrainGrid. There are some parts of the envisioned architecture that aren't yet fully implemented or universally used (new Recorder... | 2022-06-06T14:52:36 | 2022-06-29T18:36:00 | null | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/f4e82884eb9f7273aca729fbb8024f03c350ec5a/Simulator/Core/GPUModel.h#L122-L128
The code for allocating and copying memory between CPU and GPU is in subclasses of AllEdges and AllVertice... | null | {
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> After extensive testing done by the IT CSS/STEM Liaisons with the CSS remote lab computers, the Infrastructure Committee has decided th... | null | {
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I only in... | {
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Fixes the segmentation fault at the end of GPU simulations. See conversation in issue #333 for more details. | {
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"I wonder if we take away the `force_orphan: true` would the monthly script come in and wipe out the commit history for us? The point of this manual script was to not have to regenerate Doxygen files all the time. @stiber do you have a preference for what fix should be implemented? I would think removing `force_orp... | 2022-05-27T20:57:02 | 2022-06-01T21:30:44 | 2022-06-01T21:30:44 | CONTRIBUTOR | null | {
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"I have a couple of observations about this:\r\n\r\n## Can we move the method to Connections?\r\n\r\nThe CPU version of it is very similar but without the downcasting. It seems to me that the CPU version can be very easily moved to the `Connections` class since it already has or can obtain the needed information fr... | 2022-05-27T19:02:03 | 2023-09-26T05:05:07 | null | CONTRIBUTOR | null | {
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"I was able to create the clang-tidy file using the command: $ clang-tidy -dump-config >> .clang-tidy\r\nTo use the file, I ran this command: $ clang-tidy `find . -type f \\( -iname \"*.cpp\" -or -iname \"*.h\" \\) ! -path \"./Testing/li... | 2022-05-23T00:49:11 | 2023-12-07T23:40:30 | null | CONTRIBUTOR | null | {
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"The reason Graphitti is failing to build is because `log4cplus/loggingmacros.h` is being included after `IRecoder.h` in `Simulator/Core/Model.h`:\r\n\r\n```\r\n#include \"AllVertices.h\"\r\n#include \"IRecorder.h\"\r\n#include \"Layout.h\"\r\n#include <log4cplus/loggingmacros.h>\r\n#include <memory>\r\n ```\r\n\r\... | 2022-05-16T21:39:23 | 2022-05-18T01:57:57 | 2022-05-18T01:57:54 | CONTRIBUTOR | null | {
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"Actually, I'm not sure the body of the loop can be put inside the `EventBuffer` method. That loop is actually reading the equivalent of one `EventBuffer` object for each iteration. Also, it seems that there is also a need to implement a `copyToGPU()` method. Also, from conversation with @PoojaPal2021, there is a l... | 2022-05-11T16:54:09 | 2022-12-02T18:10:35 | 2022-12-02T18:10:35 | CONTRIBUTOR | null | {
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Class needs at least one additional methods:
First, we definitely need something like `EventBuffer::copyFromGPU()`. This should implement the current functionality of much of `AllSpikingNeurons::copyDevice... | {
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"I don't think we need the 911 simulation code from the JCPenny-advanceEdges branch anymore. The model has changed significantly and made this code irrelevant."
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"We determined no longer needed."
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"first version of documentation for EventBuffer changes"
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"Merging changes for Event Buffer and impacted classes. \r\nNote: This merge might break the code at the GPU side as the implementation is incomplete."
] | 2022-05-10T17:32:09 | 2022-05-10T21:48:45 | 2022-05-10T21:44:35 | CONTRIBUTOR | null | {
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It also has changes in impacted Vertex classes and Recorder classes by introducing Event Buffer.
Changes are tested with Manually by taking different simulation instances and comparing the out... | {
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"@stiber and @rashwini21, hunting this bug down wasn't easy but I finally found the source of the segmentation fault. The bug is in `AllIFNeurons_d.cu` line 63:\r\n\r\n```\r\nsummationMap_ = allVerticesDevice.summationMap_;\r\n```\r\n\r\n`summationMap_` is a host pointer in AllVertices.h but it is being assigned th... | 2022-05-06T21:51:39 | 2022-06-06T14:18:44 | 2022-06-06T14:18:44 | CONTRIBUTOR | null | {
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"This is addressed in PR #336 "
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"Looking at commit #348 we now have PlantUML class diagrams, but they are very flat and not human-friendly. It would be good to have PlantUML diagrams that are more like the hand-drawn block diagram at https://uwb-biocomputing.github.io/Graphitti/Developer/ClassDiagrams/hand-drawn.pdf"
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"How can I reproduce this bug? What input file should I use for the serialized simulation run and when deserializing it?",
"I believe that there is a serialized network file available on the research machines; we can verify this at an upcoming lab meeting. Sorry that this reply is so opaque; it's rather complicat... | 2022-05-03T17:23:36 | 2025-01-22T18:55:43 | null | CONTRIBUTOR | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/327 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/327/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/327/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/327/events | https://github.com/UWB-Biocomputing/Graphitti/issues/327 | 1,219,145,809 | I_kwDOEEdqD85IqrBR | 327 | Consider splitting unit and regression tests into three action workflows | {
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"Actually, I don't think \"build\" can be a separate workflow; not sure what I was thinking.",
"Correction: I was thinking of a workflow that just verified that the simulator could be built. If there is a way to have an action do a test build, and prevent other actions from running if the build fails, then that c... | 2022-04-28T18:59:56 | 2023-06-20T04:59:08 | null | CONTRIBUTOR | null | {
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- Build
- Unit tests
- Regression tests
The disadvantage of this is that there are two extra builds: one for the unit tests and one for the regression tests. This will add about 4 minutes total to the entire suite of tests. However, if we can condition running the unit and/or regressi... | null | {
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"Closed as superseded by #625 "
] | 2022-04-28T16:30:14 | 2024-12-03T22:12:28 | 2024-12-03T22:12:28 | CONTRIBUTOR | null | {
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