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This PR updates the graphml file for the Seattle PD simulation with the actual coordinates of the [33 Fire Stations](https://www.seattle.gov/fire/about-us/fire-stations) and [5 Police Precincts](https://www.seattle.gov/police/about-us/police-locations) that serve the Seattle PD PSAP boundaries. It also modified the scripts that generate the input files to match the caller region's vertex_id.
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This PR updates the graphml file for the Seattle PD simulation with the actual coordinates of the [33 Fire Stations](https://www.seattle.gov/fire/about-us/fire-stations) and [5 Police Precincts](https://www.seattle.gov/police/about-us/police-locations) that serve the Seattle PD PSAP boundaries. It also modified the scripts that generate the input files to match the caller region's `vertex_id`. | {
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"Could also add the ability to click on individual vertices/edges to edit single entity properties."
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"I just want to check that the GPU version passes its tests when run manually. Am I right in my impression, looking that the code, that in the creation and update of synapses on the GPU, summation point addresses are computed, and passed from one function to another, but never used? So, is it the case that the GPU ... | 2023-08-30T14:51:47 | 2023-09-27T17:31:08 | 2023-09-27T17:31:03 | COLLABORATOR | null | {
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This PR addresses the following 3 things:
01. Delete `summationPoint_ ` member variable from AllEdges
02. Delete `sumPoint ` parameters from `createEdge` and `addEdge` member functions
03. Removed the `summationPoint_` and `sumPoint` from plantUML diagrams. | {
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} | null | After the completion of issue #513, which involves the removal of `summationPoint` from AllEdges, it is worth considering renaming the `summationMap` member variable present in AllVertices- to better align with its actual functionality.
The term "summationMap" is currently misleading, as it doesn't accurately reflect its purpose. Unlike a traditional map, this variable holds a vector that stores all the summation points associated with specific vertices. Therefore, renaming it to `summationPoint` would be more descriptive. | {
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Additional Info: See comments in PR #496 | {
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closes #495
Added changes requested from last PR & duplicate code of conduct removed | {
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} | null | Referring to Issue #458, which pertains to serializing the `summationPoint_` member variable in the `AllEdges` base class, a decision was made to replace `summationPoint_` with a vector of integers. This change aimed to store indexes from `summationMap_` rather than specific addresses.
However, after a closer analysis, we realized that the indexes in the `summationPoint_` vector replicate the data already available in the `destVertexIndex_` vector. To improve the efficiency and clarity of our codebase, we should remove the `summationPoint_` vector to eliminate unnecessary duplication. | {
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This PR removes all the Layout Files previously used with the 911 models. These files are no longer needed because all vertices attributes should now be added as vertex parameters in the GraphML file used to set up the graph. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/508 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/508/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/508/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/508/events | https://github.com/UWB-Biocomputing/Graphitti/pull/508 | 1,858,707,517 | PR_kwDOEEdqD85YWdxU | 508 | [ISSUE-368] renamed unitTesting folder and added a output folder | {
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1. Renaming "Core" in the Testing folder to "UnitTesting" and making the corresponding changes in the CMAKE file and unit testing files.
2. Adding a subfolder "TestOutput" under the UnitTesting folder and adding entries in .gitignore to exclude tracking .xml and .h5 files in that folder. | {
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"@KamathScience I am assigning this to you because there are two `.xml` files in `build/output` that are yours. Should they be tracked in the repo? There are some files under build that should be, but most not. Let's document this.",
"Ack, they need not be tracked in the repo, they are created as part of the unit... | 2023-08-16T22:41:29 | 2023-09-28T23:03:01 | 2023-09-28T23:03:00 | CONTRIBUTOR | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/506 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/506/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/506/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/506/events | https://github.com/UWB-Biocomputing/Graphitti/pull/506 | 1,850,960,125 | PR_kwDOEEdqD85X8elB | 506 | [ISSUE-478] XmlRecorder records all events for all neurons | {
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"By overloading the registerVariable() function, it becomes possible for the Xml recorder to record a vector of EventBuffer."
] | 2023-08-15T06:20:11 | 2024-11-09T01:04:52 | 2023-09-06T02:06:19 | CONTRIBUTOR | null | {
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This PR creates a variable table within the XmlRecorder, which contains a list of variables that need to be recorded. With this enhancement, the XmlRecorder becomes capable of capturing and storing all event information for all neurons. | {
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"> Would be good to add README.md file(s) that describe the files within the directory.\r\n\r\nReorganized the script directories, renamed them to be more descriptive of what they contain, and added a README.md file."
] | 2023-08-11T20:14:31 | 2023-08-24T05:23:05 | 2023-08-24T05:22:09 | CONTRIBUTOR | null | {
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This PR adds a python script under Tools for modeling the call arrival process as a cluster point process. | {
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"Our initial design involves each Recorder class containing a variable table. However, issue 240 highlights that each variable has a temporal resolution, with some requiring updates every time step, while others may update less frequently, such as once per epoch. Additionally, a set of constants, such as neuron typ... | 2023-08-11T18:47:39 | 2024-04-24T06:36:10 | 2024-04-24T06:31:31 | CONTRIBUTOR | null | {
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"Create a RecordableConstant as the subclass of RecordableBase to record constant variable. \r\nThe class diagram is here [Link is here](https://github.com/UWB-Biocomputing/Graphitti/blob/8f5100c66cef39361506b21c765334f33f269ec0/docs/Developer/ClassDiagrams/recordable.puml#L13-L20)",
"For X, Y Location, in the ex... | 2023-08-11T18:43:36 | 2025-02-23T08:52:57 | 2025-02-23T08:52:57 | CONTRIBUTOR | null | {
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This issue it a sub-issue of 240
This issue involves adding an interface to the XmlRecorder so that it can record constant variables, such as X and Y location. These constant variables only need to be recorded once because these value do not change as the simulation runs. | {
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} | null | Create a recordable template for EventBuffer class and modify the code in the XmlRecorder
Currently, the EventBuffer only stores uint64_t data, but there is a need for the simulator to store other types of data such as double, To solve this problem, we need to create a recordable template for the EventBuffer class and modify the code in the XmlRecorder so that it can work with Recordable. | {
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"Done; we're using it."
] | 2023-08-11T18:02:12 | 2025-01-22T17:55:12 | 2025-01-22T17:55:10 | CONTRIBUTOR | null | {
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"Moot, given move to personal development branches."
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} | null | The graphml containing the Seattle PD PSAP graph was extracted from the King county 911 network graph. The King county graph was in turn generated using the Geographic Information System (GIS) files provided by our contacts at Washington State 911 Coordination Office.
The GIS files used for generating the graph are based on service/jurisdictional boundaries for the PSAP and Responder entities. Due to many service boundaries not being contiguous, the generated graph appears to have more responder vertices than there are in reality. For instance, the Seattle Fire Department has 41 locations some of which provide EMS only service, Fire only services, or both; but when examining the generated graph, it contains 55 Seattle FD EMS nodes and 55 Seattle FD Fire nodes. This is consistent with the Fire and EMS layers provided in the GIS files but does not correspond to the location of the Fire Stations nor with the services provided (EMS or Fire).
A more accurate approach would be to use the locations and service type provided by the [Seattle Fire Department website](https://www.seattle.gov/fire/about-us/fire-stations). The [wikipedia page for Seattle FD](https://en.wikipedia.org/wiki/Seattle_Fire_Department) also contains information about each of the stations' location and their units.
Similarly, the location of the Seattle PD stations can be obtained from [their website](https://www.seattle.gov/police/about-us/police-locations).
This can be a tedious work if we have a large network. It would be great if we can find a central source for this data. | {
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"Closing PR because I accidentally opened it against the `master` branch instead of `development`."
] | 2023-08-08T06:07:01 | 2023-08-11T20:12:58 | 2023-08-11T20:12:58 | CONTRIBUTOR | null | {
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This PR adds a python script under `Tools` for modeling the call arrival process as a cluster point process. | {
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"This branch is pretty outdated, I made a new branch and am revisiting the changes. I think this PR should be closed and a new one should be made."
] | 2023-08-08T00:30:01 | 2024-12-20T21:38:32 | 2023-12-20T20:16:07 | CONTRIBUTOR | null | {
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This PR adds creates new conditional compilation switch for Testing in CMakeLists.txt file | {
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"We need to manually check the GPU version of the simulator.",
"Closing PR as per the findings mentioned in issue #513 "
] | 2023-08-07T23:08:19 | 2023-08-29T22:29:23 | 2023-08-29T22:29:17 | COLLABORATOR | null | {
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This PR transforms `summationPoint_` into a vector of indexes, which can then be serialized and deserialized using the standard serialization methods provided by the Cereal Library.
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"Should have been closed by PR."
] | 2023-08-04T16:24:22 | 2023-11-06T23:41:57 | 2023-11-06T23:41:56 | CONTRIBUTOR | null | {
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} | null | The GraphML files have vertex locations and caller regions (in latitude and longitude); the information should be sufficient to generate a pixelated cartogram image. See Alex Neary's capstone materials in Google Drive: Readings/Lab Publications/Internal.
Likely, this will just be Python code in the Tools subdirectory. | {
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"I took care of the requested changes to attempt merging this PR."
] | 2023-08-02T00:50:12 | 2024-06-03T06:45:11 | 2024-06-03T06:42:15 | CONTRIBUTOR | null | {
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- Updates the command line option in the documentation under Student Quickstart
- Adds command line option in the documentation under Quickstart | {
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"I am facing the issue of modeling the responders' travel time and response time. Specifically, I need to figure out what kind of probability distributions are good fits and then do parameter fitting; for which data is needed.\r\n\r\nThis is a good research paper on travel time distribution: [Analyzing travel time ... | 2023-07-28T07:25:00 | 2023-11-07T02:28:24 | 2023-11-07T02:28:24 | CONTRIBUTOR | null | {
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- Responder travel time
- Responder response time
- Dispatch queue
- Units availability | {
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} | null | We need to implement the responder dispatch logic. The responder that is available, appropriate for, and closest to the emergency event is the one that is dispatched.
In order to implement this we need to model the emergency call types, in addition to time and location. Obtaining 911 data to link the calls to the emergency event types is proving more difficult than originally thought. | {
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} | null | We will model call abandonment using a patience parameter as used in the Erlang A queuing model. The following is a general description of the process as presented in the literature.
Gans et al. (2003) used the Erlang A queuing model to demonstrate that call abandonment in heavily loaded call centers significantly affects system performance. Abandonment is modeled through a `patience` parameter which is an exponentially distributed random variable with an abandonment rate θ (average patience of 1/θ).
Mandelbaum and Zeltyn (2005) suggest two methods for estimating the average patience (1/θ). The practical approach for the 911 model is to calculate the abandonment rate with the following formula:
`θ = %Abandonment / Average Wait`
Each call gets an exponentially distributed patience time. If the call has not been picked up once its patience runs out, the customer abandons the waiting queue.
References:
Gans, N., Koole, G., & Mandelbaum, A. (2003). Telephone Call Centers: Tutorial, Review, and Research Prospects. Manufacturing & Service Operations Management, 5(2), 79–141. https://doi.org/10.1287/msom.5.2.79.16071
Mandelbaum, A., & Zeltyn, S. (2007). Service Engineering in Action: The Palm/Erlang-A Queue, with Applications to Call Centers. In D. Spath & K.-P. Fähnrich (Eds.), Advances in Services Innovations (pp. 17–45). Springer. https://doi.org/10.1007/978-3-540-29860-1_2
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"Had trouble with comment indentation but it should be good now."
] | 2023-07-27T21:23:56 | 2023-08-07T23:54:43 | 2023-08-07T23:54:37 | CONTRIBUTOR | null | {
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This PR checks to make sure switches on edgeType and makes sure they have default cases, with the ability to expand with throwing exceptions in the future if the switches return 0. In principle, return 0 in switch case if error. | {
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"@KamathScience, as per our conversation this evening I looked into removing the `summation_map` from the NG911 model. The following is what I found:\r\n\r\nThe addEdge method in `AllEdges.cpp` assumes that all models would have a `summation_point` by requiring it in the method's signature. This is the reason it is... | 2023-07-26T23:42:57 | 2023-07-27T06:42:51 | null | CONTRIBUTOR | null | {
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} | null | This is a partial implementation of the 911 event queueing model. Most of the logic for the PSAP and Caller Region vertices have been implemented and `TODO` labels were added for the parts not yet implemented. Merging this branch will help divide the complete implementation into small bits (pun intended). I will create issues for all the TODOs in the comments.
The current recorder class was hacked together using some generic helper functions that I implemented in `global.h`. I expect this to be temporary until the recorded classes get refactored.
The config file that I am using for testing is `test-spd-911.xml` (for Seattle PD). Besides the config file, the 911 model requires a graphml file and the list of calls as an input file for the `test-spd-911.xml` simulation those files are `graphs\spd.graphml` (graph) and `inputs\SPD_calls.xml` (calls). The input file was created using one month of actual 911 calls received by Seattle PD PSAP during September 2020. | {
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This PR adds a pre-run check to ensure the provided serialization file path is writable before executing the simulator. | {
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Added top-level page for oxygen documentation
Added links to Graphitti landing page for testing section, fixed Code of Conduct link
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"After testing on Raiju Machine:\r\nCPU: Minimal difference\r\nGPU: Around 3 seconds faster with -j enabled"
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This PR adds:
Added "make -j" to line 18 on README.md
Added line 28 on tests.yml "run: make -j" for GitHub Actions Workflow file, noticed a 2ms time difference on raiju ./tests run with -j option enabled on GPU.
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} | null | This problem corresponds to a subtask aimed at resolving Issue 240.
In the initial/first step, we focuses on migrating the variable registration functionality from the Recorder class to the appropriate variable owner classes. Currently, we enabled the XmlRecorder to record all events for a single neuron using the EventBuffer data structure. Now we want it records all events for all neurons.
In this issue, our main concern is still with the XmlRecorder. | {
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"Andrzej Dawiec went from Graduate to Undergradate section"
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This PR Revises Contributors.md and adds Andrzej Dawiec to Undergraduate section | {
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"Merged into master"
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As a part of the onboarding task add Andrzej Dawiec to the Contributors list of Graphitti. Revised from graduate to undergraduate.
#### Files Contributors.md | {
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"I will add onto the contributing guide. ",
"Some notes:\r\n\r\n- [GitFlow article](https://datasift.github.io/gitflow/IntroducingGitFlow.html)\r\n- Need to update CONTRIBUTING.md\r\n- Should redraw diagrams, rather than copy them, so look into #501 "
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"Currently checking unit + regression tests"
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Closes #121
Closes #431
This PR documents the following:
1. Details on how to write unit tests when dealing with a Singleton Class
2. Useful Visual Studio Code extensions
3. Github etiquette
4. Update the PlantUML diagram
5. Document the `help` command line option of Graphitti
6. C++ design decisions on `override` keywords, `return-reference` from getter methods, and using `=default` & `=delete` notation
7. Minor spelling errors
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"Done check #475 for revision"
] | 2023-06-26T19:32:54 | 2023-06-27T18:45:49 | 2023-06-27T18:45:38 | CONTRIBUTOR | null | {
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As a part of the onboarding task add Andrzej Dawiec to the Contributors list of Graphitti.
#### Files:
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"> Can merge now, or we can add years for some of the students (I can search for them).\r\n\r\nSure I can wait"
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This PR adds the Contributors.txt file with all students' names.
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"Resolved on PR #505"
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A spatiotemporal cluster point process provides a reasonable framework for modeling call arrivals. Therefore, we will script the generation of calls into a .xml file using this framework. | {
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Removes the extra level in the Connections parameter node from the XML config file because it is not needed. | {
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Refactored the documentation to hopefully improve readability.
had to make another pr because too many broken files in other one. | {
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Graphitti, being a collaborative project managed on GitHub, would benefit from having an onboarding task for new joiners. This task aims to enhance their familiarity with Graphitti's GitHub environment. Currently, the proposed task involves adding new contributors' names to the contributor.txt file located in the Graphitti repository.
### Tasks
01. Create an Onboarding guide describing all the instructions
02. Create a Contributors.txt file in Graphitti | {
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"This will likely also involve modifying our `cmake` configuration files.",
"Also, would be good to do some before/after performance measurement on raiju and otachi.",
"Just finished, see pull request but results are as follows on Raiju machine:\r\n\r\nGoogle unit tests: around 2ms faster\r\nCPU Test: Minimal D... | 2023-06-14T00:23:07 | 2023-08-03T19:07:35 | 2023-08-03T19:07:35 | COLLABORATOR | null | {
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The `-j` option in the `make` command allows users to control the number of simultaneous jobs executed by `make`, thereby improving the build process efficiency of Graphitti by leveraging multiple processors or cores on the system.
#### Usage
To utilize the `-j` option, append it to the `make` command. If the specific number of jobs is not mentioned, `make` will utilize all available cores on the system.
`make -j`
#### Task
01. Update the Graphitti Documentation
02. Add `-j` to the GitHub Actions workflow file; for faster testing | {
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Currently, Graphitti utilizes a dynamically allocated bool array `inUse_` in AllEdges to store boolean values.
` unique_ptr<bool[]> inUse_;`
However, Cereal Library does not serialize or deserialize dynamically allocated arrays. So, an alternative option considered was using a vector of bool, which provides a compact representation using a single bit per element to conserve memory. However, this representation is not suitable when transferring the data to the GPU, as the GPU expects boolean values in the form of true or false rather than compact 0s and 1s.
To address this issue, a potential solution is to convert the `inUse_` to vectors of int or unsigned char. This conversion would allow for a compatible data representation that can be serialized using Cereal Libray and data can be transferred to the GPU. | {
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"Closing this issue as per the findings mentioned in issue #513 "
] | 2023-06-12T17:22:56 | 2023-08-29T22:28:15 | 2023-08-29T22:28:15 | COLLABORATOR | null | {
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The `summationPoint_` member variable is currently a vector of raw pointers in the `AllEdges` base class. `summationPoint_` stores several addresses of indexes from the `summationMap_`.
` vector<BGFLOAT *> summationPoint_;`
However, the Cereal Library does not serialize raw pointers directly. To address this issue, we have two options for serializing `summationPoint_`:
01. Exclude `summationPoint_` during serialization and recompute it after all classes have been deserialized.
02. Transform `summationPoint_` into a vector of indexes, which can then be serialized and deserialized using the standard serialization methods provided by the Cereal Library.
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Graphitti currently has two unit tests that ensure error-free serialization and deserialization processes. However, in order to further improve the reliability of these unit tests, it is essential to verify that the obtained serialized output precisely matches the expected deserialized output.
### Task
One approach could be to deserialize a file, followed by serializing it back to its original format. The idea is we can then compare the resulting serialized file with the initial one to determine if they are identical. This approach can be a validation mechanism, confirming the accuracy of the serialization process. | null | {
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- Added 3 tables to the performance.md : Initialization, Access and Sum, and Random Access and Sum.
- If you prefer a different format or have any specific requirements, please let me know. | {
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"added presentation to google drive"
] | 2023-06-05T17:47:31 | 2023-08-29T21:36:47 | 2023-08-29T21:36:46 | CONTRIBUTOR | null | {
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> Computational neuroscientists have developed a diversity of software platforms for simulating neural network models at different scales. However, each simulator has its own programming or configuration language, leading to considerable difficulty in porting models from one simulator to another. A common programming interface to multiple simulators would help to reduce or eliminate the problems of simulator diversity while retaining the benefits. PyNN is such an interface, making it possible to write a simulation script once, using the Python programming language, and run it without modification on any supported simulator (currently including NEURON, NEST, Brian, and the SpiNNaker and BrainScaleS neuromorphic hardware systems). | {
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"> Hi @stiber, I would like to work on this issue\r\n\r\nThanks for contacting us! If you think you can follow what's written there, then feel free to do so. Please fork the repo and make the change off of the master branch. See our contributing guide for more inf... | 2023-06-02T18:21:20 | 2023-06-06T17:42:23 | 2023-06-06T17:42:23 | CONTRIBUTOR | null | {
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"> Not sure if you're ready to merge quite yet. Re-request my review as needed. When you've done enough manual testing (or updated the regression tests) and are ready to merge, let me know explicitly and I will override the block due to not all tests passing, if needed.\r\n\r\nIt is not ready to merge. I discussed ... | 2023-05-31T06:12:48 | 2023-08-03T06:22:25 | 2023-08-02T00:00:05 | CONTRIBUTOR | null | {
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} | null | Fixes Issue #452
1.Remove all concrete classes in the XML Recorder except for the XmlRecorder class.
2. Change the recorder name to XmlRecorder in the related config files
3. Refactor the XmlRecorder class. Currently, this class only records Eventbuffer variable and it stores all events of a single neuron (neuron 7).
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} | null | Issue 240 involves the reengineering of the recorder class in a step-by-step manner. The initial step focuses on migrating the variable registration functionality from the Recorder class to the appropriate variable owner classes.
In this issue, our main concern is with the XmlRecorder, specifically enabling it to record all events for a single neuron using the EventBuffer data structure.
To address this issue, the following tasks need to be completed:
1. Remove all concrete classes in the XML Recorder, such as XmlGrowthRecorder and XmlSTDPRecorder, except for the XmlRecorder class. Additionally, remove any code within the project that calls these removed XML recorder classes.
2. Modify certain input files in the "configfiles" folder to specify the XmlRecorder class as the desired class name in those files.
3. Identify the classes that will serve as the owners of the variables, particularly those implementing EventBuffer variables. In this case, the AllSpikingNeurons class is the only class with an EventBuffer variable called vertexEvent_, which stores events for a neuron. Therefore, only the AllSpikingNeurons class need to register EventBuffer variables.
4. Refactor the XmlRecorder class from scratch. The EventBuffer data structure will store all the events for a neuron within the current Epoch. The XML Recorder will store the address of an EventBuffer variable in its owner class. As the simulator runs, the values in the EventBuffer will be updated, and all values in the EventBuffer vector will be outputted to a destination file. Consider the specific scenario of a single EventBuffer associated with a random neuron ( such as neuron = 7) and modify the XmlRecorder class accordingly. | {
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Refactored the documentation to hopefully improve readability. | {
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Currently, Graphitti utilizes generic CUDA functions for GPU operations. This issue suggests exploring the possibility of using [Thrust](https://docs.nvidia.com/cuda/thrust/index.html) CUDA library for GPU optimization. As per their official website, Thrust provides a higher-level interface and optimized algorithms for common GPU tasks, simplifying code maintenance.
See also issue #308.
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Moved subcategories around in the testing, user, and developer documentation categories.
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This PR replaces the usage of `resize` followed by `assign` with a single call to `assign` to initialize a vector with default values. This simplifies the code and makes it more efficient by eliminating the need to resize the vector and then fill in the default values separately.
The changes have been tested on the CPU and GPU with the medium config file.
Thanks @jardiamj for raising this issue | {
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} | null | ### Description
Currently, the vector resizing operation in Graphitti is being performed using the resize function followed by the assign function to set new values to its elements. This approach results in unnecessary reallocation of memory when the vector is resized. A better system would use the assign function as it resizes the vector and sets its elements to new values in a single step, without incurring extra memory allocations.
### Task
Remove the resize method of vector and just use assign. | {
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"Technically, we're returning a reference to the object, not a reference to the unique_ptr, right?",
"> Technically, we're returning a reference to the object, not a reference to the unique_ptr, right?\r\n\r\nYes, wrong choice of words! Corrected to say returns a reference to the object."
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Change the getter methods of AllVertices, AllEdges, Model, Layout, Connections, and Recorder to return a reference of the object than a raw pointer. | {
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check the output file extension for Hdf5 Recorders and XML Recorders | {
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Replaced `typedef` with the `using` keyword in the Graphitti codebase as it provides a more consistent syntax with the rest of the code and works well with templates. | {
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"Looks like things are shaping up nicely! When you feel like this is ready for prime time, let's solicit feedback from the lab members.",
"Fixes Issue #442 ",
"going to make new pr"
] | 2023-04-19T21:38:27 | 2023-05-10T02:12:13 | 2023-05-10T02:12:12 | CONTRIBUTOR | null | {
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Moved student quickstart under user documentation
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"I think one more file waiting (see unresolved conversation).",
"It seems that this PR is failing our style check. If it isn't obvious what the issues are, you might try running a recent version of `clang-format` to generate a reformatted version of the file(s) in question, and then do a `diff` to see what it's u... | 2023-04-12T00:46:40 | 2023-05-11T21:27:48 | 2023-05-11T21:27:48 | CONTRIBUTOR | null | {
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Following changes made in .h files present in Simulator:
1. Added #pragma once if missing
2. Removed #ifndef if required
3. Removed extra tab for the indentation if required | {
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} | null | C++ 11 introduced the `override` specifier which is used to explicitly indicate that a member function of a derived class is intended to override a virtual function from its base class.
There are multiple benefits of adding `override` specifier to our Graphitti codebase:
1. Improves code readability- The function that's meant to override from the base class is made very clear to the reader.
2. Enforces compiler checks- When a function is marked with `override`, the compiler will check whether the function is actually overriding a virtual function in the base class, providing an additional check.
3. Improve maintainability- When changes are made to the base class, `override` ensures that the derived classes are still correctly overriding the virtual functions.
Actions:
1. Add `override` specifier to all the derived classes where required.
2. Document the `override` feature in coding & cpp standards.
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Removed #ifndef.
Changes:
1. Removed line number 11,12 and 199
2. Removed extra tab for the indentation (line number 12 to 53) | {
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"Note that this requires a thorough audit of all of our `.h` files so that they are all fixed."
] | 2023-04-06T22:58:33 | 2023-05-11T21:27:49 | 2023-05-11T21:27:49 | COLLABORATOR | null | {
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} | null | A few files like `Global.h` have both `#pragma once` and `#ifdef` directives defined in the same file. Both these directives are intended to prevent multiple inclusions of header files. As per C++ standard `#pragma once` is usually sufficient to prevent multiple inclusions by itself. However, we must aim to clean these and keep which serves best based on the use case. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/426 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/426/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/426/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/426/events | https://github.com/UWB-Biocomputing/Graphitti/issues/426 | 1,656,491,802 | I_kwDOEEdqD85ivA8a | 426 | Make recording member variables private or protected | {
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"I've been giving this a little bit of thought. If the `Recorder` method that is used to register variables for recording takes them by reference, and those references are saved, then the `Recorder` class doesn't need to be a `friend` and can still access and modify private variables. Conceptually, this is because ... | 2023-04-06T00:24:58 | 2023-04-06T20:10:38 | null | COLLABORATOR | null | {
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} | null | Currently, we see that a few member variables in different classes in the Graphitti codebase are made public so that the recorder class can access them. We must think about how we can make these member variables compatible with recording variables while avoiding making them public.
Reference: [Google Style Guide-Access Control](https://google.github.io/styleguide/cppguide.html#Access_Control) | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/425 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/425/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/425/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/425/events | https://github.com/UWB-Biocomputing/Graphitti/issues/425 | 1,656,437,928 | I_kwDOEEdqD85iuzyo | 425 | Add Namespaces to Graphitti | {
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} | null | Namespaces subdivide the global scope into distinct, named scopes, and so are useful for preventing name collisions in the global scope. We should consider placing the Graphitti codebase in namespaces to prevent name conflicts in the program while allowing most code to use reasonably short names.
More about namespaces in [Google Style Guide - Namespaces](https://google.github.io/styleguide/cppguide.html#Namespaces) | null | {
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