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https://github.com/ScottKolo/suitesparse-matrix-collection-website
A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection
https://github.com/ScottKolo/suitesparse-matrix-collection-website
Last synced: 5 days ago
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A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection
- Host: GitHub
- URL: https://github.com/ScottKolo/suitesparse-matrix-collection-website
- Owner: ScottKolo
- License: mit
- Created: 2015-09-08T22:58:14.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2024-08-02T01:57:04.000Z (3 months ago)
- Last Synced: 2024-08-02T12:49:07.218Z (3 months ago)
- Language: Ruby
- Homepage:
- Size: 341 MB
- Stars: 21
- Watchers: 9
- Forks: 6
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codemeta: codemeta.json
Awesome Lists containing this project
- awesome-starred - ScottKolo/suitesparse-matrix-collection-website - A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection (others)
README
# SuiteSparse Matrix Collection
[](https://scottkolo.semaphoreci.com/projects/suitesparse-matrix-collection-website) [](https://codeclimate.com/github/ScottKolo/suitesparse-matrix-collection-website) [](https://codeclimate.com/github/ScottKolo/suitesparse-matrix-collection-website/coverage) [](https://codeclimate.com/github/ScottKolo/suitesparse-matrix-collection-website) [](http://joss.theoj.org/papers/965b1c7bba801c85e9341a3db9013ef8)
A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection. It is currently deployed at [https://sparse.tamu.edu](https://sparse.tamu.edu).
## Features and Functionality
The SuiteSparse Matrix Collection web application provides a variety of features to help the scientific computing community access the Collection more easily.
### Matrix Property Search, Sorting, and Filtering
The SuiteSparse Matrix Collection web application allows real-time filtering by the following matrix properties:
#### Matrix Size and Shape
- **Rows** - The number of rows in the matrix.
- **Columns** - The number of columns in the matrix.
- **Nonzeros** - The number of nonzero entries in the matrix.
#### Matrix Structure and Entry Type
- **Pattern symmetry** - The percent of entries that are mirrored across the matrix diagonal. The numeric value of the entries is irrelevant.
- **Numerical symmetry** - The percent of entries that are mirrored across the matrix diagonal with the identical numeric value.
- **Number of strongly connected components** - The number of strongly connected components present in the resulting graph of this sparse matrix.
- **Rutherford-Boeing type** - The type of entry in the sparse matrix. One of either Real, Complex, Integer, or Binary.
- **Structure** - Special matrix structure, including square, rectangular, symmetric, skew-symmetric, Hermitian, and unsymmetric.
- **Positive definiteness**
#### Matrix Metadata
- **Matrix name** - The specific name of the matrix.
- **Matrix group** - The group name the matrix belongs to.
- **Matrix ID** - The numeric identification number of the matrix.
- **Matrix Year** - The year the matrix was added to the Collection.
Additionally, matrix details are displayed on each matrix's individual page, including the matrix's rank, condition number, and information regarding its singular value decomposition. A variety of visualizations are also presented, including sparsity patterns, force-directed graph (or bipartite graph) visualizations (courtesy of Yifan Hu), Dulmage-Mendelsohn permuted sparsity patterns, and singular values plotted in decreasing size.
### Quick Access via URL Routing
Matrices can also be quickly accessed by URL route matching using the following URL routes:
* **Group name** and **matrix name** to go directly to a matrix page
* `https://sparse.tamu.edu//`
* [https://sparse.tamu.edu/HB/west0479](https://sparse.tamu.edu/HB/west0479)
* **Matrix ID number** to go directly to a matrix page
* `https://sparse.tamu.edu/`
* [https://sparse.tamu.edu/1230](https://sparse.tamu.edu/1230) redirects to [https://sparse.tamu.edu/GHS_indef/copter2](https://sparse.tamu.edu/GHS_indef/copter2)
* **Group name** to go directly to a group information page
* `https://sparse.tamu.edu/`
* [https://sparse.tamu.edu/Mycielski](https://sparse.tamu.edu/Mycielski)
## Other Interfaces to the Collection
For more information about interfaces to the Collection, see the [Interfaces](https://sparse.tamu.edu/interfaces) page.
## Bugs and Feature Requests
Find a problem with the website? Report it as an [Issue](https://github.com/ScottKolo/suitesparse-matrix-collection-website/issues), or suggest a fix via a [Pull Request](https://github.com/ScottKolo/suitesparse-matrix-collection-website/pulls).
## Building Locally
While the canonical deployment can be found at [https://sparse.tamu.edu](https://sparse.tamu.edu), you may wish to deploy a version of the SuiteSparse Matrix Collection website locally for testing or convenience.
The only dependencies for running the application are listed below. They can be installed using your package manager (like `apt-get` or `yum` for Linux or `brew` for macOS):
* Ruby 2.7.1 or later
* PostgreSQL 9.3 or later (and permissions to create a database)
* A JavaScript runtime environment such as node.js 12.17.0 or later
Many operating systems come with Ruby installed, and you can check which
version you have with `ruby -v`. If no Ruby installation is found, or the
version is incorrect, you can use your package manager to install a compatible
version (see [ruby-lang.org](https://www.ruby-lang.org) for more information
regarding obtaining and installing Ruby). You may also find Ruby Version
Manager ([rvm.io](https://rvm.io)) to be helpful if you need to maintain
multiple versions of Ruby.
Installing PostgreSQL and node.js also varies greatly from system to system. For example, to install PostgreSQL and node.js (required by Rails) on Ubuntu 18, you can use the following commands:
```shell
sudo apt install postgresql postgresql-contrib libpq-dev nodejs
sudo -u postgres createuser -s $(whoami); createdb $(whoami)
```
Note that after installing PostgreSQL, one needs to start it up so it is running in the background. The status can be checked using `pg_isready`. If this fails, the installation can be started manually, e.g. via `pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start`, depending on the location of your installation. If PostgreSQL was installed from a package manager, post-install information is usually displayed about how to start the PostgreSQL daemon on your platform.
For running the test suite, the following additional dependencies are required:
* Firefox 46 or later
The application is a standard Ruby on Rails web application, and can be installed with the following commands:
```shell
ruby -v # Check that Ruby 2.7.1+ is installed
pg_isready # Check that PostgreSQL database is ready
git clone https://github.com/ScottKolo/suitesparse-matrix-collection-website.git
cd suitesparse-matrix-collection-website
gem install bundler # Dependency manager
bundle config set without 'development test'
bundle install # Download and install dependencies
bundle exec rails db:setup # Generate and seed the database
bundle exec rails server # Start the Ruby on Rails server application
```
Once the Rails server starts, you can navigate in a web browser to localhost:3000 to view the web application running locally.
## Test Suite
After building and running the application locally, you can run the test suite by running
```shell
bundle exec rake
```
This will run a variety of Cucumber, rspec, and Brakeman tests that ensure the backend and user interface frontend function correctly, and that no (obvious) security issues exist. It will also report test coverage, with a detailed report generated in the `/coverage` directory.
## Acknowledgements
This website was originally part of a Software Engineering course project. The original team members are listed below:
* [Scott Kolodziej](http://www.scottkolo.com) (current maintainer)
* [Read Sandström](https://parasol.tamu.edu/people/readamus/)
* [Mohsen Aznaveh](https://parasol.tamu.edu/people/aznaveh/)
* [Jarrett David](https://parasol.tamu.edu/people/jld6827/)
* [Matthew Bullock](https://parasol.tamu.edu/people/fourcow2/)
* Matthew Henderson
We would also like to thank [Dr. Jeff Huang](https://parasol.tamu.edu/~jeff/), who taught that Software Enigneering course and impressed upon us the importance of software engineering practices, such as test-driven development and Agile.
We also owe a significant debt to [Dr. Tim Davis](http://faculty.cse.tamu.edu/davis/) for his input and guidance, as well as for creating many of the tools (and the original website) that made this project possible.
## License
Overview: This website software (except for ssget) is under the MIT License.
The matrices themselves are under the CC-BY 4.0 License.
ssget (available in [SuiteSparse/ssget](https://github.com/DrTimothyAldenDavis/SuiteSparse)
in the ssget folder is under the BSD 3-clause License.
The matrices themselves are under the
[CC-BY 4.0 license](https://creativecommons.org/licenses/by/4.0/).
Note that this license asks you to cite the source of
the matrices. That citation can be made to these references:
* Kolodziej et al., (2019). The SuiteSparse Matrix Collection Website Interface.
Journal of Open Source Software, 4(35), 1244,
[DOI](https://doi.org/10.21105/joss.01244)
* Timothy A. Davis and Yifan Hu. 2011. The University of Florida sparse matrix
collection. ACM Trans. Math. Softw. 38, 1, Article 1 (November 2011), 25 pages.
[DOI](https://doi.org/10.1145/2049662.2049663)
You should also preserve the metadata in the matrices themselves, which
includes additional citations for specific matrices. For example, the
[LAW](http://sparse.tamu.edu/LAW) set of matrices (from the Laboratory for Web
Algorithmics, Universita degli Studi di Milano) includes specific instructions
on how to properly cite the matrices. See
[sparse.tamu.edu/LAW](http://sparse.tamu.edu/LAW) for details. For the Matrix
Market format, most of the metadata appears in the header of the *.mtx
themselves.
Ideally, if you redistribute the matrices in your own applications, you should
not change them at all. This is essential for repeatability of experiments
that rely on these matrices. Modification is permitted under the CC-BY 4.0
License, but that license requires you to state the modifications you make. If
you make any such modifications, please change the filename and matrix name to
indicate that it differs from the copy of the matrix from
[sparse.tamu.edu](http://sparse.tamu.edu). Carefully describe any
modifications you make.
Last update: Mar 14, 2022.