pentapy

pentapy: A Python toolbox for pentadiagonal linear systems - Published in JOSS (2019)

https://github.com/geostat-framework/pentapy

Science Score: 100.0%

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DOI references
Found 11 DOI reference(s) in README and JOSS metadata
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Links to: joss.theoj.org, zenodo.org
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

linear-algebra linear-systems math matrix pentadiagonal-linear-systems python solvers toolbox

Last synced: 4 months ago · JSON representation ·

Repository

A Python toolbox for pentadiagonal linear systems

Basic Info

Host: GitHub
Owner: GeoStat-Framework
License: mit
Language: Python
Default Branch: main
Homepage: https://pentapy.readthedocs.io/
Size: 346 KB

Statistics

Stars: 14
Watchers: 1
Forks: 4
Open Issues: 5
Releases: 17

Topics

linear-algebra linear-systems math matrix pentadiagonal-linear-systems python solvers toolbox

Created almost 7 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Citation Zenodo

Welcome to pentapy

pentapy-LOGO

Purpose

pentapy is a toolbox to deal with pentadiagonal matrices in Python.

Pentadiagonal linear equation systems arise in many areas of science and engineering: e.g. when solving differential equations, in interpolation problems, or in numerical schemes like finite difference.

Installation

The package can be installed via pip. On Windows you can install WinPython to get Python and pip running.

pip install pentapy

There are pre-built wheels for Linux, MacOS and Windows for most Python versions.

To get the scipy solvers running, you have to install scipy or you can use the following extra argument:

pip install pentapy[all]

Instead of "all" you can also typ "scipy" or "umfpack" to get one of these specific packages.

Citation

If you use pentapy in your publication, please cite it:

Müller, (2019). pentapy: A Python toolbox for pentadiagonal linear systems. Journal of Open Source Software, 4(42), 1759, https://doi.org/10.21105/joss.01759

To cite a certain release, have a look at the Zenodo site: https://doi.org/10.5281/zenodo.2587158

References

The solver is based on the algorithms PTRANS-I and PTRANS-II presented by Askar et al. 2015.

Documentation and Examples

You can find the documentation under https://pentapy.readthedocs.org.

Solving a pentadiagonal linear equation system

This is an example of how to solve a LES with a pentadiagonal matrix.

```python import numpy as np import pentapy as pp

size = 1000

create a flattened pentadiagonal matrix

M_flat = (np.random.random((5, size)) - 0.5) * 1e-5 V = np.random.random(size) * 1e5

solve the LES with M_flat as row-wise flattened matrix

X = pp.solve(Mflat, V, isflat=True)

create the corresponding matrix for checking

M = pp.createfull(Mflat, col_wise=False)

calculate the error

print(np.max(np.abs(np.dot(M, X) - V))) ```

This should give something like: python 4.257890395820141e-08

Performance

In the following a couple of solvers for pentadiagonal systems are compared:

Solver 1: Standard linear algebra solver of Numpy np.linalg.solve
Solver 2: scipy.sparse.linalg.spsolve
Solver 3: Scipy banded solver scipy.linalg.solve_banded
Solver 4: pentapy.solve with solver=1
Solver 5: pentapy.solve with solver=2

Performance

The implementations of pentapy are almost one order of magnitude faster than the scipy algorithms for banded or sparse matrices.

The performance plot was created with perfplot. Have a look at the script: examples/03_perform_simple.py.

Requirements:

NumPy >= 1.14.5

Optional

Contact

You can contact us via info@geostat-framework.org.

License

Owner

Name: GeoStat Framework
Login: GeoStat-Framework
Kind: organization
Email: info@geostat-framework.org
Location: UFZ Leipzig

Website: https://geostat-framework.org
Twitter: GSFramework
Repositories: 7
Profile: https://github.com/GeoStat-Framework

Python framework for geostatistical simulations

JOSS Publication

pentapy: A Python toolbox for pentadiagonal linear systems

Published

October 08, 2019

DOI

10.21105/joss.01759

Volume 4, Issue 42, Page 1759

Authors

Sebastian Müller

Department of Computational Hydrosystems, UFZ -- Helmholtz Centre for Environmental Research, Leipzig, Germany, Institute of Earth and Environmental Sciences, University Potsdam, Potsdam, Germany

Editor

Vincent Knight

Citation (CITATION.bib)

@Article{muller_pentapy_2019,
AUTHOR = {M\"uller, Sebastian},
TITLE = {pentapy: {A} {Python} toolbox for pentadiagonal linear systems},
SHORTTITLE = {pentapy},
JOURNAL = {Journal of Open Source Software},
VOLUME = {4},
YEAR = {2019},
NUMBER = {42},
PAGES = {1759},
URL = {https://joss.theoj.org/papers/10.21105/joss.01759},
DOI = {10.21105/joss.01759},
ISSN = {2475-9066},
}

GitHub Events

Total

Create event: 2
Release event: 1
Issues event: 2
Delete event: 1
Issue comment event: 5
Push event: 3
Pull request event: 1

Last Year

Create event: 2
Release event: 1
Issues event: 2
Delete event: 1
Issue comment event: 5
Push event: 3
Pull request event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 154
Total Committers: 3
Avg Commits per committer: 51.333
Development Distribution Score (DDS): 0.026

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
MuellerSeb	m**b@p**e	150
Lorena A. Barba	l**a@g**u	3
derb12	5****2	1

Committer Domains (Top 20 + Academic)

gwu.edu: 1 posteo.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 15
Total pull requests: 14
Average time to close issues: 7 months
Average time to close pull requests: 22 days
Total issue authors: 6
Total pull request authors: 5
Average comments per issue: 1.87
Average comments per pull request: 1.07
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 0
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: 4 months
Issue authors: 0
Pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 1

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Top Authors

Issue Authors

MuellerSeb (6)
MothNik (5)
derb12 (1)
virgesmith (1)
joglekara (1)
inakleinbottle (1)

Pull Request Authors

MuellerSeb (7)
MothNik (4)
labarba (3)
dependabot[bot] (2)
derb12 (1)

Top Labels

Issue Labels

enhancement (5) dependencies (2)

Pull Request Labels

enhancement (6) dependencies (4)

Packages

Total packages: 2
Total downloads:
- pypi 5,027 last-month

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 20
Total maintainers: 3

pypi.org: pentapy

pentapy: A toolbox for pentadiagonal matrizes.

Homepage: https://github.com/GeoStat-Framework/pentapy
Documentation: https://pentapy.readthedocs.io
License: MIT
Latest release: 1.4.0
published 8 months ago

Versions: 17
Dependent Packages: 2
Dependent Repositories: 2
Downloads: 5,027 Last month

Rankings

Dependent packages count: 3.2%

Downloads: 7.7%

Average: 11.1%

Dependent repos count: 11.5%

Stargazers count: 16.1%

Forks count: 16.9%

Maintainers (3)

geostatframework sebastian.mueller LSchueler

Last synced: 4 months ago

conda-forge.org: pentapy

Homepage: https://github.com/GeoStat-Framework/pentapy
License: MIT
Latest release: 1.1.2
published over 3 years ago

Versions: 3
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent packages count: 28.8%

Dependent repos count: 34.0%

Average: 41.3%

Stargazers count: 50.9%

Forks count: 51.6%

Last synced: 4 months ago

Dependencies

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/download-artifact v2 composite
actions/setup-python v2 composite
actions/upload-artifact v2 composite
pypa/cibuildwheel v2.12.1 composite
pypa/gh-action-pypi-publish release/v1 composite

pyproject.toml pypi

numpy >=1.14.5

setup.py pypi

pentapy

Science Score: 100.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Welcome to pentapy

Purpose

Installation

Citation

References

Documentation and Examples

Solving a pentadiagonal linear equation system

create a flattened pentadiagonal matrix

solve the LES with M_flat as row-wise flattened matrix

create the corresponding matrix for checking

calculate the error

Performance

Requirements:

Optional

Contact

License

Owner

JOSS Publication

pentapy: A Python toolbox for pentadiagonal linear systems

Authors

Editor

Tags

Citation (CITATION.bib)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

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Committer Domains (Top 20 + Academic)

Issues and Pull Requests

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Past Year

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Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pentapy

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Maintainers (3)

conda-forge.org: pentapy

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Dependencies