BridgeStan

BridgeStan: Efficient in-memory access to the methods of a Stan model - Published in JOSS (2023)

https://github.com/roualdes/bridgestan

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 7 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: arxiv.org, joss.theoj.org
✓
Committers with academic emails
4 of 13 committers (30.8%) from academic institutions
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Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

c cpp julia python r stan

Keywords from Contributors

meshing standardization pde interpretability closember ode pypy rating wavelets hydrology

Scientific Fields

Physics Physical Sciences - 40% confidence

Last synced: 4 months ago · JSON representation ·

Repository

BridgeStan provides efficient in-memory access through Python, Julia, and R to the methods of a Stan model.

Basic Info

Host: GitHub
Owner: roualdes
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://roualdes.github.io/bridgestan
Size: 6.91 MB

Statistics

Stars: 104
Watchers: 6
Forks: 12
Open Issues: 7
Releases: 17

Topics

c cpp julia python r stan

Created over 3 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Citation

BridgeStan

BridgeStan provides efficient in-memory access through Python, Julia, Rust, and R to the methods of a Stan model, including log densities, gradients, Hessians, and constraining and unconstraining transforms. The motivation was developing inference algorithms in higher-level languages for arbitrary Stan models.

Stan is a probabilistic programming language for coding statistical models. For an introduction to what can be coded in Stan, see the Stan User's Guide.

BridgeStan is currently shipping with Stan version 2.37.0

Documentation is available at https://roualdes.us/bridgestan/

Compatibility

BridgeStan has been tested with the following operating system and C++ compiler combinations.

Linux: Ubuntu 20.04 with gcc 9.4.0
Apple: Mac OS X 12.2 with Apple clang 11.0.3
Microsoft: Windows 10 with gcc MSYS2 5.3.0

Installing BridgeStan

Installing the core of BridgeStan is as simple as installing a C++ toolchain (libraries, compiler, and the make command), and downloading this repository. To download the latest development version, you can run

shell git clone --recurse-submodules https://github.com/roualdes/bridgestan.git

For a full guide on installing, configuring, and using BridgeStan, consult the documentation

Using BridgeStan

Compiling a Stan program

To compile the Stan model in test_models/multi/multi.stan to a binary shared object (.so file), use the following.

$ cd bridgestan $ make test_models/multi/multi_model.so

This will require internet access the first time you run it in order to download the appropriate Stan compiler for your platform into <bridgestan-dir>/bin/stanc[.exe]

Example programs

This repository includes examples of calling Stan through BridgeStan in Python, Julia, R, Rust, and C.

From Python: example.py
From Julia: example.jl
From R: example.r
From Rust: example.rs
From C: example.c

Examples of other functionality can be found in the test folder for each interface.

Software using BridgeStan

We are aware of the following projects using BridgeStan.

Julia

https://github.com/sethaxen/StanLogDensityProblems.jl
https://github.com/Julia-Tempering/Pigeons.jl
https://github.com/TuringLang/TuringBenchmarking.jl

Python

https://github.com/pymc-devs/nutpie (through Rust)
https://github.com/UoL-SignalProcessingGroup/retrospectr
https://github.com/UoL-SignalProcessingGroup/SMC-NUTS

R

https://github.com/JTorgander/hmc-sandbox
https://github.com/UCL/rmcmc
https://github.com/CerulloE1996/BayesMVP/

Other

https://github.com/xhep-lab/polystan

Research using BridgeStan

If you use BridgeStan in your research, please consider citing our JOSS paper and letting us know so we can list your project here.

Acknowledgements

The Julia and Python APIs were derived from the Stan Model Server API, which in turn was derived from ReddingStan.

Thanks to Sebastian Weber (GitHub @wds15) for enabling multi-threaded calls from Julia to a single Stan model instance.

Thanks to Adrian Seyboldt (GitHub @aseyboldt) for providing the Rust wrapper.

Owner

Name: Edward A. Roualdes
Login: roualdes
Kind: user
Location: Chico, CA
Company: CSU, Chico

Website: https://roualdes.us
Repositories: 41
Profile: https://github.com/roualdes

JOSS Publication

BridgeStan: Efficient in-memory access to the methods of a Stan model

Published

July 22, 2023

DOI

10.21105/joss.05236

Volume 8, Issue 87, Page 5236

Authors

Edward A. Roualdes

California State University, Chico

Brian Ward

Center for Computational Mathematics, Flatiron Institute

Bob Carpenter

Center for Computational Mathematics, Flatiron Institute

Adrian Seyboldt

PyMC Labs

Seth D. Axen

Cluster of Excellence Machine Learning: New Perspectives for Science, University of Tübingen

Editor

Nikoleta Glynatsi

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Roualdes
  given-names: Edward A.
  orcid: "https://orcid.org/0000-0002-8757-3463"
- family-names: Ward
  given-names: Brian
  orcid: "https://orcid.org/0000-0002-9841-3342"
- family-names: Carpenter
  given-names: Bob
  orcid: "https://orcid.org/0000-0002-2433-9688"
- family-names: Seyboldt
  given-names: Adrian
  orcid: "https://orcid.org/0000-0002-4239-4541"
- family-names: Axen
  given-names: Seth D.
  orcid: "https://orcid.org/0000-0003-3933-8247"
contact:
- family-names: Roualdes
  given-names: Edward A.
  orcid: "https://orcid.org/0000-0002-8757-3463"
doi: 10.5281/zenodo.7760173
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Roualdes
    given-names: Edward A.
    orcid: "https://orcid.org/0000-0002-8757-3463"
  - family-names: Ward
    given-names: Brian
    orcid: "https://orcid.org/0000-0002-9841-3342"
  - family-names: Carpenter
    given-names: Bob
    orcid: "https://orcid.org/0000-0002-2433-9688"
  - family-names: Seyboldt
    given-names: Adrian
    orcid: "https://orcid.org/0000-0002-4239-4541"
  - family-names: Axen
    given-names: Seth D.
    orcid: "https://orcid.org/0000-0003-3933-8247"
  date-published: 2023-07-22
  doi: 10.21105/joss.05236
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5236
  title: "BridgeStan: Efficient in-memory access to the methods of a
    Stan model"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05236"
  volume: 8
title: "`BridgeStan`: Efficient in-memory access to the methods of a
  Stan model"

GitHub Events

Total

Create event: 26
Commit comment event: 8
Release event: 3
Issues event: 17
Watch event: 13
Delete event: 28
Issue comment event: 57
Push event: 107
Pull request review event: 30
Pull request review comment event: 24
Pull request event: 55
Fork event: 1

Last Year

Create event: 26
Commit comment event: 8
Release event: 3
Issues event: 17
Watch event: 13
Delete event: 28
Issue comment event: 57
Push event: 107
Pull request review event: 30
Pull request review comment event: 24
Pull request event: 55
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 425
Total Committers: 13
Avg Commits per committer: 32.692
Development Distribution Score (DDS): 0.384

Past Year

Commits: 52
Committers: 4
Avg Commits per committer: 13.0
Development Distribution Score (DDS): 0.442

Top Committers

Name	Email	Commits
Brian Ward	b**d@f**g	262
dependabot[bot]	4****]	53
Edward A. Roualdes	e**s@c**u	38
Bob Carpenter	b**r@f**g	21
Bob Carpenter	c**p@a**m	21
github-actions[bot]	4****]	17
Adrian Seyboldt	a****t	4
Seth Axen	s**h@s**m	2
Marco Inacio	m@m****m	2
Jonah Gabry	j**y@g**m	2
Rok Češnovar	r**r@f**i	1
Alex Phillips	a**s@g**m	1
Mike Lawrence	m**c@g**m	1

Committer Domains (Top 20 + Academic)

flatironinstitute.org: 2 fri.uni-lj.si: 1 marcoinacio.com: 1 sethaxen.com: 1 alias-i.com: 1 csuchico.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 78
Total pull requests: 238
Average time to close issues: 24 days
Average time to close pull requests: 3 days
Total issue authors: 27
Total pull request authors: 10
Average comments per issue: 4.49
Average comments per pull request: 1.42
Merged pull requests: 218
Bot issues: 1
Bot pull requests: 86

Past Year

Issues: 10
Pull requests: 56
Average time to close issues: 13 days
Average time to close pull requests: 1 day
Issue authors: 6
Pull request authors: 3
Average comments per issue: 1.9
Average comments per pull request: 0.45
Merged pull requests: 48
Bot issues: 1
Bot pull requests: 30

View more stats

Top Authors

Issue Authors

roualdes (13)
WardBrian (12)
nsiccha (7)
aseyboldt (7)
bob-carpenter (7)
sethaxen (4)
avehtari (4)
goedman (3)
gil2rok (2)
YuFuOliver (2)
daslu (1)
alexandrebouchard (1)
fonnesbeck (1)
dependabot[bot] (1)
fredhu0514 (1)

Pull Request Authors

WardBrian (126)
dependabot[bot] (86)
aseyboldt (7)
roualdes (5)
bob-carpenter (4)
randommm (4)
sethaxen (3)
alecksphillips (1)
mike-lawrence (1)
jgabry (1)

Top Labels

Issue Labels

enhancement (10) question (7) c-api (5) python (4) cpp (4) good first issue (4) dependencies (4) documentation (3) windows (2) help wanted (2) julia (1) code-cleanup (1) rust (1) github_actions (1)

Pull Request Labels

dependencies (89) github_actions (67) documentation (30) julia (22) python (20) enhancement (18) cpp (18) rust (18) R-lang (17) code-cleanup (13) submodules (12) c-api (9) bug (4) windows (4) help wanted (1)

Packages

Total packages: 3
Total downloads:
- julia 10 total
- cargo 19,764 total
- pypi 549 last-month

Total dependent packages: 6
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 45
Total maintainers: 3

pypi.org: bridgestan

Access the methods of a Stan model in Python.

Homepage: https://github.com/roualdes/bridgestan
Documentation: https://bridgestan.readthedocs.io/
License: BSD-3-Clause
Latest release: 2.6.2
published 8 months ago

Versions: 16
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 549 Last month

Rankings

Dependent packages count: 7.0%

Average: 19.4%

Downloads: 20.8%

Dependent repos count: 30.5%

Maintainers (2)

WardBrian roualdes

Last synced: 4 months ago

juliahub.com: BridgeStan

BridgeStan provides efficient in-memory access through Python, Julia, and R to the methods of a Stan model.

Homepage: https://roualdes.github.io/bridgestan
Documentation: https://docs.juliahub.com/General/BridgeStan/stable/
License: BSD-3-Clause
Latest release: 2.6.2
published 9 months ago

Versions: 16
Dependent Packages: 5
Dependent Repositories: 0
Downloads: 10 Total

Rankings

Dependent repos count: 9.9%

Stargazers count: 13.7%

Forks count: 19.4%

Average: 20.5%

Dependent packages count: 38.9%

Last synced: 4 months ago

crates.io: bridgestan

Rust interface for BridgeStan

Homepage: https://roualdes.github.io/bridgestan/latest/
Documentation: https://docs.rs/bridgestan/
License: BSD-3-Clause
Latest release: 2.6.2
published 8 months ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 19,764 Total

Rankings

Forks count: 15.6%

Stargazers count: 16.2%

Dependent repos count: 16.5%

Average: 23.9%

Downloads: 35.3%

Dependent packages count: 36.1%

Maintainers (1)

roualdes

Last synced: 4 months ago

Dependencies

R/DESCRIPTION cran

R6 >= 2.4.0 imports
testthat >= 3.0.0 suggests

.github/workflows/docs.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
ad-m/github-push-action master composite
julia-actions/setup-julia v1 composite

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actions/checkout v3 composite
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docs/requirements.txt pypi

breathe *
ipykernel *
ipython *
ipywidgets *
myst-parser *
nbsphinx *
pydata-sphinx-theme *
sphinx >5
sphinx-copybutton *

python/pyproject.toml pypi

BridgeStan

Science Score: 100.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

BridgeStan

Compatibility

Installing BridgeStan

Using BridgeStan

Compiling a Stan program

Example programs

Software using BridgeStan

Julia

Python

R

Other

Research using BridgeStan

Acknowledgements

Owner

JOSS Publication

BridgeStan: Efficient in-memory access to the methods of a Stan model

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: bridgestan

Rankings

Maintainers (2)

juliahub.com: BridgeStan

Rankings

crates.io: bridgestan

Rankings

Maintainers (1)

Dependencies