AnyPyTools

AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System - Published in JOSS (2019)

https://github.com/anybody-research-group/anypytools

Science Score: 98.0%

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
✓
DOI references
Found 6 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
○
Committers with academic emails
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Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

anybody python

Keywords from Contributors

pde

Scientific Fields

Mathematics Computer Science - 84% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Python tools and utilities for working with the AnyBody Modelling System

Basic Info

Host: GitHub
Owner: AnyBody-Research-Group
License: mit
Language: Python
Default Branch: master
Homepage: https://anybody-research-group.github.io/anypytools
Size: 7.95 MB

Statistics

Stars: 20
Watchers: 14
Forks: 9
Open Issues: 3
Releases: 65

Topics

anybody python

Created about 14 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Citation

AnyPyTools

AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. It enables reproduceable research with the AnyBody Modeling System, and bridges the gap to whole ecosystem of open source scientific Python.

The AnyPyTools Python package enables batch processing, parallization of model simulations, model sensitivity studies, and parameter studies, using either Monte-Carlo (random sampling) or Latin hypercube sampling. It makes reproducible research much easier and replaces the tedious process of manually automating the musculoskeletal simulations and aggregating the results.

If you use the library for publications please cite as:

Lund et al., (2019). AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. Journal of Open Source Software, 4(33), 1108, https://doi.org/10.21105/joss.01108

Installation

Download and install the pixi package manager
After installation open a command prompt in you project directory and type:

bash pixi init pixi add anypytools pixi install

This will install a virtual environment with python, anypytools and all dependencies. You can then run you scripts in the virtual environment by typing by prefixing the command with pixi run: e.g. pixi run python myscript.py

The library is also available on PyPi for installing using pip.

Usage

The simplest case:

python from anypytools import AnyPyProcess app = AnyPyProcess() macro = [ 'load "Model.main.any"', 'operation Main.Study.InverseDynamics', 'run', ] app.start_macro(macro)

Please see the Jupyter Notebook based tutorial, or check the the following for more information:

AnyPyTools's Documentation

Don't panic

Owner

Name: AnyBody-Research-Group
Login: AnyBody-Research-Group
Kind: organization
Location: Aalborg University, Denmark

Website: http://www.biomechanics.m-tech.aau.dk/
Repositories: 11
Profile: https://github.com/AnyBody-Research-Group

JOSS Publication

AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System

Published

January 07, 2019

DOI

10.21105/joss.01108

Volume 4, Issue 33, Page 1108

Authors

Morten Enemark Lund

AnyBody Technology A/S, Denmark, Department of Materials and Production, Aalborg University, Denmark

John Rasmussen

Department of Materials and Production, Aalborg University, Denmark

Michael Skipper Andersen

Department of Materials and Production, Aalborg University, Denmark

Editor

Tania Allard

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lund"
  given-names: "Morten Enemark"
  orcid: "https://orcid.org/0000-0001-9920-4051"
title: "AnyPyTools"
version: 2.0.4
doi: 10.5281/zenodo.5187643
date-released: 2021-08-12
url: "https://github.com/AnyBody-Research-Group/AnyPyTools"
preferred-citation:
  type: article
  authors:
  - family-names: "Lund"
    given-names: "Morten Enemark"
    orcid: "https://orcid.org/0000-0001-9920-4051"
  - family-names: "Rasmussen"
    given-names: "John"
    orcid: "https://orcid.org/0000-0003-3257-5653"
  - family-names: "Andersen"
    given-names: "Michael Skipper"
    orcid: "https://orcid.org/0000-0001-8275-9472"
  doi: "10.21105/joss.01108"
  journal: "Journal of Open Source Software"
  month: 1
  start: 1108 # First page number
  title: "AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System"
  issue: 33
  volume: 4
  year: 2018

GitHub Events

Total

Release event: 11
Watch event: 2
Delete event: 4
Issue comment event: 1
Push event: 44
Pull request event: 14
Create event: 23

Last Year

Release event: 11
Watch event: 2
Delete event: 4
Issue comment event: 1
Push event: 44
Pull request event: 14
Create event: 23

Committers

Last synced: 5 months ago

All Time

Total Commits: 767
Total Committers: 10
Avg Commits per committer: 76.7
Development Distribution Score (DDS): 0.018

Past Year

Commits: 30
Committers: 1
Avg Commits per committer: 30.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Morten Enemark Lund	m**d@g**m	753
abrg-data-access	8****s	4
Kasper Pihl Rasmussen	k**r@g**m	2
kpr	k**r@a**m	2
The Gitter Badger	b**r@g**m	1
Matei Sarivan	ms@a****m	1
JohnRasmussenAnyBody	4****y	1
Enrico Depieri	d**o@g**m	1
BKE	b**e@a**m	1
Arfon Smith	a****n	1

Committer Domains (Top 20 + Academic)

anybodytech.com: 3 gitter.im: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 18
Total pull requests: 113
Average time to close issues: 11 months
Average time to close pull requests: 7 days
Total issue authors: 8
Total pull request authors: 7
Average comments per issue: 1.28
Average comments per pull request: 0.16
Merged pull requests: 109
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 14
Average time to close issues: N/A
Average time to close pull requests: about 5 hours
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.14
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

melund (10)
sebastianskejoe (2)
elnormo (1)
trallard (1)
ghost (1)
depierie (1)
KasperPRasmussen (1)
neildhir (1)

Pull Request Authors

melund (114)
KasperPRasmussen (2)
MateiSarivan (2)
gitter-badger (1)
arfon (1)
abrg-data-access (1)
sebastianskejoe (1)

Top Labels

Issue Labels

Pull Request Labels

hacktoberfest-accepted (3)

Packages

Total packages: 2
Total downloads:
- pypi 445 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 125
Total maintainers: 1

pypi.org: anypytools

Python tools and utilities for working with the AnyBody Modeling System

Homepage: https://anybody-research-group.github.io/anypytools-docs/
Documentation: https://anybody-research-group.github.io/anypytools-docs/
License: MIT License
Latest release: 1.17.1
published 6 months ago

Versions: 70
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 445 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 11.4%

Stargazers count: 13.6%

Downloads: 19.4%

Average: 24.4%

Dependent repos count: 67.3%

Maintainers (1)

melund

Last synced: 4 months ago

conda-forge.org: anypytools

AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. Its main purpose is to launch AnyBody simulations and collect results. It has a scheduler to launch multiple instances of AMS utilising computers with multiple cores. AnyPyTools makes it possible to run parameter and Monte Carlo studies more efficiently than from within the AnyBody Modeling System.

Homepage: https://github.com/AnyBody-Research-Group/AnyPyTools
License: MIT
Latest release: 1.9.0
published about 3 years ago

Versions: 55
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 44.0%

Forks count: 44.7%

Stargazers count: 46.3%

Dependent packages count: 51.2%

Last synced: 4 months ago

Dependencies

.github/workflows/docs.yaml actions

actions/checkout v2 composite
mamba-org/setup-micromamba main composite
peaceiris/actions-gh-pages v3 composite

.github/workflows/test.yml actions

actions/checkout v3 composite
psf/black stable composite

pyproject.toml pypi

numpy *
scipy *
tqdm *

docs/environment.yml conda

cloud_sptheme
h5py
ipython
ipywidgets
jinja2 <3.1
myst-parser
nbsphinx
numpy
pytest
python 3.9.*
scipy
sphinx <4
tqdm

environment.yml conda

build
cloud_sptheme 1.10.1.post20200504175005.*
h5py
ipywidgets
pandas
pydoe
pygments_anyscript
python 3.11.*
scipy
setuptools
tqdm
twine

AnyPyTools

Science Score: 98.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

AnyPyTools

Installation

Usage

Owner

JOSS Publication

AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

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Last Year

Committers

All Time

Past Year

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Committer Domains (Top 20 + Academic)

Issues and Pull Requests

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Packages

pypi.org: anypytools

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Maintainers (1)

conda-forge.org: anypytools

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Dependencies