Package Health Score

78 / 100

security
No known security issues
popularity
Small
maintenance
Healthy
community
Sustainable

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Popularity

Small

GitHub Stars: 196
Forks: 51
Contributors: 30

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package alchemlyb, we found that it has been starred 196 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Sep 19, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 23
Open PR: 5
Last Release: 2 months ago
Last Commit: 19 days ago

Further analysis of the maintenance status of alchemlyb based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that alchemlyb demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: No
Contributors: 30
Funding: No

With more than 10 contributors for the alchemlyb repository, this is possibly a sign for a growing and inviting community.

We found a way for you to contribute to the project! Looks like alchemlyb is missing a Code of Conduct.

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Package

Python Versions Compatibility: >=3.10

Age: 8 years
Latest Release: 2 months ago
Dependencies: 5 Direct
Versions: 23
Maintainers: 3
Wheels: OS Independent

Not sure how to use alchemlyb?

To help you get started, we've collected the most common ways that alchemlyb is being used within popular public projects.

Becksteinlab / MDPOW / mdpow / estimators / ti_.py View on Github

import alchemlyb.estimators
import numpy as np
import pandas as pd
import numkit

class TI(alchemlyb.estimators.TI):
    """Thermodynamic integration (TI) estimator

    Parameters
    ----------

    verbose : bool, optional
        Set to True if verbose debug output is desired.

    Attributes
    ----------

    delta_f_ : DataFrame
        The estimated dimensionless free energy difference between each state.
    d_delta_f_ : DataFrame
        The estimated statistical uncertainty (one standard deviation) in
        dimensionless free energy differences.

View more ways to use alchemlyb

alchemlyb: the simple alchemistry library

alchemlyb makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:

Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, NAMD and other simulation codes.
Subsamplers for obtaining uncorrelated samples from timeseries data (including extracting independent, equilibrated samples Chodera2016 as implemented in the pymbar package).
Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) Shirts2008 and BAR (from pymbar) and thermodynamic integration (TI).

Documentation

The documentation is hosted on Read the Docs.

Installation

Install via pip from PyPi (alchemlyb):

pip install alchemlyb

or as a conda package from the conda-forge (alchemlyb) channel:

conda install -c conda-forge alchemlyb

Update with pip:

pip install --update alchemlyb

or with conda run:

conda update -c conda-forge alchemlyb

to get the latest released version.

Getting involved

Contributions of all kinds are very welcome.

If you have questions or want to discuss alchemlyb please post in the alchemlyb Discussions.

If you have bug reports or feature requests then please get in touch with us through the Issue Tracker.

We also welcome code contributions: have a look at our Developer Guide. Open an issue with the proposed fix or change in the Issue Tracker and submit a pull request against the alchemistry/alchemlyb GitHub repository.

References

Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.
Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.

alchemlyb dependencies

loguru numpy pyarrow scikit-learn scipy

FAQs

What is alchemlyb?

the simple alchemistry library. Visit Snyk Advisor to see a full health score report for alchemlyb, including popularity, security, maintenance & community analysis.

Is alchemlyb popular?

The python package alchemlyb receives a total of 1,410 weekly downloads. As such, alchemlyb popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is alchemlyb well maintained?

We found that alchemlyb demonstrated a healthy version release cadence and project activity. It has a community of 30 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is alchemlyb safe to use?

The python package alchemlyb was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 4 November-2024, at 22:09 (UTC).

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alchemlyb

the simple alchemistry library For more information about how to use this package see README

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Package

Not sure how to use alchemlyb?

alchemlyb: the simple alchemistry library

Documentation

Installation

Getting involved

References

alchemlyb dependencies

FAQs

What is alchemlyb?

Is alchemlyb popular?

Is alchemlyb well maintained?

Is alchemlyb safe to use?

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Package Health Score

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Direct Usage Popularity

Security and license risk for latest version

Commit Frequency

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Snyk Vulnerability Scanner

Not sure how to use alchemlyb?

alchemlyb: the simple alchemistry library

Documentation

Installation

Getting involved

References

alchemlyb dependencies

FAQs

What is alchemlyb?

Is alchemlyb popular?

Is alchemlyb well maintained?

Is alchemlyb safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

Fix identified vulnerabilities

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