Package Health Score

75 / 100

security
No known security issues
popularity
Small
maintenance
Sustainable
community
Active

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Popularity

Small

GitHub Stars: 10.74K
Forks: 1.59K
Contributors: 430

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package acryo, we found that it has been starred 10,742 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Mar 7, 2024
Direct Vulnerabilities: 0
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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

Sustainable

Commit Frequency

Open Issues: 744
Open PR: 160
Last Release: 2 months ago
Last Commit: 1 year ago

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

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

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: No
Contributors: 430
Funding: Yes

A good and healthy external contribution signal for acryo project, which invites more than one hundred open source maintainers to collaborate on the repository.

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

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Package

Python Versions Compatibility: >=3.9

Age: 2 years
Latest Release: 2 months ago
Dependencies: 0 Direct
Versions: 20
Maintainers: 1
Wheels: OS Independent

Readme

acryo

acryo is an extensible cryo-EM/ET toolkit for Python.

The purpose of this library is to make data analysis of cryo-EM/ET safer, efficient, reproducible and customizable for everyone. Scientists can avoid the error-prone CLI-based data handling, such as writing out the results to the files every time and manage all the result just by the file names.

📘 Documentation

Install

Use pip

pip install acryo -U

From source

git clone git+https://github.com/hanjinliu/acryo.git
cd acryo
pip install -e .

Features

Out-of-core and parallel processing during subtomogram averaging/alignment to make full use of CPU.
Extensible and ready-to-use alignment models.
Manage subtomogram loading tasks from single or multiple tomograms in the same API.
Tomogram and tilt series simulation.
Masked PCA clustering.

Code Snippet

import polars as pl
from acryo import SubtomogramLoader, Molecules  # acryo objects
from acryo.tilt import single_axis  # missing wedge model
from acryo.pipe import soft_otsu  # data input pipelines

# construct a loader
loader = SubtomogramLoader.imread(
    "path/to/tomogram.mrc",
    molecules=Molecules.from_csv("path/to/molecules.csv"),
)

# filter out bad alignment in polars way
loader_filt = loader.filter(pl.col("score") > 0.7)

# averaging
avg = loader_filt.average(output_shape=(48, 48, 48))

# alignment
aligned_loader = loader.align(
    template=avg,                           # use the average as template
    mask=soft_otsu(sigma=2, radius=2),      # apply soft-Otsu to template to make the mask
    tilt=single_axis((-45, 45), axis="y"),  # range of tilt series degrees.
    cutoff=0.5,                             # lowpass filtering cutoff
    max_shifts=(4, 4, 4),                   # search space limits
)

FAQs

What is acryo?

An extensible cryo-EM/ET toolkit for Python. Visit Snyk Advisor to see a full health score report for acryo, including popularity, security, maintenance & community analysis.

Is acryo popular?

The python package acryo receives a total of 452 weekly downloads. As such, acryo popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is acryo well maintained?

We found indications that acryo maintenance is sustainable demonstrating some project activity. We saw a total of 430 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is acryo safe to use?

The python package acryo 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 24 April-2024, at 22:41 (UTC).

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acryo

An extensible cryo-EM/ET toolkit for Python. For more information about how to use this package see README

Ensure you're using the healthiest python packages

Package Health Score

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Popularity

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Security

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Community

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Package

Readme

acryo

Install

Use pip

From source

Features

Code Snippet

FAQs

What is acryo?

Is acryo popular?

Is acryo well maintained?

Is acryo safe to use?

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Scan your app for vulnerabilities

Fix identified vulnerabilities

Monitor for new issues

Package Health Score

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Direct Usage Popularity

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Commit Frequency

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Snyk Vulnerability Scanner

Readme

acryo

Install

Use pip

From source

Features

Code Snippet

FAQs

What is acryo?

Is acryo popular?

Is acryo well maintained?

Is acryo 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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