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Open Source Science

https://github.com/cgevans/mixes

https://github.com/cgevans/mixes

Science Score: 59.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: cgevans
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Size: 488 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 1
  • Open Issues: 8
  • Releases: 7
Created almost 4 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

Documentation Status Codecov GitHub Workflow Status PyPI PyPI - Python Version DOI

For DNA 28, our poster as a Jupyter notebook is available here. Our documentation is in the process of being written (latest git documentation is here); we also have a tutorial notebook (WIP).

This package, alhambra_mixes, is a separate package containing the alhambra.mixes library from alhambra modified to be more compatible with Python < 3.10. Continued development on mixes will take place here, and alhambra will be made to depend on this. The name may change soon to something more unique.

The mixes package is a Python library to systematically, efficiently, and safely design recipes for mixes of many components, intended primarily for DNA computation experiments. The library recursively tracks individual components through layers of intermediate mixes, performs checks to ensure those layers of mixes are possible, and allows verification that final samples will contain the correct components at the correct concentrations. Incorporating reference information from files such as DNA synthesis order details, the library generates recipes for straightforward pipetting, even in mixes with many components at different concentrations spread across several plates.

Changelog

v0.6.1

  • Adds html_with_borders_tablefmt again (and import printing).

v0.6.0

  • Optional ECHO liquid handler support, with the 'echo' feature (eg, pip install --upgrade alhambra_mixes[echo]). Uses kithairon, which does require Python ≥ 3.10.

v0.5.0

An interim version release while larger changes are being made, so that users can make use of several important new features, and the pypi-available version fits well with the latest documentation.

  • Adds an Experiment class that can hold mixes and components, and keep track of volumes, etc.
  • Adds volume/consumption tracking.
  • Adds master/split mix functions.
  • Fixes numerous minor bugs.

Owner

  • Name: Constantine Evans
  • Login: cgevans
  • Kind: user

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 10
  • Pull request event: 2
  • Create event: 2
Last Year
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 10
  • Pull request event: 2
  • Create event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 279
  • Total Committers: 3
  • Avg Commits per committer: 93.0
  • Development Distribution Score (DDS): 0.38
Past Year
  • Commits: 11
  • Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.455
Top Committers
Name Email Commits
Constantine Evans c****t@c****u 173
David Doty d****y@u****u 104
Damien Woods d****s@m****e 2
Committer Domains (Top 20 + Academic)
mu.ie: 1 ucdavis.edu: 1 costi.eu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 17
  • Total pull requests: 21
  • Average time to close issues: 7 days
  • Average time to close pull requests: 9 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 1.06
  • Average comments per pull request: 1.62
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 11 hours
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 2.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dave-doty (10)
  • cgevans (6)
  • nsiles (1)
Pull Request Authors
  • cgevans (14)
  • dave-doty (9)
Top Labels
Issue Labels
enhancement (5) bug (1) invalid (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 70 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
pypi.org: alhambra-mixes

Many-component mix library for molecular programming

  • Homepage: https://github.com/cgevans/mixes
  • Documentation: https://alhambra-mixes.readthedocs.io
  • License: BSD 3-Clause License Copyright (c) 2024, Constantine Evans and other contributors. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.6.1
    published over 1 year ago
  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 70 Last month
Rankings
Dependent packages count: 2.9%
Average: 20.4%
Downloads: 27.5%
Dependent repos count: 30.6%
Maintainers (1)
cevans
Last synced: 7 months ago

Dependencies

.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v1 composite
  • psf/black stable composite
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite
pyproject.toml pypi
  • attrs >= 22.1
  • numpy *
  • openpyxl *
  • pandas *
  • pint >= 0.20
  • tabulate *
  • toml *
  • typing_extensions >= 4.2