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Open Source Science

mc-peptide

https://github.com/doncamilom/mc-peptide

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.1%) to scientific vocabulary
Last synced: 8 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: doncamilom
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 7.4 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

tests PyPI PyPI - Python Version Documentation Status Cookiecutter template from @SchwallerGroup Learn more @SchwallerGroup


Gather, modify, and model MacroCyclic Peptide data with LLMs!

🔥 Usage

Extract macrocyclic peptide data out of a single paper.

bash mc_peptide extract -f data/papers/wang/ --llm=gpt-4-turbo

👩‍💻 Installation

The most recent code and data can be installed directly from GitHub with:

bash $ pip install git+https://github.com/schwallergroup/mc-peptide.git

✅ Citation

```bibtex

@Misc{mcpeptide, author = { }, title = { mcpeptide - }, howpublished = {Github}, year = {2023}, url = {https://github.com/schwallergroup/mc-peptide } } ```

🛠️ For Developers

See developer instructions ### 👐 Contributing Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See [CONTRIBUTING.md](https://github.com/schwallergroup/mc-peptide/blob/master/.github/CONTRIBUTING.md) for more information on getting involved. ### Development Installation To install in development mode, use the following: ```bash $ git clone git+https://github.com/schwallergroup/mc-peptide.git $ cd mc-peptide $ pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/schwallergroup/mc-peptide/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/schwallergroup/mc-peptide.git $ cd mc-peptide $ tox -e docs $ open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). ### 📦 Making a Release After installing the package in development mode and installing `tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/mc_peptide/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this step 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after.

Owner

  • Name: Andres
  • Login: doncamilom
  • Kind: user
  • Company: EPFL @schwallergroup

Citation (CITATION.cff) 

cff-version: 1.0.2
message: "If you use this software, please cite it as below."
title: "mc_peptide"
authors:
  - name: ""
version: 0.0.1
doi:
url: "https://github.com/schwallergroup/mc-peptide"

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 11
  • Total Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.091
Past Year
  • Commits: 11
  • Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.091
Top Committers
Name Email Commits
Andres d****m@g****m 10
marcelmmc m****d@g****m 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite
pyproject.toml pypi