pytoda
pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/
Basic Info
Statistics
- Stars: 28
- Watchers: 4
- Forks: 7
- Open Issues: 0
- Releases: 15
Topics
Metadata Files
README.md
PyToDa
Overview
pytoda - PaccMann PyTorch Dataset Classes
A python package that eases handling biochemical data for deep learning applications with pytorch.
Installation
pytoda ships via PyPI:
sh
pip install pytoda
Documentation
Please find the full documentation here.
Development
For development setup, we recommend to work in a dedicated conda environment:
sh
conda env create -f conda.yml
Activate the environment:
sh
conda activate pytoda
Install in editable mode:
sh
pip install -r dev_requirements.txt
pip install --user --no-use-pep517 -e .
Examples
For some examples on how to use pytoda see here
References
If you use pytoda in your projects, please cite the following:
bib
@article{born2021data,
title={Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2},
author={Born, Jannis and Manica, Matteo and Cadow, Joris and Markert, Greta and Mill, Nil Adell and Filipavicius, Modestas and Janakarajan, Nikita and Cardinale, Antonio and Laino, Teodoro and Martinez, Maria Rodriguez},
journal={Machine Learning: Science and Technology},
volume={2},
number={2},
pages={025024},
year={2021},
publisher={IOP Publishing}
}
Owner
- Name: PaccMann
- Login: PaccMann
- Kind: organization
- Email: drugilsberg@gmail.com
- Repositories: 19
- Profile: https://github.com/PaccMann
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jannis Born | j****b@z****m | 135 |
| pyup.io bot | g****t@p****o | 39 |
| Matteo Manica | d****g@g****m | 19 |
| Joris | j****w@g****m | 10 |
| Greta Markert | g****e@z****m | 7 |
| Nikita Janakarajan | n****7@g****m | 5 |
| Matteo Manica | t****e@z****m | 5 |
| Yoel Shoshan | y****s@i****m | 4 |
| annaweber209 | 5****9 | 1 |
| Nil Adell Mill | n****1@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 23
- Total pull requests: 79
- Average time to close issues: 6 months
- Average time to close pull requests: 11 days
- Total issue authors: 7
- Total pull request authors: 9
- Average comments per issue: 1.7
- Average comments per pull request: 0.75
- Merged pull requests: 49
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 14 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jannisborn (12)
- C-nit (4)
- drugilsberg (3)
- annaweber209 (1)
- YoelShoshan (1)
- niladell (1)
- hmkim (1)
Pull Request Authors
- pyup-bot (38)
- jannisborn (30)
- C-nit (6)
- niklexical (2)
- YoelShoshan (1)
- drugilsberg (1)
- niladell (1)
- annaweber209 (1)
- M4kxjcxv (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 1,433 last-month
- Total dependent packages: 0
- Total dependent repositories: 5
- Total versions: 10
- Total maintainers: 1
pypi.org: pytoda
pytoda: PaccMann PyTorch Dataset Classes.
- Homepage: https://github.com/PaccMann/paccmann_datasets
- Documentation: https://pytoda.readthedocs.io/
- License: MIT
-
Latest release: 1.1.6
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- better-apidoc ==0.3.1 development
- black >=22.3.0 development
- flake8 ==3.8.4 development
- flask ==1.1.2 development
- flask_login ==0.5.0 development
- mypy ==0.800 development
- myst-parser ==0.13.3 development
- pytest ==6.1.1 development
- pytest-cov ==2.10.1 development
- six ==1.15.0 development
- sphinx ==3.4.3 development
- sphinx-autodoc-typehints ==1.11.1 development
- sphinx_rtd_theme ==0.5.1 development
- PubChemPy >=1.0.4
- SmilesPE >=0.0.3
- Unidecode >=1.1.2
- dill >=0.3.3
- diskcache >=5.0.3
- importlib_resources >=5.2.2
- numpy >=1.19.0
- pandas >=1.0.0
- pyfaidx >=0.6.0
- rdkit-pypi >=2021.9.3
- scikit-learn >=0.23.0
- selfies >=2.0.0
- torch >=1.4.0,<1.9
- upfp >=0.0.5
- SmilesPE >=0.0.3
- Unidecode *
- dill >=0.3.3
- diskcache *
- importlib_resources *
- numpy *
- pandas *
- pubchempy *
- pyfaidx *
- rdkit-pypi >=2021.9.3
- scikit-learn *
- selfies >=2.0.0
- torch >=1.4.0
- upfp *
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