TO DO: Add other badges.
A command line interface for automatically extracting relevant metadata from code repositories (readme, configuration files, documentation, etc.).
This repository is extracted from https://github.com/SciCodes/somef-core/issues
Authors: Daniel Garijo, Allen Mao, Miguel Ángel García Delgado, Haripriya Dharmala, Vedant Diwanji, Jiaying Wang, Aidan Kelley, Jenifer Tabita Ciuciu-Kiss, Luca Angheluta and Juanje Mendoza.
Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the following categories (if present), listed in alphabetical order:
- Acknowledgement: Text acknowledging funding sources or contributors
- Build file: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
- Citation: Preferred citation as the authors have stated in their readme file. SOMEF recognizes Bibtex, Citation File Format files and other means by which authors cite their papers (e.g., by in-text citation). We aim to recognize the following properties:
- Title: Title of the publication
- Author: list of author names in the publication
- URL: URL of the publication
- DOI: Digital object identifier of the publication
- Date published
- Code of conduct: Link to the code of conduct of the project
- Code repository: Link to the GitHub/GitLab repository used for the extraction
- Contact: Contact person responsible for maintaining a software component
- Continuous integration: Link to continuous integration service(s)
- Contribution guidelines: Text indicating how to contribute to this code repository
- Contributors: Contributors to a software component
- Creation date: Date when the repository was created
- Date updated: Date of last release.
- Description: A description of what the software does
- Documentation: Where to find additional documentation about a software component
- Download URL: URL where to download the target software (typically the installer, package or a tarball to a stable version)
- Executable examples: Jupyter notebooks ready for execution (e.g., files, or through myBinder/colab links)
- FAQ: Frequently asked questions about a software component
- Forks count: Number of forks of the project
- Forks url: Links to forks made of the project
- Full name: Name + owner (owner/name)
- Full title: If the repository is a short name, we will attempt to extract the longer version of the repository name
- Identifier: Identifier associated with the software (if any), such as Digital Object Identifiers. DOIs associated with publications will also be detected.
- Images: Images used to illustrate the software component
- Installation instructions: A set of instructions that indicate how to install a target repository
- Invocation: Execution command(s) needed to run a scientific software component
- Issue tracker: Link where to open issues for the target repository
- Keywords: set of terms used to commonly identify a software component
- License: License and usage terms of a software component
- Logo: Main logo used to represent the target software component
- Name: Name identifying a software component
- Owner: Name and type of the user or organization in charge of the repository
- Package distribution: Links to package sites like pypi in case the repository has a package available.
- Package files: Links to package files used to wrap the project in a package.
- Programming languages: Languages used in the repository
- Related papers: URL to possible related papers within the repository stated within the readme file (from Arxiv)
- Releases (GitHub only): Pointer to the available versions of a software component. For each release, somef will track the following properties:
- Description: Release notes
- Author: Agent responsible of creating the release
- Name: Name of the release
- Tag: version number of the release
- Date of publication
- Date of creation
- Link to the html page of the release
- Id of the release
- Link to the tarball zip and code of the release
- Repository status: Repository status as it is described in repostatus.org.
- Requirements: Pre-requisites and dependencies needed to execute a software component
- Stargazers count: Total number of stargazers of the project
- Support: Guidelines and links of where to obtain support for a software component
- Support channels: Help channels one can use to get support about the target software component
- Usage examples: Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it
We use different supervised classifiers, header analysis, regular expressions, the GitHub/Gitlab API to retrieve all these fields (more than one technique may be used for each field) and language specific metadata parsers (e.g., for package files). Each extraction records its provenance, with the confidence and technique used on each step. For more information check the output format description
The documentation for somef-core is available at https://somef-core.readthedocs.io/en/latest/
Journal publication (preferred):
@article{10.1162/qss_a_00167,
author = {Kelley, Aidan and Garijo, Daniel},
title = "{A Framework for Creating Knowledge Graphs of Scientific Software Metadata}",
journal = {Quantitative Science Studies},
pages = {1-37},
year = {2021},
month = {11},
issn = {2641-3337},
doi = {10.1162/qss_a_00167},
url = {https://doi.org/10.1162/qss_a_00167},
eprint = {https://direct.mit.edu/qss/article-pdf/doi/10.1162/qss\_a\_00167/1971225/qss\_a\_00167.pdf},
}
Conference publication (first):
@INPROCEEDINGS{9006447,
author={A. {Mao} and D. {Garijo} and S. {Fakhraei}},
booktitle={2019 IEEE International Conference on Big Data (Big Data)},
title={SoMEF: A Framework for Capturing Scientific Software Metadata from its Documentation},
year={2019},
doi={10.1109/BigData47090.2019.9006447},
url={http://dgarijo.com/papers/SoMEF.pdf},
pages={3032-3037}
}
- Python 3.9 or Python 3.10 (default version support)
SOMEF has been tested on Unix, MacOS and Windows Microsoft operating systems.
If you face any issues when installing SOMEF, please make sure you have installed the following packages: build-essential, libssl-dev, libffi-dev and python3-dev.
We are currently working on this
To run somef_core, please follow the next steps:
Clone this GitHub repository
git clone https://github.com/KnowledgeCaptureAndDiscovery/somef-core.git
We use Poetry to ensure library compatibility. It can be installed as follows:
curl -sSL https://install.python-poetry.org | python3 -
This option is recommended over installing Poetry with pip install.
Now Poetry will handle the installation of SOMEF-core and all its dependencies configured in the toml file.
To test the correct installation of poetry run:
poetry --version
Install somef and all their dependencies.
cd /somef-core
poetry install
Now we need to access our virtual environment, to do so you have to install the poetry plugin shell and run the following command:
pip install poetry-plugin-shell
After shell is set up, you can run the following comand to access the virtual environment
poetry shell
Test SOMEF installation
somef --helpIf everything goes fine, you should see:
Usage: somef_core [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
Commands:
configure Configure credentials
describe Running the Command Line Interface
version Show somef version.We are working on this section
Before running SOMEF for the first time, you must configure it appropriately (you only need to do this once). Run:
somef_core configureAnd you will be asked to provide the following:
- A GitHub authentication token [optional, leave blank if not used], which SOMEF uses to retrieve metadata from GitHub. If you don't include an authentication token, you can still use SOMEF. However, you may be limited to a series of requests per hour. For more information, see https://help.github.com/en/github/authenticating-to-github/creating-a-personal-access-token-for-the-command-line
- The path to the trained classifiers (pickle files). If you have your own classifiers, you can provide them here. Otherwise, you can leave it blank
If you want somef to be automatically configured (without GitHUb authentication key and using the default classifiers) just type:
somef_core configure -aFor showing help about the available options, run:
somef_core configure --helpWhich displays:
Usage: somef_core configure [OPTIONS]
Configure GitHub credentials and classifiers file path
Options:
-a, --auto Automatically configure SOMEF
-h, --help Show this message and exit.$ somef_core describe --help
SOMEF Command Line Interface
Usage: somef_core describe [OPTIONS]
Running the Command Line Interface
Options:
Input: [mutually_exclusive, required]
-r, --repo_url URL Github/Gitlab Repository URL
-d, --doc_src PATH Path to the README file source
-i, --in_file PATH A file of newline separated links to GitHub/
Gitlab repositories
Output: [required_any]
-o, --output PATH Path to the output file. If supplied, the
output will be in JSON
-c, --codemeta_out PATH Path to an output codemeta file
-p, --pretty Pretty print the JSON output file so that it
is easy to compare to another JSON output
file.
-m, --missing The JSON will include a field
somef_missing_categories to report with the
missing metadata fields that SOMEF was not
able to find.
-kt, --keep_tmp PATH SOMEF will NOT delete the temporary folder
where files are stored for analysis. Files
will be stored at the
desired path
-h, --help Show this message and exit.The following command extracts all metadata available from https://github.com/dgarijo/Widoco/.
somef_core describe -r https://github.com/dgarijo/Widoco/ -o test.json If you want to contribute with a pull request, please do so by submitting it to the dev branch.