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Read CFF formatted CITATION file from a GitHub url or local file and convert it to BibTeX, EndNote, RIS, Codemeta, .zenodo.json, or plain JSON

Project description

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cffconvert

Read CFF formatted CITATION file from a GitHub url and convert it to various formats, such as:

  1. BibTeX
  2. EndNote
  3. RIS
  4. codemeta
  5. plain JSON
  6. Zenodo JSON

Supported types of GitHub URL:

  1. https://github.com/<org>/<repo>
  2. https://github.com/<org>/<repo>/tree/<sha>
  3. https://github.com/<org>/<repo>/tree/<tagname>
  4. https://github.com/<org>/<repo>/tree/<branchname>

cffconvert does not support the full CFF spec yet.

For users

Install

There are a few options:

Option 1 (preferred): install in user space.

Ensure that the user space directory ~/.local/bin/ is on the PATH.

pip3 install --user cffconvert

Option 2 (not preferred): install in virtual environment

virtualenv -p /usr/bin/python3.5 myvenv3
source myvenv3/bin/activate
pip3 install cffconvert

Option 3 (not preferred): install globally

Note: this option needs sudo rights.

sudo -H pip3 install cffconvert

Option 4 (not preferred): install with conda

See https://stackoverflow.com/questions/41060382/using-pip-to-install-packages-to-anaconda-environment

conda install pip
pip install cffconvert

Command line interface

See cffconvert’s options:

cffconvert --help

Shows:

Usage: cffconvert [OPTIONS]

Options:
  -if, --infile TEXT          Path to the CITATION.cff input file.
  -of, --outfile TEXT         Path to the output file.
  -f, --outputformat TEXT     Output format: bibtex|cff|codemeta|endnote|ris|zenodo
  -u, --url TEXT              URL of the repo containing the CITATION.cff (currently only github.com is supported; may
                              include branch name, commit sha, tag name). For example: 'https://github.com/citation-
                              file-format/cff-converter-python' or 'https://github.com/citation-file-format/cff-
                              converter-python/tree/master'
  --validate                  Validate the CITATION.cff found at the URL or supplied through '--infile'
  -ig, --ignore-suspect-keys  If True, ignore any keys from CITATION.cff that are likely out of date, such as
                              'commit', 'date-released', 'doi', and 'version'.
  --verbose                   Provide feedback on what was entered.
  --version                   Print version and exit.
  --help                      Show this message and exit.

Example usage, retrieve CITATION.cff from URL with curl, output as BibTeX:

curl https://raw.githubusercontent.com/citation-file-format/cff-converter-python/44a8ad35d94dd50a8b5924d8d26402ae0d162189/CITATION.cff > CITATION.cff
cffconvert -f bibtex

Results in:

@misc{YourReferenceHere,
author = {
            Jurriaan H. Spaaks and
            Tom Klaver
         },
title  = {cff-converter-python},
month  = {1},
year   = {2018},
doi    = {10.5281/zenodo.1162057},
url    = {https://github.com/citation-file-format/cff-converter-python}
}

Example usage, let cffconvert retrieve CITATION.cff from URL, output as codemeta.json:

cffconvert -f codemeta -u https://github.com/citation-file-format/cff-converter-python/tree/master -of codemeta.json

Contents of file codemeta.json:

{
    "@context": [
        "https://doi.org/10.5063/schema/codemeta-2.0",
        "http://schema.org"
    ],
    "@type": "SoftwareSourceCode",
    "author": [
        {
            "@type": "Person",
            "affiliation": {
                "@type": "Organization",
                "legalName": "Netherlands eScience Center"
            },
            "familyName": "Spaaks",
            "givenName": "Jurriaan H."
        },
        {
            "@type": "Person",
            "affiliation": {
                "@type": "Organization",
                "legalName": "Netherlands eScience Center"
            },
            "familyName": "Klaver",
            "givenName": "Tom"
        },
        {
            "@type": "Person",
            "affiliation": {
                "@type": "Organization",
                "legalName": "Netherlands eScience Center"
            },
            "familyName": "Verhoeven",
            "givenName": "Stefan"
        }
    ],
    "codeRepository": "https://github.com/citation-file-format/cff-converter-python",
    "datePublished": "2018-05-22",
    "identifier": "https://doi.org/10.5281/zenodo.1162057",
    "keywords": [
        "citation",
        "bibliography",
        "cff",
        "CITATION.cff"
    ],
    "license": "http://www.apache.org/licenses/LICENSE-2.0",
    "name": "cffconvert",
    "version": "0.0.5"
}

Convert the contents of a local file CITATION.cff into the format used by .zenodo.json files (see Zenodo’s API docs), while ignoring any keys that are likely out of date:

cffconvert -f zenodo --ignore-suspect-keys

Results in (note absence of date-released, doi, and version):

{
    "creators": [
        {
            "affiliation": "Netherlands eScience Center",
            "name": "Spaaks, Jurriaan H."
        },
        {
            "affiliation": "Netherlands eScience Center",
            "name": "Klaver, Tom"
        },
        {
            "affiliation": "Netherlands eScience Center",
            "name": "Verhoeven, Stefan"
        }
    ],
    "keywords": [
        "citation",
        "bibliography",
        "cff",
        "CITATION.cff"
    ],
    "license": {
        "id": "Apache-2.0"
    },
    "title": "cffconvert"
}

For developers

Install

# get a copy of the cff-converter-python software
git clone https://github.com/citation-file-format/cff-converter-python.git
# change directory into cff-converter-python
cd cff-converter-python
# make a Python3.5 virtual environment named .venv35
virtualenv -p /usr/bin/python3.5 .venv35
# activate the virtual environment
source ./.venv35/bin/activate
# install any packages that cff-converter-python needs
pip install -r requirements.txt
# install any packages used for development such as for testing
pip install -r requirements-dev.txt
# install the cffconvert package using symlinks
pip install --editable .

Running tests

# (from the project root)

# run unit tests
pytest test/

# run tests against live system (GitHub)
pytest livetest/

For maintainers

Making a release

# make sure the release notes are up to date

# run the live tests and unit tests, make sure they pass

# git push everything, merge into master as appropriate

# verify that everything has been pushed and merged by testing as follows
cd $(mktemp -d)
git clone https://github.com/citation-file-format/cff-converter-python.git
cd cff-converter-python
virtualenv -p /usr/bin/python3.5 myvenv3
source myvenv3/bin/activate
pip install -r requirements.txt
pip install -r requirements-dev.txt
pytest test/
pytest livetest/

# register with PyPI test instance https://test.pypi.org

# remove these directories if you have them
rm -rf dist
rm -rf cffconvert-egg.info
# make a source distribution:
python setup.py sdist
# install the 'upload to pypi/testpypi tool' aka twine
pip install twine
# upload the contents of the source distribtion we just made
twine upload --repository-url https://test.pypi.org/legacy/ dist/*

# checking the package
# pip install --user --index-url https://test.pypi.org/simple/ cffconvert

# check that the package works as it should when installed from pypitest

# FINAL STEP: upload to PyPI
twine upload dist/*

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
cffconvert-1.0.1.tar.gz (16.5 kB) Copy SHA256 hash SHA256 Source None Jul 25, 2018

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