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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| #!/usr/bin/env python | ||
| """Synchronize authors and contributor metadata. | ||
| This script synchronizes the metadata provided in the CITATION.cff and | ||
| the contributors.yaml file with the metadata stored in the .zenodo.json | ||
| file. | ||
| All authors should be listed in the CITATION.cff file, while contributors | ||
| should be listed in the contributors.yaml file. | ||
| Both files use the [citation file-format][1] for [person objects][2]. | ||
| [1] https://citation-file-format.github.io/ | ||
| [2] https://citation-file-format.github.io/1.0.3/specifications/#/person-objects | ||
| """ | ||
| from dataclasses import dataclass | ||
|
|
||
| import click | ||
| import json | ||
| from ruamel.yaml import load, Loader | ||
|
|
||
|
|
||
| @dataclass | ||
| class Contributor: | ||
| last_names: str | ||
| first_names: str | ||
| affiliation: str | ||
| orcid: str = None | ||
|
|
||
| @classmethod | ||
| def from_citation_author(cls, **citation): | ||
| return cls( | ||
| last_names=citation.pop('family-names'), | ||
| first_names=citation.pop('given-names'), | ||
| **citation) | ||
|
|
||
| def as_zenodo_creator(self): | ||
| ret = dict( | ||
| name='{} {}'.format(self.first_names, self.last_names), | ||
| affiliation=self.affiliation) | ||
| if self.orcid: | ||
| ret['orcid'] = self.orcid.lstrip('https://orcid.org/') | ||
| return ret | ||
|
|
||
|
|
||
| @click.command() | ||
| @click.pass_context | ||
| @click.option('--check', default=False, is_flag=True, | ||
| help="Return with non-zero exit code if metadata needs to be updated.") | ||
| @click.option('-i', '--in-place', type=bool, is_flag=True, | ||
| help="Modify metadata in place.") | ||
| def sync(ctx, in_place=False, check=True): | ||
|
|
||
| with open('CITATION.cff', 'rb') as file: | ||
| citation = load(file.read(), Loader=Loader) | ||
| authors = [ | ||
| Contributor.from_citation_author(**author) | ||
| for author in citation['authors']] | ||
|
|
||
| with open('contributors.yaml', 'rb') as file: | ||
| contributors = load(file.read(), Loader=Loader)['contributors'] | ||
| contributors = [Contributor.from_citation_author( | ||
| **contributor) for contributor in contributors] | ||
|
|
||
| with open('.zenodo.json', 'rb') as file: | ||
| zenodo = json.loads(file.read()) | ||
| zenodo_updated = zenodo.copy() | ||
| zenodo_updated['creators'] = [a.as_zenodo_creator() for a in authors] | ||
| zenodo_updated['contributors'] = [c.as_zenodo_creator() | ||
| for c in contributors if c not in authors] | ||
| for key in ('version', 'keywords'): | ||
| zenodo_updated[key] = citation[key] | ||
|
|
||
| modified = json.dumps(zenodo, sort_keys=True) != json.dumps(zenodo_updated, sort_keys=True) | ||
| if modified: | ||
| if in_place: | ||
| with open('.zenodo.json', 'wb') as file: | ||
| file.write(json.dumps(zenodo_updated, indent=4, sort_keys=True).encode('utf-8')) | ||
| else: | ||
| click.echo(json.dumps(zenodo_updated, indent=4, sort_keys=True)) | ||
| if check: | ||
| ctx.exit(1) | ||
| else: | ||
| click.echo("No changes.", err=True) | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| sync() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,44 +1,78 @@ | ||
| { | ||
| "description": "<p>The signac framework aids in the management of large and heterogeneous data spaces. It provides a simple and robust data model to create a well-defined indexable storage layout for data and metadata. This makes it easier to operate on large data spaces, streamlines post-processing and analysis and makes data collectively accessible.</p>", | ||
| "license": "BSD-3-Clause", | ||
| "upload_type": "software", | ||
| "creators": [ | ||
| "contributors": [ | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Carl S. Adorf" | ||
| "name": "Benjamin Swerdlow", | ||
| "orcid": "0000-0001-6240-1430" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Paul M. Dodd" | ||
| "name": "Jens Glaser", | ||
| "orcid": "0000-0003-1852-3849" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Vyas Ramasubramani" | ||
| "name": "Timothy Moore", | ||
| "orcid": "0000-0002-5709-7259" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Benjamin Swerdlow" | ||
| "name": "Yuan Zhou" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Jens Glaser" | ||
| "affiliation": "Air Force Science and Technology Fellowship Program", | ||
| "name": "Eric Harper", | ||
| "orcid": "0000-0002-7058-1686" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Bradley Dice" | ||
| "name": "Kelly Wang" | ||
| } | ||
| ], | ||
| "access_right": "open", | ||
| "related_identifiers": [ | ||
| "creators": [ | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Carl Simon Adorf", | ||
| "orcid": "0000-0003-4962-2495" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Vyas Ramasubramani", | ||
| "orcid": "0000-0001-5181-9532" | ||
| }, | ||
| { | ||
| "scheme": "url", | ||
| "identifier": "https://dx.doi.org/10.1016/j.commatsci.2018.01.035", | ||
| "relation": "isSupplementedBy" | ||
| "affiliation": "University of Michigan", | ||
| "name": "Bradley D. Dice", | ||
| "orcid": "0000-0002-9983-0770" | ||
| }, | ||
| { | ||
| "affiliation": "Boise State University", | ||
| "name": "Mike Henry", | ||
| "orcid": "0000-0002-3870-9993" | ||
| }, | ||
| { | ||
| "affiliation": "University of Michigan", | ||
| "name": "Paul M. Dodd" | ||
| }, | ||
| { | ||
| "scheme": "url", | ||
| "identifier": "arXiv://1611.03543 [cs.DB]", | ||
| "relation": "isSupplementedBy" | ||
| "affiliation": "University of Michigan", | ||
| "name": "Sharon C. Glotzer", | ||
| "orcid": "0000-0002-7197-0085" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "description": "The signac framework helps users manage and scale file-based workflows, facilitating data reuse, sharing, and reproducibility.\n\nIt provides a simple and robust data model to create a well-defined indexable storage layout for data and metadata. This makes it easier to operate on large data spaces, streamlines post-processing and analysis and makes data collectively accessible.", | ||
| "doi": "10.5281/zenodo.2581327", | ||
| "keywords": [ | ||
| "python", | ||
| "data management", | ||
| "reproducibility", | ||
| "sharability", | ||
| "workflow", | ||
| "scientific computing" | ||
| ], | ||
| "license": { | ||
| "id": "http://www.opensource.org/licenses/BSD-3-Clause" | ||
| }, | ||
| "title": "signac", | ||
| "version": "1.1.0" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| # YAML 1.2 | ||
| --- | ||
| cff-version: "1.0.3" | ||
| title: signac | ||
| version: 1.1.0 | ||
| abstract: | | ||
| The signac framework helps users manage and scale file-based workflows, facilitating data | ||
| reuse, sharing, and reproducibility. It provides a simple and robust data model to create | ||
| a well-defined indexable storage layout for data and metadata. This makes it easier to | ||
| operate on large data spaces, streamlines post-processing and analysis and makes data | ||
| collectively accessible. | ||
| doi: 10.5281/zenodo.2581327 | ||
| authors: | ||
| - | ||
| family-names: Adorf | ||
| given-names: "Carl Simon" | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0003-4962-2495" | ||
| - | ||
| family-names: Ramasubramani | ||
| given-names: Vyas | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0001-5181-9532" | ||
| - | ||
| family-names: Dice | ||
| given-names: "Bradley D." | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0002-9983-0770" | ||
| - | ||
| family-names: Henry | ||
| given-names: Mike | ||
| affiliation: "Boise State University" | ||
| orcid: "https://orcid.org/0000-0002-3870-9993" | ||
| - | ||
| family-names: Dodd | ||
| given-names: "Paul M." | ||
| affiliation: "University of Michigan" | ||
| - | ||
| family-names: Glotzer | ||
| given-names: "Sharon C." | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0002-7197-0085" | ||
| keywords: | ||
| - python | ||
| - "data management" | ||
| - reproducibility | ||
| - sharability | ||
| - workflow | ||
| - "scientific computing" | ||
| license: "http://www.opensource.org/licenses/BSD-3-Clause" | ||
| message: > | ||
| Development and deployment supported by MICCoM, as part of the Computational | ||
| Materials Sciences Program funded by the U.S. Department of Energy, Office of | ||
| Science, Basic Energy Sciences, Materials Sciences and Engineering Division, | ||
| under Subcontract No. 6F-30844. Project conceptualization and implementation | ||
| supported by the National Science Foundation, Award # DMR 1409620. | ||
| repository-code: https://github.com/glotzerlab/signac | ||
| references: | ||
| - type: article | ||
| - authors: | ||
| - | ||
| family-names: Adorf | ||
| given-names: "Carl Simon" | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0003-4962-2495" | ||
| - | ||
| family-names: Dodd | ||
| given-names: "Paul M." | ||
| affiliation: "University of Michigan" | ||
| - | ||
| family-names: Ramasubramani | ||
| given-names: Vyas | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0001-5181-9532" | ||
| - | ||
| family-names: Glotzer | ||
| given-names: "Sharon C." | ||
| affiliation: "University of Michigan" | ||
| orcid: "https://orcid.org/0000-0002-7197-0085" | ||
| - title: "Simple data and workflow management with the signac framework" | ||
| - journal: "Comput. Mater. Sci." | ||
| - volume: 146 | ||
| - number: C | ||
| - year: 2018 | ||
| - pages: 9 | ||
| - doi: "10.1016/j.commatsci.2018.01.035" | ||
| ... |
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