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Add CFF citation support and contribution instructions (#25)
* Add CFF citation support and contribution instructions * Delete footer.md * remove author information from supplementary pages I.e., examples, schemas, etc.
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‎ngff_spec/CITATION.cff‎

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cff-version: 1.2.0
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message: Please cite the following works when using this project.
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abstract: >-
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A growing community is constructing a next-generation file format (NGFF) for
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bioimaging to overcome problems of scalability and heterogeneity. Organized by
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the Open Microscopy Environment (OME), individuals and institutes across
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diverse modalities facing these problems have designed a format specification
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process (OME-NGFF) to address these needs. Those community members have built
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the format itself – OME-Zarr – along with tools and data resources available
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today to increase FAIR access and remove barriers in the scientific process.
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The current momentum offers an opportunity to unify a key component of the
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bioimaging domain — the file format that underlies so many personal,
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institutional, and global data management and analysis tasks.
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title: Next-generation file format specification
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authors:
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- family-names: NGFF-community
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given-names: ''
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identifiers:
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- type: doi
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value: 10.1038/s41592-021-01326-w
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description: Original Nature Methods article (2021)
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- type: doi
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value: 10.1101/2023.02.17.528834v2
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description: OME-Zarr preprint (2023)
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keywords:
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- FAIR
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- community
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- bioimaging
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- data
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- cloud
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- format
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license: CC-BY-4.0
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url: https://ngff.openmicroscopy.org
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repository: https://github.com/ome/ngff-spec
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preferred-citation:
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type: article
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doi: 10.1038/s41592-021-01326-w
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journal: Nature Methods
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month: 11
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start: 1496
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end: 1498
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title: >-
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OME-NGFF: a next-generation file format for expanding bioimaging data-access
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strategies
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issue: 12
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volume: 18
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year: 2021
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authors:
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- given-names: Josh
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family-names: Moore
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orcid: https://orcid.org/0000-0003-4028-811X
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- given-names: Chris
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family-names: Allan
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- given-names: Sébastien
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family-names: Besson
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orcid: https://orcid.org/0000-0001-8783-1429
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- given-names: Jean-Marie
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family-names: Burel
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orcid: https://orcid.org/0000-0002-1789-1861
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- given-names: Erin
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family-names: Diel
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orcid: https://orcid.org/0000-0003-2526-3512
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- given-names: David
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family-names: Gault
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- given-names: Kevin
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family-names: Kozlowski
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- given-names: Dominik
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family-names: Lindner
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orcid: https://orcid.org/0000-0001-8038-1250
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- given-names: Melissa
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family-names: Linkert
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- given-names: Trevor
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family-names: Manz
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orcid: https://orcid.org/0000-0001-7694-5164
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- given-names: Will
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family-names: Moore
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orcid: https://orcid.org/0000-0002-7264-8338
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- given-names: Constantin
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family-names: Pape
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orcid: https://orcid.org/0000-0001-6562-7187
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- given-names: Christian
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family-names: Tischer
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orcid: https://orcid.org/0000-0003-4105-1990
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- given-names: Jason R.
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family-names: Swedlow
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orcid: https://orcid.org/0000-0002-2198-1958
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type: software
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repository-code: https://github.com/ome/ngff

‎ngff_spec/citing.md‎

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Citing
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======
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---
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title: Citing
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author: ""
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---
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(citing)=
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[Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4)

‎ngff_spec/contribute.md‎

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---
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author: ""
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---
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# Contribution guide
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Contributions to the spec text, examples and schemas are highly welcome
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You'll find the built webpages under `_build/html`.
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## First contribution
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If you haven't contributed to the spec before,
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please add yourself as an author in the `ngff_spec/myst.yml` metadata file.
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This should look like this, for example:
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```yaml
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- name: John A. Doe
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id: jdoe
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orcid: xxxx-xxxx-xxxx-xxxx
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github: jdoe
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affiliations:
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- id: key
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institution: ICSLDJ University
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city: Doeburg
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ror: https://ror.org/....
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- name: Jane Doe
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affiliations: key
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```
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For more information see [myst documentation on author formatting](https://mystmd.org/guide/frontmatter#frontmatter-authors).
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When you submit your first PR,
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make sure to rebuild the `CITATION.cff` file in the root of this repository.
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To do so, run the following command:
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```bash
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cd ngff_spec/ && jupyter book build --cff
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```
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Copy the generated `CITATION.cff` file from `ngff_spec/CITATION.cff` to the root of this repository
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and submit it along with your PR.
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### Text format
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Contributions should conform to [Semantic Line Breaks (SemBr)](https://sembr.org/),

‎ngff_spec/examples.md‎

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---
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title: NGFF metadata JSON Examples
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short_title: JSON Examples
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author: ""
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---
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This section contains JSON examples for various metadata layouts.

‎ngff_spec/myst.yml‎

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- format: pdf
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template: plain_latex_book
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output: exports/book.pdf
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- format: cff
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type: software
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identifiers:
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- type: doi
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value: 10.1038/s41592-021-01326-w
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description: Original Nature Methods article (2021)
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- type: doi
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value: 10.1101/2023.02.17.528834v2
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description: OME-Zarr preprint (2023)
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repository-code: 'https://github.com/ome/ngff'
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url: 'https://ngff.openmicroscopy.org'
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abstract: >-
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A growing community is constructing a next-generation file
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format (NGFF) for bioimaging to overcome problems of
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scalability and heterogeneity. Organized by the Open
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Microscopy Environment (OME), individuals and institutes
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across diverse modalities facing these problems have
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designed a format specification process (OME-NGFF) to
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address these needs. Those community members have built
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the format itself – OME-Zarr – along with tools and data
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resources available today to increase FAIR access and
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remove barriers in the scientific process. The current
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momentum offers an opportunity to unify a key component of
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the bioimaging domain — the file format that underlies so
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many personal, institutional, and global data management
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and analysis tasks.
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keywords:
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- FAIR
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- community
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- bioimaging
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- data
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- cloud
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- format
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license: CC-BY-4.0
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preferred-citation:
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type: article
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doi: "10.1038/s41592-021-01326-w"
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journal: "Nature Methods"
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month: 11
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start: 1496
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end: 1498
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title: "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies"
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issue: 12
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volume: 18
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year: 2021
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authors:
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- given-names: "Josh"
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family-names: "Moore"
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orcid: "https://orcid.org/0000-0003-4028-811X"
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- given-names: "Chris"
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family-names: "Allan"
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- given-names: "Sébastien"
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family-names: "Besson"
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orcid: "https://orcid.org/0000-0001-8783-1429"
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- given-names: "Jean-Marie"
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family-names: "Burel"
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orcid: "https://orcid.org/0000-0002-1789-1861"
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- given-names: "Erin"
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family-names: "Diel"
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orcid: "https://orcid.org/0000-0003-2526-3512"
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- given-names: "David"
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family-names: "Gault"
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- given-names: "Kevin"
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family-names: "Kozlowski"
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- given-names: "Dominik"
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family-names: "Lindner"
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orcid: "https://orcid.org/0000-0001-8038-1250"
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- given-names: "Melissa"
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family-names: "Linkert"
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- given-names: "Trevor"
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family-names: "Manz"
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orcid: "https://orcid.org/0000-0001-7694-5164"
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- given-names: "Will"
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family-names: "Moore"
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orcid: "https://orcid.org/0000-0002-7264-8338"
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- given-names: "Constantin"
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family-names: "Pape"
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orcid: "https://orcid.org/0000-0001-6562-7187"
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- given-names: "Christian"
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family-names: "Tischer"
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orcid: "https://orcid.org/0000-0003-4105-1990"
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- given-names: "Jason R."
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family-names: "Swedlow"
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orcid: "https://orcid.org/0000-0002-2198-1958"
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toc:
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- file: specification.md
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- file: examples.md

‎ngff_spec/pre_build.py‎

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index_md = """---
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title: NGFF metadata JSON Examples
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short_title: JSON Examples
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author: ""
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---
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This section contains JSON examples for various metadata layouts.
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index_md += f"\n## {example}\n"
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# add header
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markdown_content = f"""# {example}\n\n
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markdown_content = f"""---
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title: {example} Examples
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author: ""
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---
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This document contains JSON examples for {example} metadata layouts.
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os.makedirs(output_directory, exist_ok=True)
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schema_files = glob.glob(os.path.join(schema_source_dir, '*.schema'), recursive=True)
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index_markdown = """# JSON Schemas
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index_markdown = """---
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title: NGFF metadata JSON Schemas
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short_title: JSON Schemas
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author: ""
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---
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This section contains JSON schemas for various metadata layouts.
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Find below links to auto-generated markdown pages or interactive HTML pages for each schema.
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with open(output_path_md, 'r') as md_file:
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md_content = md_file.read()
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crossref = f"schemas:{Path(schema_file).stem}"
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md_content = f"({crossref})=\n\n{md_content}"
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md_content = f"""---
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author: ""
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---
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({crossref})=\n\n{md_content}
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"""
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with open(output_path_md, 'w') as md_file:
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md_file.write(md_content)
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‎ngff_spec/schemas.md‎

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# JSON Schemas
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---
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title: NGFF metadata JSON Schemas
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short_title: JSON Schemas
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author: ""
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---
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This section contains JSON schemas for various metadata layouts.
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Find below links to auto_generated markdown pages or interactive HTML pages for each schema.
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Find below links to auto-generated markdown pages or interactive HTML pages for each schema.
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| Schema | Markdown | HTML |
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|--------|----------|------|

‎ngff_spec/version_history.md‎

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---
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author: ""
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---
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# Version History
2-
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(history)=
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All notable changes to this project will be documented in this file.

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