JOSS Paper

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git,env,*build,bids-examples,coverage_html,schema.json
+skip = *.js,*.svg,*.eps,.git,env,*build,bids-examples,coverage_html,schema.json,docs/paper/paper.bib
 ignore-words-list = te,ans,nin
 builtin = clear,rare

docs/paper/.gitignore

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+*.html
+*.pdf
+*.docx

docs/paper/checklist.md

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+## General checks
+
+Repository:
+
+Is the source code for this software available at the https://github.com/JamesPHoughton/pysd/?
+
+License:
+
+Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
+
+Contribution and authorship:
+
+Has the submitting author (@rogersamso) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
+
+Substantial scholarly effort:
+
+Does this submission meet the scope eligibility described in the JOSS guidelines
+
+## Functionality
+
+Installation:
+
+Does installation proceed as outlined in the documentation?
+
+Functionality:
+
+Have the functional claims of the software been confirmed?
+
+Performance:
+
+If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
+
+## Documentation
+
+A statement of need:
+
+Do the authors clearly state what problems the software is designed to solve and who the target audience is?
+
+Installation instructions:
+
+Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
+
+Example usage:
+
+Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
+
+Functionality documentation:
+
+Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
+
+Automated tests:
+
+Are there automated tests or manual steps described so that the functionality of the software can be verified?
+
+Community guidelines:
+
+Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
+
+## Software paper
+
+Summary:
+
+Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
+
+A statement of need:
+
+Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
+
+State of the field:
+
+Do the authors describe how this software compares to other commonly-used packages?
+
+Quality of writing:
+
+Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
+
+References:
+
+Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

docs/paper/metadata.py

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+# yml front matter for paper from citaton.cff file
+
+import ruamel.yaml
+from pathlib import Path
+from rich import print
+
+from datetime import datetime
+
+yaml = ruamel.yaml.YAML()
+yaml.indent(mapping=2, sequence=4, offset=2)
+
+CITATION_CFF = Path(__file__).parent.parent.parent.joinpath("CITATION.cff")
+
+first_author = "Gau"
+sort_authors_alphabetically = True
+
+
+def return_author_order(author_list, first_author):
+    """Return the order of authors in the paper."""
+    author_order = [x["family-names"].strip() for x in author_list]
+    if sort_authors_alphabetically:
+        author_order = sorted(author_order)
+    author_order.pop(author_order.index(first_author))
+    author_order.insert(0, first_author)
+    print(author_order)
+    return author_order
+
+
+def main():
+    with open(CITATION_CFF, encoding="utf8") as f:
+        citation = yaml.load(f)
+
+    author_order = return_author_order(citation["authors"], first_author)
+    author_names = [x["family-names"].strip() for x in citation["authors"]]
+
+    author_list = []
+    affiliation_list = []
+
+    for this_author_name in author_order:
+
+        author = citation["authors"][author_names.index(this_author_name)]
+
+        this_author = {
+            "name": f"{author['given-names']} {author.get('family-names', '')}".strip()
+        }
+
+        if author.get("orcid", None) is not None:
+            this_author["orcid"] = author.get("orcid").replace("https://orcid.org/", "")
+
+        if author.get("affiliation") is not None:
+
+            this_affiliation = author.get("affiliation")
+            affiliation_list_names = [x["name"] for x in affiliation_list]
+
+            if this_affiliation not in affiliation_list_names:
+                affiliation_list.append(
+                    {"name": this_affiliation, "index": len(affiliation_list) + 1}
+                )
+
+            affiliation_list_names = [x["name"] for x in affiliation_list]
+            this_author["affiliation"] = (
+                affiliation_list_names.index(this_affiliation) + 1
+            )
+
+        author_list.append(this_author)
+
+    content = {
+        "title": "",
+        "tags": citation["keywords"],
+        "authors": author_list,
+        "affiliations": affiliation_list,
+        "date": datetime.now().strftime("%Y-%m-%d"),
+        "bibliography": "paper.bib",
+    }
+
+    with open("metadata.yml", "w", encoding="utf8") as output_file:
+        return yaml.dump(content, output_file)
+
+
+if __name__ == "__main__":
+    main()

docs/paper/metadata.yml

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+---
+title: ''
+tags:
+- MATLAB
+- Octave
+- brain imaging data structure
+- MRI
+- MEG
+- EEG
+- iEEG
+- PET
+- microscopy
+
+authors:
+- name: Rémi Gau
+  orcid: 0000-0002-1535-9767
+  affiliation: 1
+- name: Marco Barilari
+  orcid: 0000-0002-3313-3120
+  affiliation: 1
+- name: Ceren Battal
+  orcid: 0000-0002-9844-7630
+  affiliation: 1
+- name: Nikita Beliy
+- name: Rotem  Botvinik-Nezer
+- name: Jeanne Caron-Guyon
+  orcid: 0000-0001-8681-5267
+  affiliation: 1
+- name: Phillips Chrisophe
+  orcid: 0000-0002-4990-425X
+- name: Tanguy Duval
+  orcid: 0000-0002-1228-5192
+- name: Guillaume Flandin
+  orcid: 0000-0003-0077-7859
+- name: Andrew Janke
+- name: Michèle MacLean
+  orcid: 0000-0002-0174-9326
+  affiliation: 2
+- name: Christopher Madan
+  orcid: 0000-0003-3228-6501
+- name: Henk Mutsaerts
+  orcid: 0000-0003-0894-0307
+- name: Guiomar Niso
+  orcid: 0000-0001-5872-8924
+- name: Martin Norgaard
+  orcid: 0000-0003-2131-5688
+- name: Robert Oostenveld
+  orcid: 0000-0002-1974-1293
+- name: Cyril Pernet
+  orcid: 0000-0003-4010-4632
+- name: Iqra Shahzad
+  orcid: 0000-0002-8724-7668
+  affiliation: 1
+- name: Michał Szczepanik
+  orcid: 0000-0002-4028-2087
+affiliations:
+- name: Université catholique de Louvain
+  index: 1
+- name: Université de Montréal
+  index: 2
+date: '2022-10-21'
+bibliography: paper.bib