JOSS paper draft

.gitignore

@@ -23,3 +23,8 @@ docs/_build
 # test related
 test.rea
 test*.f*
+
+# paper
+paper.pdf
+paper/.bundle
+paper/.whedon

codemeta.json

@@ -0,0 +1,68 @@
+{
+    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+    "@type": "Code",
+    "identifier": "pymech",
+    "name": "pymech",
+    "version": "1.4.0",
+    "description": "A Python suite of routines for Nek5000 and Simson.",
+    "license": "GNU General Public License v3 or later (GPLv3+), OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "author": [
+        {
+            "@id": "https://orcid.org/0000-0002-2979-6327",
+            "@type": "Person",
+            "email": "[email protected]",
+            "givenName": "Ashwin Vishnu",
+            "familyName": "Mohanan",
+            "affiliation": "Stockholm University, Stockholm, Sweden"
+        },
+        {
+            "@type": "Person",
+            "givenName": "Guillaume",
+            "familyName": "Chauvat",
+            "affiliation": "KTH Royal Institute of Technology, Stockholm, Sweden"
+        },
+        {
+            "@type": "Person",
+            "givenName": "Nicolo",
+            "familyName": "Fabbiane",
+            "affiliation": "ONERA, Paris, France"
+        },
+        {
+            "@type": "Person",
+            "givenName": "Jacopo",
+            "familyName": "Canton",
+            "affiliation": "ETH Zürich, Zürich, Switzerland"
+        }
+
+    ],
+    "audience": [
+        {
+            "@type": "Audience",
+            "audienceType": "Science/Research"
+        }
+    ],
+    "codeRepository": "https://github.com/jcanton/pymech.git",
+    "issueTracker": "https://github.com/jcanton/pymech/issues",
+    "programmingLanguage": "Python",
+    "datePublished": "2020-03-12",
+    "dateModified": "2020-11-16",
+    "dateCreated": "2016-01-21",
+    "keywords": [
+        "CFD",
+        "fluid dynamics",
+        "post-processing",
+        "Nek5000",
+        "SIMSON",
+        "file I/O"
+    ],
+    "title": "Pymech: A Python suite of routines for Nek5000 and Simson",
+    "provider": {
+        "@id": "https://pypi.org",
+        "@type": "Organization",
+        "name": "The Python Package Index",
+        "url": "https://pypi.org"
+    },
+    "runtimePlatform": "Python 3",
+    "url": "https://github.com/jcanton/pymech",
+    "operatingSystem": "OS Independent"
+}

paper/Makefile

@@ -0,0 +1,23 @@
+# Setup Ruby and execute `bundle install` to get whedon
+OPENJOURNALS_PATH := .whedon/resources
+
+draft: paper.pdf
+
+paper.pdf: paper.md paper.bib
+	pandoc -o paper.pdf -V documentclass=scrartcl -V geometry:margin=1in --pdf-engine=xelatex --citeproc paper.md
+
+
+joss: paper.md paper.bib .whedon
+	pandoc \
+    --defaults=joss-defaults.yaml \
+		--data-dir=$(OPENJOURNALS_PATH) \
+		--resource-path=.:$(OPENJOURNALS_PATH) \
+		--csl=$(OPENJOURNALS_PATH)/apa.csl \
+		--template=$(OPENJOURNALS_PATH)/joss/latex.template \
+		--lua-filter=$(OPENJOURNALS_PATH)/time.lua \
+  	--metadata=aas_logo_path:$(OPENJOURNALS_PATH)/joss/aas-logo.png \
+  	--metadata=logo_path:$(OPENJOURNALS_PATH)/joss/logo.png \
+  	$<
+
+.whedon:
+	git clone https://github.com/openjournals/whedon $@

paper/generate_metadata.py

@@ -0,0 +1,79 @@
+"""Generate pandoc metadata from codemeta.json"""
+import sys
+from collections import OrderedDict
+from json import load
+from pathlib import Path
+from datetime import datetime
+
+import ruamel.yaml
+
+
+here = Path.cwd()
+
+with (here.parent / "codemeta.json").open() as fp:
+    cm = load(fp)
+
+
+#  print(cm)
+
+
+def ordered_set(iterable):
+    return OrderedDict.fromkeys(iterable).keys()
+
+
+uniq_affiliations = list(ordered_set(author["affiliation"] for author in cm["author"]))
+
+
+def make_author(author):
+    data = {
+        "name": " ".join([author["givenName"], author["familyName"]]),
+        "affiliation": uniq_affiliations.index(author.get("affiliation", "")) + 1,
+    }
+    orcid_url = author.get("@id")
+    if orcid_url:
+        data.update({"orcid": Path(orcid_url).name})
+    return data
+
+
+def make_affiliations():
+    return [{"name": name, "index": i + 1} for i, name in enumerate(uniq_affiliations)]
+
+
+def make_date(date):
+    date_parsed = datetime.strptime(date, "%Y-%m-%d")
+    return datetime.strftime(date_parsed, "%d %B %Y")
+
+
+# Prepare data for metadata output
+data = {
+    "title": cm.get("title", ""),
+    "tags": cm.get("keywords", []),
+    "authors": [make_author(_) for _ in cm.get("author", [{}])],
+    "affiliations": make_affiliations(),
+    "date": make_date(cm.get("dateModified", "")),
+    "bibliography": "paper.bib",
+}
+
+
+# FIXME: New API wraps dictionaries
+# yaml = ruamel.yaml.YAML(typ='safe')
+# yaml.compact(seq_seq=False, seq_map=False)
+# yaml.allow_unicode = True
+# yaml.indent(sequence=4, offset=2, mapping=4)
+def dump(data, dest):
+    # yaml.dump(data, dest)
+    ruamel.yaml.dump(
+        data,
+        dest,
+        explicit_start=True,
+        allow_unicode=True,
+        Dumper=ruamel.yaml.RoundTripDumper,
+    )
+
+
+dest = sys.stdout
+dump(data, dest)
+#  output = here / "metadata.yaml"
+#  dest = output.open("w")
+#  with output.open("w") as dest:
+#      dump(data, dest)

paper/joss-defaults.yaml

@@ -0,0 +1,48 @@
+# Combined from joss/defaults.yaml and docker-defaults.yaml file in whedon repository
+from: markdown
+to: latex
+output-file: paper.pdf
+standalone: true
+
+# note that structured variables may be specified:
+variables:
+  archive_doi: 'DOI unavailable'
+  doi_batch_id: 'N/A'
+  editor_url: 'https://example.com'
+  formatted_doi: 'DOI unavailable'
+  repository: 'NO_REPOSITORY'
+  review_issue_url: 'N/A'
+  paper_url: 'NO PAPER URL'
+  joss_resource_url: 'N/A'
+  journal_abbrev_title: 'JOSS'
+  journal_alias: 'joss'
+  journal_issn: '2475-9066'
+  journal_name: 'Journal of Open Source Software'
+  journal_url: 'https://joss.theoj.org/'
+
+metadata:
+  citation_author: '¿citation_author?'
+  editor_name: 'Pending Editor'
+  issue: '¿ISSUE?'
+  page: '¿PAGE?'
+  published: 'N/A'
+  reviewers:
+    - 'Pending Reviewers'
+  submitted: 'N/A'
+  volume: '¿VOL?'
+
+# resource-path: [".", '/usr/local/share/openjournals']
+
+filters:
+  - citeproc
+
+# ERROR, WARNING, or INFO
+verbosity: INFO
+
+pdf-engine: xelatex
+dpi: 300
+
+default-image-extension: ".png"
+reference-links: true
+fail-if-warnings: true
+

paper/paper.bib

@@ -0,0 +1,81 @@
+
+@book{AyachitParaView2015,
+  title = {The {{ParaView Guide}}: {{A Parallel Visualization Application}}},
+  shorttitle = {The {{ParaView Guide}}},
+  author = {Ayachit, Utkarsh},
+  year = {2015},
+  publisher = {{Kitware, Inc.}},
+  address = {{Clifton Park, NY, USA}},
+  isbn = {978-1-930934-30-6}
+}
+
+@book{Chevalier.etalSIMSON2007,
+  title = {{{SIMSON}}: A Pseudo-Spectral Solver for Incompressible Boundary Layer Flows},
+  shorttitle = {{{SIMSON}}},
+  author = {Chevalier, Mattias and Schlatter, Philipp and Lundbladh, Anders and Henningson, Dan S.},
+  year = {2007},
+  publisher = {{Mekanik, Kungliga Tekniska h\"ogskolan}},
+  address = {{Stockholm}},
+  url = {https://www.mech.kth.se/~mattias/simson-user-guide-v4.0.pdf},
+  annotation = {OCLC: 234048689},
+  isbn = {978-91-7178-838-2},
+  language = {en}
+}
+
+@inproceedings{Childs.etalContract2005,
+  title = {A Contract Based System for Large Data Visualization},
+  booktitle = {{{VIS}} 05. {{IEEE Visualization}}, 2005.},
+  author = {Childs, H. and Brugger, E. and Bonnell, K. and Meredith, J. and Miller, M. and Whitlock, B. and Max, N.},
+  year = {2005},
+  month = oct,
+  pages = {191--198},
+  doi = {10.1109/VISUAL.2005.1532795},
+  keywords = {Concurrent computing,contract based system,Contracts,Data analysis,data flow computing,data visualisation,Data visualization,featured visualization tool,Geometry,Graphics,Hardware,Laboratories,Pipelines,Rendering (computer graphics),very large databases,VisIt data flow network design}
+}
+
+@article{Harris.etalArray2020,
+  title = {Array Programming with {{NumPy}}},
+  author = {Harris, Charles R. and Millman, K. Jarrod and {van der Walt}, St{\'e}fan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and {van Kerkwijk}, Marten H. and Brett, Matthew and Haldane, Allan and {del R{\'i}o}, Jaime Fern{\'a}ndez and Wiebe, Mark and Peterson, Pearu and {G{\'e}rard-Marchant}, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
+  year = {2020},
+  month = sep,
+  volume = {585},
+  pages = {357--362},
+  publisher = {{Nature Publishing Group}},
+  issn = {1476-4687},
+  doi = {10.1038/s41586-020-2649-2},
+  url = {https://www.nature.com/articles/s41586-020-2649-2},
+  urldate = {2020-09-25},
+  journal = {Nature},
+  language = {en},
+  number = {7825}
+}
+
+@article{Hoyer.HammanXarray2017,
+  title = {Xarray: {{N}}-{{D}} Labeled {{Arrays}} and {{Datasets}} in {{Python}}},
+  shorttitle = {Xarray},
+  author = {Hoyer, Stephan and Hamman, Joe},
+  year = {2017},
+  month = apr,
+  volume = {5},
+  pages = {10},
+  publisher = {{Ubiquity Press}},
+  issn = {2049-9647},
+  doi = {10.5334/jors.148},
+  url = {http://openresearchsoftware.metajnl.com/articles/10.5334/jors.148/},
+  urldate = {2021-03-09},
+  journal = {Journal of Open Research Software},
+  keywords = {data analysis,data; data handling,multidimensional,netCDF,pandas,Python},
+  language = {en},
+  number = {1}
+}
+
+@misc{NEK50002019,
+  title = {{{NEK5000}} Version 19.0},
+  year = {2019},
+  month = dec,
+  url = {https://nek5000.mcs.anl.gov/},
+  urldate = {2021-03-17},
+  howpublished = {Argonne National Laboratory, Illinois}
+}
+
+