Submission for Issue #79

papers/LCAX-HyxnZh0ct7/README

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+codebase:
+https://github.com/ArnoutDevos/r2d2
+
+issue:
+https://github.com/reproducibility-challenge/iclr_2019/issues/79

papers/LCAX-HyxnZh0ct7/ReScience_src/Makefile

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+# From  https://tex.stackexchange.com/questions/40738/how-to-properly-make-a-latex-project
+# -----------------------------------------------------------------------------
+# You want latexmk to *always* run, because make does not have all the info.
+# Also, include non-file targets in .PHONY so they are run regardless of any
+# file of the given name existing.
+.PHONY: clean
+
+# The first rule in a Makefile is the one executed by default ("make"). It
+# should always be the "all" rule, so that "make" and "make all" are identical.
+
+all: draft
+draft: draft.pdf
+final: final.pdf
+
+
+# CUSTOM BUILD RULES
+# -----------------------------------------------------------------------------
+metadata-draft.tex: metadata-draft.yaml
+	./yaml-to-latex.py -i $< -o $@
+
+metadata-final.tex: metadata-final.yaml
+	./yaml-to-latex.py -i $< -o $@
+
+
+# MAIN LATEXMK RULE
+# -----------------------------------------------------------------------------
+# -pdf tells latexmk to generate PDF directly (instead of DVI).
+# -pdflatex="" tells latexmk to call a specific backend with specific options.
+# -use-make tells latexmk to call make for generating missing files.
+# -interaction=nonstopmode keeps the pdflatex backend from stopping at a
+# missing file reference and interactively asking you for an alternative.
+draft.pdf: draft.tex content.tex metadata-draft.tex
+	latexmk -pdf -pdflatex="xelatex -interaction=nonstopmode" -use-make draft.tex
+
+final.pdf: final.tex content.tex metadata-final.tex
+	latexmk -pdf -pdflatex="xelatex -interaction=nonstopmode" -use-make final.tex
+
+clean:
+	@latexmk -CA
+	@rm -f *.bbl
+	@rm -f *.run.xml

papers/LCAX-HyxnZh0ct7/ReScience_src/README.md

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+### [ReScience C](https://rescience-c.github.io/) article template
+
+This repository contains the Latex (optional) template for writing a ReScience
+C article and the (mandatory) YAML metadata file. For the actual article,
+you're free to use any software you like as long as you enforce the proposed
+PDF style. For the fonts, you'll need:
+
+* [Source Serif Pro (Adobe Systems)](https://github.com/adobe-fonts/source-serif-pro) by F. Grießhammer. 
+* [The Roboto family of fonts (Google)](https://github.com/google/roboto) by C. Robertson.
+* [Source Code Pro (Adobe Systems)](https://github.com/adobe-fonts/source-code-pro) by P.D. Hunt.
+
+The fonts are available for [download from Google Fonts](https://fonts.google.com/selection?selection.family=Roboto|Roboto+Condensed|Roboto+Mono|Roboto+Slab|Source+Code+Pro|Source+Serif+Pro&query=source+code+pro).
+
+A tool is available for the latex template that produces latex definitions from
+the metadata file. If you use another software, make sure that metadata and PDF
+are always synced.
+
+
+#### Usage
+
+For a submission, fill in information in
+[metadata-draft.yaml](./metadata-draft.yaml), modify [content.tex](content.tex)
+and type:
+
+```bash
+$ make draft
+```
+
+After acceptance, fill in [metadata-final.yaml](./metadata-final.yaml) and type:
+
+```bash
+$ make final
+```
+

papers/LCAX-HyxnZh0ct7/ReScience_src/article.py

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+# ReScience yaml parser
+# Released under the BSD two-clauses licence
+
+import yaml
+
+class Contributor:
+    def __init__(self, role, name, orcid="", email="", affiliations=[]):
+        self.role = role
+        self.name = name
+        self.fullname = name
+        self.lastname = self.get_lastname(name)
+        self.abbrvname = self.get_abbrvname(name)
+        self.orcid = orcid
+        self.email = email
+        self.affiliations = affiliations
+
+    def get_abbrvname(self, name):
+        if not name: return ""
+
+        if ',' in name:
+            lastname = name.split(",")[0]
+            firstnames = name.split(",")[1].strip().split(" ")
+        else:
+            lastname = name.split(" ")[-1]
+            firstnames = name.split(" ")[:-1]
+        abbrvname = ""
+        for firstname in firstnames:
+            if "-" in firstname:
+                for name in firstname.split("-"):
+                    abbrvname += name[0].strip().upper() + '.-'
+                abbrvname = abbrvname[:-1]
+            else:
+                abbrvname += firstname[0].strip().upper() + '.'
+        return abbrvname + " " + lastname
+
+
+    def get_lastname(self, name):
+        if not name: return ""
+        # Rougier, Nicolas P.
+        if ',' in name:
+            lastname = name.split(",")[0].strip()
+            firstname = name.split(",")[1].strip()
+        # Nicolas P. Rougier
+        else:
+            lastname = name.split(" ")[-1]
+            firstname = name.split(" ")[:-1]
+        return lastname
+
+
+class Affiliation:
+    def __init__(self, code, name, address=""):
+        self.code = code
+        self.name = name
+        self.address = address
+
+class Repository:
+    def __init__(self, name, url, doi):
+        self.name = name
+        self.url = url
+        self.doi = doi
+
+class Replication:
+    def __init__(self, cite, bib, url, doi):
+        self.cite = cite
+        self.bib = bib
+        self.url = url
+        self.doi = doi
+
+class Review:
+    def __init__(self, url, doi):
+        self.url = url
+        self.doi = doi
+
+class Date:
+    def __init__(self, date):
+        try:
+            import dateutil.parser
+
+            date = dateutil.parser.parse(date)
+            self.date = date
+            self.year = date.year
+            self.month = date.month
+            self.day = date.day
+            self.textual = self.date.strftime("%d %B %Y")
+        except:
+            import datetime
+            now = datetime.datetime.now()
+            self.date = now
+            self.year = now.year
+            self.month = now.month
+            self.day = now.day
+            self.textual = ""
+
+    def __str__(self):
+        return self.textual
+        #return self.date.strftime("%d %B %Y")
+
+    def __repr__(self):
+        return self.textual
+        # return self.date.strftime("%d %B %Y")
+
+
+class Article:
+    def __init__(self, data):
+        self.title = ""
+        self.absract = ""
+        self.type = ""
+        self.domain = ""
+        self.language = ""
+        self.bibliography = ""
+        self.keywords = []
+        self.authors = []
+        self.editors = []
+        self.reviewers = []
+        self.affiliations = []
+        self.code = ""
+        self.data = ""
+        self.contact = ""
+
+        self.review = ""
+        self.replication = ""
+
+        self.date_received = ""
+        self.date_accepted = ""
+        self.date_published = ""
+
+        self.journal_name = ""
+        self.journal_issn = ""
+        self.journal_volume = ""
+        self.journal_issue = ""
+        self.article_number = ""
+        self.article_doi = ""
+        self.article_url = ""
+
+        self.parse(data)
+
+        # Build authors list
+        self.authors_short = "" # Family names only
+        self.authors_abbrv = "" # Abbreviated firsnames + Family names
+        self.authors_full = ""  # Full names
+
+        n = len(self.authors)
+        if n > 3:
+            self.authors_short = self.authors[0].lastname + " et al."
+            self.authors_abbrv = self.authors[0].abbrvname + " et al."
+            self.authors_full = self.authors[0].fullname + " et al."
+        elif n==1:
+            self.authors_short += self.authors[0].lastname
+            self.authors_abbrv += self.authors[0].abbrvname
+            self.authors_full += self.authors[0].fullname
+        else:
+            for i in range(n-2):
+                self.authors_short += self.authors[i].lastname + ", "
+                self.authors_abbrv += self.authors[i].abbrvname + ", "
+                self.authors_full += self.authors[i].fullname + ", "
+
+            if n >= 2:
+                self.authors_short += self.authors[n-2].lastname + " and "
+                self.authors_short += self.authors[n-1].lastname
+
+                self.authors_abbrv += self.authors[n-2].abbrvname + " and "
+                self.authors_abbrv += self.authors[n-1].abbrvname
+
+                self.authors_full += self.authors[n-2].fullname + " and "
+                self.authors_full += self.authors[n-1].fullname
+
+
+
+    def parse(self, data):
+        document = yaml.load(data)
+
+        self.title = document.get("title", "")
+        self.abstract = document.get("abstract","") or ""
+        self.keywords = document["keywords"] or ""
+        self.type = document["type"] or ""
+        self.domain = document["domain"] or ""
+        self.language = document["language"] or ""
+        self.bibliography = document["bibliography"] or ""
+
+        # Miscellaneous dates
+        dates = {key:value for data in document["dates"]
+                           for key, value in data.items()}
+        self.date_received = Date(dates["received"] or "")
+        self.date_accepted = Date(dates["accepted"] or "")
+        self.date_published = Date(dates["published"] or "")
+
+        # Add authors
+        for item in document["authors"]:
+            role = "author"
+            name = item["name"] or ""
+            orcid = item.get("orcid","") or ""
+            email = item.get("email","") or ""
+            if item["affiliations"] is not None:
+                if len(str(item["affiliations"])) > 1:
+                    affiliations = item["affiliations"].split(",")
+                    if "*" in affiliations:
+                        affiliations.remove("*")
+                        author = Contributor(role, name, orcid, email, affiliations)
+                        self.add_contributor(author)
+                        self.contact = author
+                    else:
+                        author = Contributor(role, name, orcid, email, affiliations)
+                        self.add_contributor(author)
+                else:
+                    affiliations = list(str(item["affiliations"]))
+                    author = Contributor(role, name, orcid, email, affiliations)
+                    self.add_contributor(author)
+
+
+        # Add author affiliations
+        for item in document["affiliations"]:
+            self.affiliations.append(
+                Affiliation(item["code"],
+                            item["name"],
+                            item.get("address", "")))
+
+
+        # Add editor & reviewers
+        for item in document["contributors"]:
+            role = item["role"]
+            name = item["name"] or ""
+            orcid = item.get("orcid","") or ""
+            contributor = Contributor(role, name, orcid)
+            self.add_contributor(contributor)
+
+
+        # Code repository (mandatory)
+        if "code" in document.keys():
+            code = {key:value for data in document["code"]
+                              for key, value in data.items()}
+            self.code = Repository("code",
+                                   code.get("url","") or "",
+                                   code.get("doi","") or "")
+        else:
+            raise IndexError("Code repository not found")
+
+        # Data repository (optional)
+        if "data" in document.keys():
+            data = {key:value for data in document["data"]
+                              for key, value in data.items()}
+            self.data = Repository("data",
+                                   data.get("url","") or "",
+                                   data.get("doi","") or "")
+        else:
+            self.data = Repository("data", "", "")
+
+        # Review
+        review = {key:value for review in document["review"]
+                            for key, value in review.items()}
+        self.review = Review(review.get("url","") or "",
+                             review.get("doi","") or "")
+
+        # Replication
+        replication = {key:value for replication in document["replication"]
+                                 for key, value in replication.items()}
+        self.replication = Replication(replication["cite"] or "",
+                                       replication["bib"] or "",
+                                       replication["url"] or "",
+                                       replication["doi"] or "")
+
+        # Article number & DOI
+        article = {key:value for article in document["article"]
+                             for key, value in article.items()}
+        self.article_number = article["number"] or ""
+        self.article_doi = article["doi"] or ""
+        self.article_url = article["url"] or ""
+
+        # Journal volume and issue
+        journal = {key:value for journal in document["journal"]
+                             for key, value in journal.items()}
+        self.journal_name = str(journal.get("name",""))
+        self.journal_issn = str(journal.get("issn", ""))
+        self.journal_volume = journal["volume"] or ""
+        self.journal_issue = journal["issue"] or ""
+
+
+    def add_contributor(self, contributor):
+        if contributor.role == "author":
+            self.authors.append(contributor)
+        elif contributor.role == "editor":
+            self.editors.append(contributor)
+        elif contributor.role == "reviewer":
+            self.reviewers.append(contributor)
+        else:
+            raise(IndexError)
+
+
+
+# -----------------------------------------------------------------------------
+if __name__ == '__main__':
+
+    with open("metadata.yaml") as file:
+        article = Article(file.read())
+        print(article.authors_full)
+        print(article.authors_abbrv)
+        print(article.authors_short)