rescience/rescience-submission

ReScience submission repository

The ReScience Journal

ReScience is a platinum open-access peer-reviewed journal that targets computational research and encourages the explicit replication of already published research promoting new and open-source implementations in order to ensure the original research is reproducible. To achieve such a goal, the whole editing chain is radically different from any other traditional scientific journal. ReScience lives on github where each new implementation is made available together with the comments, explanations and tests. Each submission takes the form of a pull request that is publicly reviewed and tested in order to guarantee any researcher can re-use it. If you ever replicated a computational result from the literature, ReScience is the perfect place to publish this new implementation. Reproducible Science is Good. Replicated Science is better.

The Editorial Board

Note: This repository contains the first volumes of ReScience. Articles were submitted as pull requests to ReScience-submissions, which were merged upon acceptance with a reference added to this repository. The new ReScience C workflow is a bit different and based on two new repositories: one for submissions and another one containing the accepted articles. The entry point for ReScience remains its Web site.

Archives

• Volume 4 - Issue 1
• Volume 3 - Issue 1
• Volume 2 - Issue 1
• Volume 1 - Issue 1

rescience-submission's Issues

Problem with pandoc-crossref

Dear ReScience Team,

since two weeks, I try to install pandoc-crossref on my linux-mint system. Sadly, the interplay of cabal and the ghc brings always a lot of errors. Because of this, I want to ask, if it possible to create the *.pdf without pandoc and pandoc-crossref ? Is it maybe possible, that I just recreate the *.tex file for my own, without pandoc?

Many thanks in advance!

Re-implementation of open source methods in another language

Dear Rescience editors. In the course of our work, we have created a Python implementation of a method that was previously available as open-source R code. Is this implementation within the scope of Rescience? Thanks! cc:@kpolimis, @bhazelton

Possible outdated pandoc command in the Makefile

I just had to modify the pandoc command in the Makefile, replacing --latex-engine with --pdf-engine as with my 2.6 version of pandoc as when pandoc tries to use --latex-engine I get the error --latex-engine has been removed. Use --pdf-engine instead. and looking in the pandoc help this appears to be the case.

I'm fumbling around a bit with this stuff though, so before issuing a PR to update the Makefile, I thought I might check to see if this will be an issue for others.

Xelatex issues with FontAwesome on macOS

Compiling the article with the template provided by ReScience can lead to a confusing issue for users of macOS using MacTex, as I just experienced. It is well described here by someone else that stumbled into this one month ago: https://tex.stackexchange.com/questions/369068/how-can-i-use-the-fontawesome-package-with-xelatex

I solved this by opening the otf file located in /usr/local/texlive/2017/texmf-dist/fonts/opentype/public/fontawesome/FontAwesome.otf with Font Book, and installing it as a regular font.

We may want to include something about that in the README.md (possibly along with including FontAwesome.otf directly in the repo to make it easier) or solve the problem in some other way.

Unable to install pandoc-crossref that's required by the Makefile

Hiya,

I've been trying to install pandoc-crossref that's required by the makefile, but I can't seem to get it to work somehow. I've also filed a ticket upstream, but they're not quite sure what's happening either.

pandoc-crossref.txt

This is a Fedora 26 system here. Anyone else seeing this?

article pandoc and tex problem

Greetings,

I tried to use the provided template after installing the latest TeX Live, pandoc, pandoc-crossref but I get these errors:

allStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:113:48 in pandoc-types-1.17.0.5-8QF4dYNSmQFGMk7bUzM7GZ:Text.Pandoc.JSON
pandoc: Error running filter /home/sepehr/.cabal/bin/pandoc-crossref
Filter returned error status 1
Makefile:10: recipe for target 'rescience-template.tex' failed
make: *** [rescience-template.tex] Error 83

I tried without a sandbox, but I get the same error. I tried installing pandoc-crossref 0.1.5.6 but cabal gets stuck forever.

pandoc-crossref filter out of date

In my initial attempts at c03fe28 I was using the latest version of pandoc-crossref (0.1.6.3) and getting this error:

pandoc-crossref: Error in $[6][0]: When expecting a product of 3 values, encountered an Array of 2 elements instead pandoc: Error running filter /root/.cabal/bin/pandoc-crossref

Apparently this error gets thrown when the filter is designed for a different version of pandoc-types. I solved the issue by using an earlier version of pandoc-crossref (0.1.5.6). Anyway, I think the filter needs to be updated.

pandoc command revision?

Probably need to change:
--bibliography=article.bib
to
--bibliography=your_article_name.bib

(And thanks for the journal, it looks very interesting; I hope to soon make a submission.)

Use binder for notebooks

mybinder.org lets people run jupyter notebooks from github repos in the cloud for free -- it might significantly decrease install issues for reviewers.

Changes in pandoc-crossref

It seems that pandoc-crossref is now installed by default in:
~/Library/Haskell/bin/pandoc-crossref
So the compilation insctructions sould be udated (they refer to ~/.cabal/bin/pandoc-crossref)

Can the Makefile load the amsmath package?

The amsmath LaTeX package is required when using math environments such as cases. Can it be loaded in the Makefile?

Change the name of the pdf

In the first published article, the name of the pdf has not been changed, which makes the downloaded file have a less than optimal name ("article"). I'm wondering if changing the name to "your_article_name.md" would be suggestive enough for the user of the submission repo to actually change the name of the file!

pandoc + xelatex chocking on the \tightlist tex command.

I get a

! Undefined control sequence.
l.227 \tightlist

which apparently comes from a "new" feature of pandoc that has not been integrated in the template. I will propose a PR modifying the template, but it asks the bigger question of maybe forking the default latex template to integrate the changes these guys make along the way.