3 ms·

Reason: A Shell for Research Papers in Rust

27 points by jaywonchung 3y ago

evolve2k 3y ago
I have all my papers in Zotero which I assume has a folder full of PDFs somewhere on my system. Can I plug reason into my existing workflow?
- deleted 3y ago
  [deleted]
- jaywonchung 3y ago
  Ah, integration with other tools is currently what I didn't think about too much, but I completely agree with the need. People usually have their own way to manage references. Basically all of the states of Reason (i.e., the paperbase) is a single YAML file that looks like this: https://github.com/jaywonchung/reason/blob/master/examples/metadata.yaml https://github.com/jaywonchung/reason/blob/master/examples/m... Pretty much every command is reading from or writing to this file, or both. So, if you can find a way to convert that to the Reason YAML format, you'll be able to use Reason at least as a paper browser, opener, and note taker. Is there anything more that you envision in integrating Reason with your Zotero workflow?
  - patrick451 3y ago
    I'm confused about the use case for this tool if it's neither meant to be a reference manager (which it must not be given how little information is stored in the yaml) and it's also not meant to integrate with existing reference managers. So it seems that really using it means I'd be managing a database of papers in two places. Also if you're already using a flat file as a database, why not just use bibtex? That format is commonly provided by publishers already, and has a much higher chance of being compatible with existing reference managers. E.g., it's the native format of JabRef and helm-bibtex, though I'm not sure about zotero. Either way, bibtex is usually going to be needed if you want to cite one of these papers.
    - jaywonchung 3y ago
      Right, fair question. I've tried many reference managers over several years but not one of them really felt like home. Their PDF viewer was lacking the features I wanted (e.g., jumping back to the original place after clicking an internal link, Sioyek-like preview windows), filtering wasn't expressive enough, etc, and above all, I just wanted to be in the command line. So, currently, I don't use any reference management software. In my current paper writing workflow I simply do not need one, as I have a giant `ref.bib` file that I constantly append with relevant papers in my field, and I can just throw that into my LaTeX project to get all the references I can possibly want. Then, I use `reason` as a glue tool that simply tracks the PDF location and markdown location of each paper, allowing me to use my favorite text editor (nvim) and favorite PDF viewer (Sioyek) without being tied to any reference management software. To be fair, I may be missing out on some of the great features reference managers might be providing. Please feel free to enlighten me :)
      - evolve2k 3y ago
        Incase it’s of any value, thought I’d share my situation and where your tool might fit. Im currently completing a phd and having a dev background wanted a good text based workflow, specifically the Zettelkasten method using Zotero and Obsidian, something like this: https://m.youtube.com/watch?v=mMpVMuGBGe8&pp=ygUiWmV0ZWxrYXNrZW4gbWV0aG9kIG9ic2lkaWFuIHpvdGVybw%3D%3D https://m.youtube.com/watch?v=mMpVMuGBGe8&pp=ygUiWmV0ZWxrYXN... I use Zotero as the reference manager, I can get academic articles “PDFs” into it via many means. I’ve then wired up Obsidian, which is just a folder of Markdown files in a way that links to Zotero and I can drop reference links in the docs I write in obsidian that link to Zotero. I do my writing in obsidian, and then can export to word at which time references to Zotero are auto generated into proper academic references and a useable bibliography. I’ve documented the whole workflow here in the hope others use it to and contribute improvements: https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide/tree/main https://github.com/evolve2k/obsidian-pandoc-academic-word-do... Linking Zotero and Obsidian together it’s recommended to use the Better Bibtex plug-in. Bibtex very much can be used for this workflow but CSLJSON is also supported. For your tools consider supporting Bibtex and/or CSLJSON and you’ll be able to be folded into many workflows. My existing workflow solves “article collection & collaborative collection” (Zotero) followed on to academic paper writing and generating via an obsidian markdown workflow. What I’m personally missing is the cli way to ask quick questions about my Zotero articles dataset. I think that’s a great place for your tool. Also while I started with Bibtex my research showed that longer bibliographies work better with CSLJSON, it’s basically like Bibtex but as a json format. Worth a look: https://github.com/citation-style-language/schema https://github.com/citation-style-language/schema Here’s the relevant part of my workflow where I stick Zotero and obsidian together by configuring Bibtex/CSLJSON. https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide/blob/main/setup-zotero-obsidian.md https://github.com/evolve2k/obsidian-pandoc-academic-word-do...

27 points by jaywonchung 3y ago

I have all my papers in Zotero which I assume has a folder full of PDFs somewhere on my system. Can I plug reason into my existing workflow?

deleted 3y ago
[deleted]
jaywonchung 3y ago
Ah, integration with other tools is currently what I didn't think about too much, but I completely agree with the need. People usually have their own way to manage references. Basically all of the states of Reason (i.e., the paperbase) is a single YAML file that looks like this: https://github.com/jaywonchung/reason/blob/master/examples/metadata.yaml https://github.com/jaywonchung/reason/blob/master/examples/m... Pretty much every command is reading from or writing to this file, or both. So, if you can find a way to convert that to the Reason YAML format, you'll be able to use Reason at least as a paper browser, opener, and note taker. Is there anything more that you envision in integrating Reason with your Zotero workflow?
- patrick451 3y ago
  I'm confused about the use case for this tool if it's neither meant to be a reference manager (which it must not be given how little information is stored in the yaml) and it's also not meant to integrate with existing reference managers. So it seems that really using it means I'd be managing a database of papers in two places. Also if you're already using a flat file as a database, why not just use bibtex? That format is commonly provided by publishers already, and has a much higher chance of being compatible with existing reference managers. E.g., it's the native format of JabRef and helm-bibtex, though I'm not sure about zotero. Either way, bibtex is usually going to be needed if you want to cite one of these papers.
  - jaywonchung 3y ago
    Right, fair question. I've tried many reference managers over several years but not one of them really felt like home. Their PDF viewer was lacking the features I wanted (e.g., jumping back to the original place after clicking an internal link, Sioyek-like preview windows), filtering wasn't expressive enough, etc, and above all, I just wanted to be in the command line. So, currently, I don't use any reference management software. In my current paper writing workflow I simply do not need one, as I have a giant `ref.bib` file that I constantly append with relevant papers in my field, and I can just throw that into my LaTeX project to get all the references I can possibly want. Then, I use `reason` as a glue tool that simply tracks the PDF location and markdown location of each paper, allowing me to use my favorite text editor (nvim) and favorite PDF viewer (Sioyek) without being tied to any reference management software. To be fair, I may be missing out on some of the great features reference managers might be providing. Please feel free to enlighten me :)
    - evolve2k 3y ago
      Incase it’s of any value, thought I’d share my situation and where your tool might fit. Im currently completing a phd and having a dev background wanted a good text based workflow, specifically the Zettelkasten method using Zotero and Obsidian, something like this: https://m.youtube.com/watch?v=mMpVMuGBGe8&pp=ygUiWmV0ZWxrYXNrZW4gbWV0aG9kIG9ic2lkaWFuIHpvdGVybw%3D%3D https://m.youtube.com/watch?v=mMpVMuGBGe8&pp=ygUiWmV0ZWxrYXN... I use Zotero as the reference manager, I can get academic articles “PDFs” into it via many means. I’ve then wired up Obsidian, which is just a folder of Markdown files in a way that links to Zotero and I can drop reference links in the docs I write in obsidian that link to Zotero. I do my writing in obsidian, and then can export to word at which time references to Zotero are auto generated into proper academic references and a useable bibliography. I’ve documented the whole workflow here in the hope others use it to and contribute improvements: https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide/tree/main https://github.com/evolve2k/obsidian-pandoc-academic-word-do... Linking Zotero and Obsidian together it’s recommended to use the Better Bibtex plug-in. Bibtex very much can be used for this workflow but CSLJSON is also supported. For your tools consider supporting Bibtex and/or CSLJSON and you’ll be able to be folded into many workflows. My existing workflow solves “article collection & collaborative collection” (Zotero) followed on to academic paper writing and generating via an obsidian markdown workflow. What I’m personally missing is the cli way to ask quick questions about my Zotero articles dataset. I think that’s a great place for your tool. Also while I started with Bibtex my research showed that longer bibliographies work better with CSLJSON, it’s basically like Bibtex but as a json format. Worth a look: https://github.com/citation-style-language/schema https://github.com/citation-style-language/schema Here’s the relevant part of my workflow where I stick Zotero and obsidian together by configuring Bibtex/CSLJSON. https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide/blob/main/setup-zotero-obsidian.md https://github.com/evolve2k/obsidian-pandoc-academic-word-do...