Workflows with Markdown

Mac & Windows (Desktop)
#41

All i wish for is a way to see my markdown note for an item and open the note in the default software if I need to edit it.
I don’t need sync either for that, even though it would have been a nice feature if the body of the notes also was synced to a text field viewable in “preview mode” or something in Aeon…
much of the same you write… I actually do link the Markdown files (directly as files on disk) and the Zotero items (as Zotero URL’s) when needed, just like you…

Some reason the default editor can’t be Obsidian from Plottr?
I did buy a license for that software, but dropped out when they went subscription based, it just didn’t give me that much, that I couldn’t do in other software, most of my projects are based on historical events and objects so it was important for me to actually see the dates in the timeline…

Digression
but I do use Obsidian extensively, and testing Foam for VSC.
Here is a little printscreen of a little part of a project displayed using the Juggl plugin because it can save to cytoscape.json that can be opened in the Cytoscape desktop software:

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#42

Can’t be Obsidian from any file link because Obsidian needs to know vault before it can open a file. So it can’t be default .md editor.
I can see that Plottr wouldn’t fit your use case at all.
I had a look at Foam once. I’ve looked at all similar programs, I think. I dislike VSCode, so Foam would never have been for me.

Nice graph.

#43

Aaah, yes of course… I forget about that all the time…

I use Zettlr as default MD Editor, but in addition I have set up VS Codium (no telemetric) with only a minimal of Markdown extension incl. Foam plus I have added the graphviz and joplin extension for VSC.
Only reason I use VSC is because it can open so many different files and has a extension for nearly anything, so it can be a helpful tool when I find something strange, or just want to look at huge text files that Notepad++ use a decade to open…

Thanks… it is larger, but Juggl struggle with large graphs…

#44

One semi-related item idea that has been suggested a few times is a pop-out editor for notes etc. that provides a larger, more comfortable space to write those notes.

It is feasible this could be expanded to be somewhat of a markdown editor in future, allowing the basics of rich text into our notes (i.e. bold, italic, links and perhaps lists… but not tables etc.).

Full text export of narrative related items
#45

Of course you do! :grinning: Citations, Zotero etc.

Prompted me to check mine. Noticed that there has just been an SSL issue, so I’ve switched to the v2 beta (I had updated to 1.8.9 after the iFrame security issues in May). I don’t actually use it often, but I like having it as one of my options.

#46

A pop-up editor would be nice, but even a viewer, something similar to Okular or Quicklook for Windows (I know there is a lot better viewer for Mac, this was just two examples that I use myself).

I think there are multiple text editor libraries that support both RTF and Markdown, but programming for me is just a theoretical knowledge… i.e. I can read the logics, but when I try to do it myself, it seems that I never get it right… :rofl:

Personally I use markdown tables a lot for lists, so supporting preview of them would be nice, editing them is not necessary, we can do that in the Markdown editor of choice…

So an export/import or sync would be nice, you could add the important data you need to the YAML header of each file…

A simple viewer that will display the content of a linked file of correct format, and that can open the linked file in a default editor if needed, I think is more than enough for most users using markdown files…
And if you use the right viewer/editor, it would even display linked pdf’s, docx, etc.
Click a link or button to open it in default editor, do the changes, save it, click “refresh” and the preview in Aeon will show the updated content… (If you don’t find a way to auto refresh.).

Back to sync
To be able to sync both a folder structure and content both ways between a folder with markdown files and the content of the files would be amazing, and you could use YAML to define Properties, and the body of the markdown note could be text in a text field for the editor you mentioned.
If it was a push-pull auto sync, it would be possible to edit the notes in your preferred markdown editor while timeline is open and the changes would be updated IRL time, that way you could actually use the markdown editor as a companion to Aeon…
(Yes, I do understand this is a lot of technically obstacles to plow through, so it is just some thoughts for a “perfect” solution).

As an example of how I do it today and did it in version 2.
I create a link to a file, i.e. one of my markdown research notes for that object (item), If I don’t have any research notes for the object, I will create my folder structure of:

  • Research Journal for {Name of object}
    • Research Logs for {Name of object}
    • Research Plans for {Name of object}
    • Research Notes for {Name of object}

and add a Markdown file for the research objects where it belong…
I also distinguish between research notes and other notes about the object, and can also have my own notes in a research- journal/log/plan/notes, that is not a research note…

It is a lot of extra work, but I have “lost” so much information because I have written it down “somewhere”, never to be found again… and it is even more work to find that information again, if even possible…

Even more digression
All this is also why I applaud any software that have some good interchangeable formats or even implement interoperability to other tools… I really love the idea of “open data open source”, Open Data being the most important of those…

(I am so good at really spinning way of topic)

#47

I don’t love YAML solutions: although readable, they tend to be program specific in use. And it’s very easy for files to become overburdened with a ton of YAML definitions.

#48

Are there? I don’t know any. I’m assuming that you mean .rtf and .md (or variant) files.

#49

How many key pair that is used is up to the user, but it is a way of adding structured data to a file with unstructured text…

I am not sure I understand “program specific” in this context…
YAML is only data key pair… so for Aeon, that can be 2 key pairs:
aeonSyncID: 123456BB
aeonLastSdata: 2021-10-110T18:34:56

I use a lot of custom YAML in my notes, in average maybe 15-20 key pair for most notes types, never had problems with that in the software that fully support it except that some software is case sensitive (don’t support uppercase first letter in key name)…
But of course there are some software that only look for its own key pairs, then its not for much use…

#50

Those Aeon pairs would be program specific to Aeon.
Unless you decided to set up another program to work with them.
My general concern is that I don’t like lots of stuff taking space in my plaintext files. YAML has a tendency to accumulate. I have a preference either to keep stuff out of YAML (I only use inline tags, for example) or to only have pairs with multiple uses (though I have none of these currently).

I have a design issue with it. It’s a method of creating a faux database using only plaintext files; for me, that’s okay for very simple uses, but non-optimal design otherwise. Countless Obsidian plugins have been produced adding line after line in the YAML; looks fine when the YAML is hidden, but use an editor that shows the whole file and there’s too much crud.

#51

Aaah, Yes, then we agree…

I mostly use YAML as data about my own data…
Obsidian and Foam (and partially Zettlr) read those keys and they can be utilized in the software…

i.e. if it is a research note for a person, I have the birth date, the name, type etc. in addition to tags aliases etc.
Some of this keys are used globally for all my notes, others is type specific.
i.e. a ship has an owner that most likely is a Shipping Company…
A Place might have an “enclosed by” or “encloses” key (taken from Gramps).
Some of this is actually redundant data, since I also use a folder structure for hierarchical structures… But I have learned that it is better to have one “field” to much, than that one is missing…

I mostly use this keys to configure the graph view, or via Juggl, create properties/attributes for a network graph file that can be saved in Juggl.
It make me be able to open a network graph of my whole folder structure in Cytoscape Desktop (network graph software) for more advanced analyzes and styling of the graphs.

#52

I noticed someone recommending the Obsidian Itinerary plugin to construct a timeline; uses YAML, as they tend to do. Not sure I’d want to do that myself.

#54

I use few plugins and very little YAML. I like my plaintext to be plain, else we end with the same design issues as docx etc. If I need a database, I prefer to use a database.
But I suspect I’m in a minority of Obsidian users, many of whom appear to want the same features as a database program.

#55

I do agree with you for most parts…

But since I use my Markdown for research mostly, it can be useful to have some extra functions so that I don’t need to use 2-3-4-5 extra applications just for my Notes and any illustrations…

I think my usage of Obsidian also differ largely from most other users…
I have one Note for each “object” and link the other objects as I go with wiki-links… I use it as much as a “freeform” relation builder and analyzer where I can relate objects and people both in unstructured and structured text… regardless of what type of object it is…

So if I find a list in a newspaper with 1200-2000 names of ships and their positions, I create a Source Note (and I add the newspaper to Zotero of course) for that List, adds all the ships and the information, starts creating wiki-links, when I need to, I create notes for this ships, the ports (or other positions and the date), as I find new lists, or other types of list I do the same thing, building up a “database” and a network graph of this information…
In addition I add Crew Lists to this and links those to the ships…
But I also add newspaper articles about both locations people and objects as unstructured text, and can link anything of “importance” to “the rest”, i.e. an article about a torpedoed ship, articles about new ships, other data for the crew members etc.
If I need to I can export excel or csv tables to markdown, and I can save the graph with my notes to a network graph file format using Juggl if I need more styling or analyzing feature…
I can also add my genealogy to this if I want to (I have a few sailors in my family, it was actually there it all started :rofl: ).
So the Markdown files for me has been a HUB for interoperability between a few different software I use…

I have actually found multiple connections with this approach that I didn’t find in either Excel, Access or postgresql nor in my genealogy software of choice that is actually kind of advanced (Gramps).

But if you use it for writing or notetaking, I agree fully with you, no need to bloat your notes mor than necessary…

I don’t use most of the plugins for Obsidian, but there is a few I find useful… At the start I added a lot of them, but find myself disabling and removing most of them…

Same is it with VSC and Foam to, I have somme extensions that are helpful to read other formats I have used, i.e. graphviz, and I use VSC to find and replace text in folders of text files, i.e. if I know I have 200 MD files with the name of a ship, and I want all of them to be wiki-links with aliases, I use VSC to search and replace that text… I could have used Notepad++ for the same, but find it to have become sluggish for those kind of operations, and since I am using Windows, I don’t have the text and file handling tools of Linux.

so as a “HUB” for other software usage, it would have been great to be able to use the notes in Aeon also, but for it to become useful for me, the text and not only the folder structure and YAML of the Notes should also be utilized somehow, and to not bloat the file of Aeon with all the Notes and Text, I thought that just be able to open and read linked files would be helpful, manually linking the files, and then if they want to have auto-sync, synchronize the files in the folder after they have been mapped/linked instead of adding all the text to text fields in Aeon… Of course, on export there must be some choices same if they want to also sync with Scrivener…
But for me personally, I don’t need, and actually don’t want to have all the text in yet another software, specially because many of my “notes” is structured data (tables). and most of the information will already be there in the form of the structure of the files and folders.

And if there should be a “full” support for a timeline based on the markdown files, there also had to be some kind of utilization of the links in the notes, i.e. every link is a relation in Aeon, but it would be problematic to create anything useful with that without the use of YAML, i.e. for setting type of note, dates, etc.

I really wish for a “perfect” software, but think we still need to work with some compromises… :rofl:

#56

I wish you well with it. Only using your own specific entries will help, I’m sure. The underlying constraint with databases is speed and size. Iirc Obsidian uses json for its indices. Have no idea what it’s max practical size will be for your mix of YAML etc, but I’m pretty sure it will be lower than a number of database designs.

#57

Thanks you, :slight_smile:

Yes, it will be way lower than a database, but some have tested it with between 30-100k notes and it works…

I have tested with 80k files with only a simple header and it was no speed reduction with that…

But the good thing with Obsidan is that it is easy to split up to multiple “vaults” if needed…

I also have a neo4j database and a mongodb database, but I am not really good at those type of queries and development frontend guis for those systems, but my plan is to get it all into a database solution some time, just need to find a platform where it also is possible to “publish” some reports and articles…

The problem with all databases is the frontend, how to use the data, and how to present it…
My system now is easy, I can just write directly “in the data”…

But… that is a digression from the topic…

At the moment, with a few thousand notes and a little over 2k sources in Zotero, it still works…

#58

I think this is very much on topic. It’s a workflow with markdown incorporating Aeon Timeline. Whole different ballgame to Scrivener and Ulysses since so much more is possible - and feels to me that you’re pushing some of those boundaries, which is very interesting.

#59

For the moment, Timeline has an advantage with this because the inspector makes links quickly accessible for all entries. Plottr’s hover system is faster, but doesn’t yet allow clicking on the hover content.

#60

Yes, the only “problem” with it is that it’s in the link “section”, the good thing is that it can also open application URL’s i.e. “zotero://”, for those applications that support it.

That is actually all I need, but it would be nice if it was tied to the different multiline text field I use, maybe supporting a quick view preview as an object for the properties in addition to multiline and singleline text… because I am fine with just creating a link for the notes I need and open them in default editor (or using Obsidans rather obscure URL’s, might be I have been stupid and installed a wrong plugin… haha), if I want to do some editing, adding text, etc.

But how the developers choose to implement it, either via sync of properties and other structures like folders and files, or the variant I have written about, I will let them decide…

I’m going to take a look at Athens Research now, see what it’s all about…

it’s still “alpha”, so… but maybe it is something “more” than the rest, or maybe not…

EDIT 2 min later… Nope… Database based :rofl:

#61

On consideration, I think that markdown export is less important than OPML import/export. In practice, import/export between markdown and OPML is easy and already structured.

I can imagine a wide range of preferences on ideal structures for markdown exports. But many markdown programs will import/export OPML - Typora, Logseq (though I’ve not tested exactly what that does). And OPML would also enable it to work with virtually all mindmap and outline programs. And Scrivener uses it, potentially avoiding the need for Sync (I personally would always prefer a shared file in a compatible format to a sync between two databases) - though a number of forum posts suggest that the OPML is somewhat limited. I suspect AT would be better easier since there’s potentially a lot of user choice over the attributes being imported or exported.

I’m not saying I wouldn’t like a markdown export, simply that OPML would be higher on my priority list, even if I can already achieve the same result via Scrivener sync.