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animint2 Reference Website #97
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@tdhock, sorry—I'm gonna ask you to do something for me. I would do it myself, but I don't have security clearance (or whatever it's called). 😅 Could you go to But for now I just wanna set up a preliminary site in your repo instead of my fork. Also, Thanks! As always, no rush. :> |
I did that, does it work for you? |
Thanks! Lemme run the |
Hmm. When you deployed the site, in
are you using GitHub Actions or are you deploying from the |
It says Deploy from a branch, is that ok? Can I give you access some how so you can do this config? |
Yeah, deploy from a branch should be right. Weird that it works from my fork but throws up a Feel free to give me access, and I'll happily return it when the GitHub Pages site is set up. But I'm not sure how to do it. Maybe give me admin powers? I can't find anything about whether admins have power over setting up Pages, though. If you have more modular control, feel free to give me access only to the Pages settings or something. But I haven't been able to find anything about that. |
Hypothesis: I'm using my personal access token, which maybe probably doesn't work for this repo since it's not mine. I may need you to generate a token for this repo and send it to me. When I started this project, I had no idea it would require so many tedious little tasks from you, which I apologize for. Do you think I should continue this stuff from my fork instead? Of course, that has other problems and probably increases your future workload in exchange for a reduced workload now. 🤔 |
OK thanks for the info. I'm not sure how to give you admin access, because I think github changed their web site since the last time I did that. I don't know if this will help, but I saw a message saying "create an organization to grant access controls" so I created the animint organization, and invited you. |
Thanks! I joined but the animint organization doesn’t seem to have access to any repositories. I don’t know if it’s because the Don’t worry about it, though. If it’s okay with you: I can just do stuff on my fork and at some later date we can have an electron meeting and figure it out this GUI stuff together. And I can just merge my fork into a branch here later, too. |
hi @ampurr and @Faye-yufan I gave you admin access to this repo (recently transferred to animint/animint2 from tdhock/animint2) does that work for you? |
@tdhock: It works! Thank you very much. :> |
Hi @tdhock , yes it works, thank you! |
Status update: I'm currently working on editing If there's anything I should really make sure to include or exclude, please let me know. 🐱 |
for sure include screenshots, installation, and basic usage example. anything else you want to delete please move to a wiki page. |
Okay, will do! What do you mean by "anything else you want to delete please move to a wiki page"? |
There is a wiki on this github repo, https://github.com/animint/animint2/wiki and you could move the README section "Differences with Other Packages" to a new wiki page with that name. |
Sorry, I'm still confused. My fault, not yours. But I took some time to think about it and I'm less confused than before. So I'm going to try and say what I'm doing. And then I'm going to say some possible interpretations of what you're requesting. Then you can let me know if any of the interpretations are correct. I generated I'm confused partly cuz I'm not deleting anything from Some interpretations:
EDIT: Interpretation 2 said the READMEs were in sync when they should've said they cannot be in sync. Whoops. |
yes for 1, and actually just delete the org file in your PR please. |
Understood. Will do. Thanks for clarifying. :> |
Today I learned that I do not know how GitHub's milestone thingy works. |
Status update: added the "Differences with other packages" section from No plans to add anything else to the wiki. |
Minor status update: I'm unable to include basic usage examples in the README. Why? GitHub doesn't support JavaScript in its READMEs, and animints are made of sugar and spice and also JavaScript. I'm moving the examples to a vignette and including a link in the Use section. |
Status update: work on the examples vignette is going all right. The biggest difficulty is selecting a built-in dataset that shows off |
Just simulate the data. You’re demonstrating some package features, not doing science. 😛 |
Ah-ha. From the pkgdown reference site: " |
Status UpdateI've moved the quick start guide to a "Get started" section on the nav-bar. On a related note, I got the animints working... Is what I wanna say. What actually happened is that renaming the file and moving it to its own section somehow got the animints to work. So it's not accurate to say that I got the animints working. Why did this work? I can't think of any plausible hypotheses. This is so strange. |
Unrelated: In the animint2 repo, I think this issue has the most comments by far. Possibly the highest word count, too. A graphomanic's paradise and a reader's nightmare. 😅 |
Status UpdateThis workday was CSS-heavy. I've managed to hack together code annotations in the comments. Except for the hash sign, I think it looks a little bit better than Quarto's solution. Since I had no control over the HTML of the codeblock, I'm pretty proud of my workaround solution. (Maybe I'll be less proud when I wake up. 😛) Due to certain limitations in CSS's Quarto's solution is to use Unrelated: I've managed to increased the gap between the animints and the paragraphs following them. Make it easier to read. |
Status UpdateGot the CSS for the explanations for the code annotation working. Gonna throw together a PR to see how my commits test and then I'm gonna sleep. 😴 |
Status update: I moved |
the progress seems good, but now I get 404 from https://animint.github.io/animint2/articles/quick-start.html did you delete it? |
@tdhock, I moved it to its own space on the navbar. It's here now: https://animint.github.io/animint2/articles/animint2.html |
Status Update
|
Hi thanks for sharing. Looks great overall. Glad you could get the line numbering and animint rendering to work. Can you please document the solution to those issues somewhere? (maybe on the wiki?)
cute_present <- cute_1 |>
animint(first = list(Cat = c("Archibald", "Muffin"))) as cute_present <- animint(
cute_1,
first=list(Cat = c("Archibald", "Muffin")) For the animated plot, there is a warning,
can you please specify Also can you add a section which adds a second plot with clickSelects? maybe plot some aggregate vs Day, with Also can you please move the data/aes to inside the geom? (this is more consistent with the other tutorials, and more generally useful, since in animints, different layers tend to have different data sets and aes) For example cute_1 <- meowtrics |>
ggplot() +
geom_point() +
aes(x = Day, y = Cuteness, group = Cat, color = Cat) could be changed to cute_1 <- ggplot()+
geom_point(aes(
x = Day,
y = Cuteness,
group = Cat,
color = Cat),
data = meowtrics) or, alternatively, if you think the current version has some kind of advantage, can you please show both versions, discuss how they give the same result, and also discuss the relative advantage/disadvantage of each approach/syntax? Thanks! |
Thanks for the thorough feedback! I'll make the changes and then get back to you. :> |
Changes to the Quick GuideRefactoring the Code
Substantial Changes
|
As an aside, turns out that while you can't get code annotations in R Markdown, you can get line numbers for codeblocks. I'm proud of my hacky workaround, but maybe line numbers are better? 🤔 |
Status UpdateI've finished most of the changes. The quick start guide on the website is currently a mess, though. Currently I'm stuck on the linked animints (with |
looks like good progress. |
Thanks for the correction! I'll fix that. Yup! That did it, thanks. Still working on the linked animints. Everything seems right, but it produces a static data viz instead of an animint. Still trying to figure that out. |
rather than linked animints do you mean linked plots in a single animint? That is what it should be, there is no way to link two different animints. if you share your code, I can help |
Yes, I meant linked plots in a single animint. I assumed that plots and animints had a one-to-one correspondence (cuz I thought "animint" referred to interactive data viz). What exactly is an animint? 😅 Thanks—I really appreciate the offer. 😄 I actually just figured it out. After hours debugging and re-reading and thinking that my code basically looked the same as the code in the manual, I realized that the problem was basically a typo. Whoops. Now the linked plots work. Thanks again! 🐈 |
Status UpdateI've finished with the linked plots and fixed the mistake with If there are any other minor changes I should make, please let me know, and I'll make them. If there are any major changes I should make, also let me know, and I'll make them after GSOC ends. The work product submission deadline is coming up and I wanna dedicate at least most of a day to it. In other news, [1] I tried a bunch of things but I'm real tired and don't wanna list them out. |
Status update: I've replaced the Markdown footnotes (which weren't working and relied on an external JS lib) with HTML ones. |
Quick guide status update: I've edited my writing and cleaned up typos. |
Hi again thanks for the updates. things are improving for sure.
I would suggest changing the title "Advanced: Linked Plots" by removing the word "Advanced" -- the normal usage of animint is to have at least two linked plots which use clickSelects and showSelected. Using only one plot is typically only in teaching. In Conclusion can you please add a link to the Animint2 Manual? Your quick start guide is roughly equivalent to Chapters 2-4, so I would mention something like "You can see another presentation of the same material in more depth in Chapters 2-4 of the Animint2 Manual, https://rcdata.nau.edu/genomic-ml/animint2-manual/Ch02-ggplot2.html#multi-panel" Thanks again for your great work. |
Sure thing. I'll make those changes and let you know when it's done. :> Will probably use an |
New checklists: Changes to the Quick Start Guide
Address Alt Text Redundancy
Aesthetic Improvements
|
Status Update
|
hi @ampurr is this the token you were using to push the gh-pages web site from your own personal computer? or? |
Hey, @tdhock. :> Yeah, this is the token I used to push the website from my personal computer. People need to renew every year or so, which is kinda annoying. I think the classic token can be permanent. Having never used GitHub Actions, I dunno if this token is necessary for GitHub Actions or not. 😅 It's possible that I might one day figure out auto deploy for this site. But I've still got a few changes I need to make to the site (which you're requested and which I've been terribly slow at addressing). So, no promises on the auto deploy front. |
For ClarityWell, when I update the website, it does activate a GitHub workflow, which I think is a subset or synonym of a GitHub action. I'm not clear on that, since I've only read a limited subset of the GitHub documentation. If you're using "GitHub action" in the sense that GitHub starts a workflow in the background when I update the site, then this token is necessary for at least some GitHub actions. I hope my response is relevant to your guess about this token being necessary or unnecessary for GitHub Actions. Sorry if it isn't. 😓 |
Here's the thread that will track the development of the
animint2
reference website. 🐈The text was updated successfully, but these errors were encountered: