DIYbiosphere/sphere

A collaborative database of Do-it-Yourself Biology initiatives

Mac Cowell

@100ideas

I am setting up netlify to deploy from @diybiosphere/sphere

one nice thing about netlify is that it can be setup to provide 'staging' builds for any commits / PRs so we can see how the changes work without updating the 'production' site

Mac Cowell

@100ideas

ok here it is http://staging.diybio.org

you have access https://app.netlify.com/sites/diybiosphere-staging/overview

if you want to see the logs

I don't have the auto-stage-prs set up yet

it just automatically regenerates anytime we make changes to sphere repo

hmm my commits to bbkopenscience are not quite working

Mac Cowell

@100ideas

cool got it working

@jasonbobe in the future just put header.jpg and logo.jpg in the folder with the markdown file

but don't add a logo entry to the yaml frontmatter of the md file

jekyll finds the sibling header/logo file if it is named header or logo as above and associates it with the yaml when the site is built

not like this: https://github.com/DIYbiosphere/sphere/commit/57192515da6ec14247c7f4c3739fec386f64d112#diff-67da456c47233c206f18df87b5417d3d

apparently events will only show up if they have a header.jpg or if the yaml includes header:image:___

Mac Cowell

@100ideas

also look at this: https://github.com/DIYbiosphere/sphere/blob/master/_labs/Biocurious/Biocurious.md

the yaml frontmatter defines logo: http://...

but the directory also has logo.png

so which one do you think is actually loaded?

confusing, right?

Mac Cowell

@100ideas

@sabgaby I cleaned up most of the stale branches in the github repo. I made a local git archive of most of them first if there is a branch you want me to put back

$ git_latest_commits
2019-05-09 23:49:31 +0000 Travis 81 minutes ago     origin/gh-pages
2019-05-09 16:55:54 -0700 Mac Cowell 75 minutes ago     origin/staging
2019-05-09 16:55:54 -0700 Mac Cowell 75 minutes ago     origin/master
2018-03-19 09:24:12 +0100 Gabriela A. Sanchez 1 year, 2 months ago     origin/update-docs
2018-03-16 21:16:53 +0100 Gabriela A. Sanchez 1 year, 2 months ago     origin/mapping
2018-02-28 13:10:39 +0100 Gabriela A. Sanchez 1 year, 2 months ago     origin/last-changes
2018-02-05 13:29:33 +0100 sabgaby 1 year, 3 months ago     origin/dynamic-design
2017-11-21 13:48:46 +0100 sabgaby 1 year, 6 months ago     origin/new-design
2017-11-15 21:37:12 +0100 sabgaby 1 year, 6 months ago     origin/redesign

here's what's left

$ git_latest_commits
2019-05-09 23:49:31 +0000 Travis 2 hours ago     origin/gh-pages
2019-05-09 16:55:54 -0700 Mac Cowell 2 hours ago     origin/staging
2019-05-09 16:55:54 -0700 Mac Cowell 2 hours ago     origin/master

Mac Cowell

@100ideas

@/all hey all, we switched the hosting over to netlify. the travis-ci gh-pages build is still available at sphere-gh.diybio.org

if you want to preview changes or commits, try to make them in the staging branch, then create a pull request to merge staging into master. If you do this, netlify will react and create a preview build of the changes without updating the production build. It will post a message in the Pull Request thread. Click the "details" link button in the last netlify message you see.

Basically (looking at you @jasonbobe) if you are using the github.com web editor to make changes, do it from the staging branch then make a PR - that way you can get netlify previews

Mac Cowell

@100ideas

@sabgaby @jasonbobe we now have free "open-source plan" hosting from netlify - it's the same as their pro plan, but free for FOSS projects like us. I will invite you both to the team. Besides hosting diybiosphere, we could also create other projects and have them hosted at netlify with our plan.

Mac Cowell

@100ideas

closed all open issues - will revisit some of them as time permits upgrading site

Jason Bobe

@jasonbobe

@100ideas this is awesome. thank you for doing all of these upgrades!

I think I may need to resubmit a few entries that caught up in the broken Travis route. I'll try to do it myself and if I run into any problems, i'll let you know. thanks again. stoked!

Jason Bobe

@jasonbobe

@100ideas i need some help understanding the process for publishing entries to the site. I added this entry inside of the "networks" collection:

https://github.com/DIYbiosphere/sphere/tree/master/_networks/CitizenScienceGlobalPartnership

Citizen Science Global Partnership

I added it last night, but today it does not appear on the site.

Do I need to take action via Netlify to publish somehow?

thanks

@100ideas I also added ToolFoundry last night and it is not published

https://github.com/DIYbiosphere/sphere/tree/master/_incubators/ToolFoundry

^ you might really like to check out this accelerator

Jason Bobe

@jasonbobe

@100ideas maybe we can set-up a time to walk through some of these issues together, so I can start publishing entries effectively. i've got a backlog! I know you've only got 1 day per month, so we might need to plan ahead!

Mac Cowell

@100ideas

hmm that's weird. I see the commit and netlify shows that it triggered a deploy https://app.netlify.com/sites/diybiosphere/deploys

it looks like the commit right before it (for feles bio) did deploy correctly DIYbiosphere/sphere@08b5ed0

Mac Cowell

@100ideas

so Citizen Science Global Partnership is getting served https://sphere.diybio.org/networks/citizenscienceglobalpartnership/

Mac Cowell

@100ideas

if you go to the most recent deploy log (I just triggered it and turned on more logging) you can see many of the projects (all?) get processed in two phases, an initial one, and then one that reports "rendering ... #excerpt"

like this

5:10:54 AM:   Pre-Render Hooks: _projects/KombuchaGenomics/KombuchaGenomics.md
5:10:54 AM:   Rendering Markup: _projects/KombuchaGenomics/KombuchaGenomics.md
5:10:54 AM:   Rendering Layout: _projects/KombuchaGenomics/KombuchaGenomics.md
5:10:54 AM:      Layout source: site
5:10:54 AM:          Rendering: _projects/KombuchaGenomics/KombuchaGenomics.md/#excerpt
5:10:54 AM:   Pre-Render Hooks: _projects/KombuchaGenomics/KombuchaGenomics.md/#excerpt
5:10:54 AM:   Rendering Markup: _projects/KombuchaGenomics/KombuchaGenomics.md/#excerpt

https://app.netlify.com/sites/diybiosphere/deploys/5cdc01b0c9cbde07ce78ac6b

I think the missing pages are getting skipped for the #excerpt thing

I think that is it

toolfoundry doesn't show up in search

but the page is there if you go to the url https://sphere.diybio.org/incubators/toolfoundry/

Mac Cowell

@100ideas

I think I got algolia reconfigured

Jason Bobe

@jasonbobe

:smile:

cons1

@cons1

hello everyone! Can you recommend some books to start learning about amateur gene editing and analyzing? What disciplines should I learn?

𝓲𝓸𝓸𝓷𝓮𝓻

@iooner_twitter

Hi!

Still ppl here ?

Ibn G. Alhadid

@ibnugamal_twitter

Hi, guys!
It's Hadid from Degenics (https://www.degenics.com/).
Degenics is a startup that combines Blockchain, Genetics & Molecular Biology, and Bioinformatics to help its users to sequence their DNA anonymously.
If you happen to be running a DIY lab that could do human DNA sequencing, please contact me at ibnu@degenics.com because we want you to become one of our sequencing lab partners!
Thanks!

Nate158

@0634034090Nate

Danny Chan

@danwchan:diybio.fun

[m]

Hello? Is anybody in this chat room

Jason Bobe

@jasonbobe

I don't think too many!

Danny Chan

@danwchan:diybio.fun

[m]

Oh nice I just got connected via the matrix protocol. So I'll be here at least :D I saw Mac did some stuff on the website. Last I spoke to James Parsons he said he was working on a wordpress version of the site but that's all I know. Nice to have chat space to throw around some ideas about the site.

Jason Bobe

@jasonbobe

what is the matrix protocol?

Danny Chan

@danwchan:diybio.fun

[m]

it's a decentralised chat network with an emphasis on unifying different chat platforms (and DMs). I think gitter might be using it under the hood or else it's fully interoperable with it. I'm using it for internal biotech without borders stuff and I use to bridge into slack and discord channels I am a part of and services with DMs (not mastodon [yet?] though)

Jason Bobe

@jasonbobe

https://matrix.org/ wild!

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