openplantpathology / openplantpathology

Open Plant Pathology website

OpenPlantPathology

This repository contains the code for the Open Plant Pathology website, https://www.openplantpathology.org/.

Code of Conduct

Please note that the OpenPlantPathology project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

openplantpathology's Issues

Build a Docker to contain OPP Notes

Using a Rocker Docker we could share OPP Notes in a controlled environment that users could interact with and run the Notes easily using RStudio.

This could include all notes (assuming we end up with more than just the one we now have) and would make a nice portable way to distribute the notes.

correct header logo for "code" and not "codes"

the title says it all

Allow kniting directory even without new members

Use Hugo to build entire site?

If we provide a script is it possible to build the members' dashboard using Hugo as well rather than knitting locally?

https://github.com/rstudio/blogdown/blob/master/docs/02-hugo.Rmd#static-files

Separate domains by a comma in directory table

Subject says it all

Directory: middle initials/names are shown as "NA" for those without an entry

As raised by Thomas Adams in Slack.

Use academicons for ORCID in directory

see: https://jpswalsh.github.io/academicons/

Main header is slow to load

An SVG shouldn't be that slow to load.

Suggest remove embedded PNG files?

Handle webpages gracefully

If there is no homepage but if there is a Twitter account then you end up with something like:

NAhttp://www.emr.ac.uk/staff/andrew-armitage-2/NANANA | NAhttps://github.com/adarmitageNANANA

rather than the proper icons

Remove disqus?

See thread from Noam Ross on Twitter, with Bob Rudis response: https://twitter.com/hrbrmstr/status/1135915244532822018

Maëlle Salmon has a blog post on using Utterances (GitHub issues): https://masalmon.eu/2019/10/02/disqus/

Change author name Reim->Heim

Hi everyone,

could you please change my name Reim-> Heim?

Could I do this myself? If so, please explain how to implement this change.

Happy Sunday,
Rene

Check url for "https" or "http" and prepend as necessary

Check if user enters full properly formed URL with "http://" or only the url, e.g. github.com and prepend the full https:// to the entry.

Add link to multivariate analysis webpage from OPP

Currently we have links to PDF and Code but a github.io page exists. Would be good to link directly to that as well.

Use continous integration to build and deploy site

Rather than building the site locally and pushing, use Travis or Circle-CI to build the site and deploy it to Netlify using Docker.

This will help with reproducibility aspects of the teaching notes and simplify the code base.

Geocode locations for users using ggmap

Rather than making the user enter lon/lat values, simply use ggmap to geocode the city location.

This makes it much more simple for the user when entering data and makes the data less likely to contain errors when constructing the directory website.

Link for "More Virtual Seminars" is missing on main page

I've tried to manually fix this since it's not working somewhere in the partials, but it's missing again.

Not sure what's wrong in the partials, but I'd hard coded it and that appears to not be working now either.

Need to investigate further.

Make Scrollbar appear in RMarkdown code chunks (html view)

Use googlesheets to read spreadsheet directly into R

Don't use readxl, read directly from Google

Add useR!2018 presentation to OPP webpage

Directory geocoding fails

I'd been using Google to geocode locations, but I think that the free trial I had been using has expired and we may now have to pay for it.

This package, https://github.com/jessecambon/tidygeocoder, uses OSM to geocode, which may be an option?

tweak the html template to not display header image on post but on twitter card

I will work on this

Simon Williams' Post-Seminar Activities

• Remove iCal link, Zoom URL and calendar time conversion from the announcement
• Download and edit video
• Upload video to YouTube channel
• Add links to YouTube in video = "" and slides on OSF using custom URL for DOI
• Email author ([email protected] ) asking for the slides
• Add slides to OSF.io (optional)
• Tweet about video on YouTube and slides on OSF

Simon Williams' Pre-Seminar Activities

• Request Zoom Webinar from USQ.
• Add Announcement to OPP Homepage.
• Tweet to announce seminar at least one week before the seminar.
• Tweet reminder again two days prior to the seminar.
• Tweet day of the seminar.
• Add Zoom link to the announcement page.
• Add iCal to the announcement page.
• Add time conversion to the announcement page.

Link to Editor's websites and clean up code of editor's page

The links are sending visitors to a blank page. Include links to institutional pages of each author or include the icons on top of the editor's name

Handle missing lat/lon values

Currently the directory file will not knit if any lat/lon values are missing.

Need to check values to ensure exist and are valid when knitting or exclude from map output.

New OPP logo website header?

Should we use the OPP logo as in the shirt and hex sticker - with the acronym and the description below? it would help promote the brand.

Please add another webinar to the Queensland APPS series

https://www.youtube.com/watch?v=kkAdiwlP8fs

Domains in directory may contain duplicates

"Population biology" and "Population Biology" both appear.

Suggest implementing drop down lists in the spreadsheet with available options to help ensure consistent data entry.

https://productivityspot.com/drop-down-list-in-google-sheets/