MBON marinebon.org Webite

:warning: deprecated.

Most of this site has been abandoned in favor of a wordpress site.

Information about the new site is in marinebon/marinebon_wordpress_website.

This site remains hosted, however, and some parts of this site are used by the new site via iframe elements.

The parts of this site linked are listed here:

This is a work-in-progress rebuild of the marinebon.org website. Details on how to make edits are below. This site is built using wowchemy and although some basic tasks are outlined below the excellent wowchemy docs are highly recommended reading.

Site Editing Workflow

If you're just getting started here it is likely you just want to edit content on one of the pages. There are several ways to do this but a checklist for how to do this in the easiest way is below. Other common tasks are outlined below (like editing the nav menu) and for more information see the wowchemy getting started page.

General content editing workflow checklist

The basics of how to edit content on an existing page. Note that the "home" page is different and weird because it is currently using wowchemy widgets.

1. Edit website content files in /content/ and commit the changes to github using one of:
   • https://marinebon2.netlify.app/admin/ Netlify CMS
   • Github website file editor interface
   • prose.io file editor interface
   • a local dev workflow
2. Your git commit will show up in the commit history and be saved in github's copy of the git repo.
3. The new commit will trigger Netlify to build and deploy the site. The job will show up at app.netlify.com/sites/marinebon2/deploys.
4. Once the status of the Netlify deploy build is "Published" your changes should be live on the project website marinebon2.netlify.app.
   • Errors in the build can be debugged by looking at the deploy log on netlify

Above is the most basic workflow for editing the content on this website but advanced users can also develop using the typical git workflow and hugo to do test builds without needing to commit and rely on Netlify builds.

Adding a "news" post

1. create a file named index.md within /content/post for your news post.
   • create a folder for the index.md by editing the name of index.md, adding your folder name followed by a /. Github should automatically create the folder. Watch the .gif here for further clarification.
2. copy and modify the "header section" from another article's index.md. The "header" is everything at the top of the file between the pair of three dashes (---)
3. use markdown syntax inside the index.md file to write your article
4. commit the file to github. The site will rebuild to include your article within minutes (as described in the general editing workflow above)
5. (optional) to add an image to the post upload it to the news post's folder and name it featured.png
   • alternatively: you can name the image anything you like; just change the image:filename:featured part of the index.md header

Editing publications

Updating publications requires a bit of technical know-how for now, but this can be automated easily in the future. The most important step below is the first one. Once you have completed step (1) then a site admin can quickly and easily complete the remaining steps. A prerequisite to these steps is to have a .bibtex file. .bibtex files are human-readable adn can be generated a number of ways. MBON's references are currently managed using Zotero, instructions for exporting a .bibtex can be found on this old issue post.

based on wowchemy instructions to import-from-bibtex

1. modify /content/publication/MBON_publications.bib
   • if you are not familiar with bibtex then you can still edit this file easily using the github website.
     1. find the publication on google scholar
     2. click the "cite this" button
     3. select "bibtex"
     4. copy and paste the entry into the .bib file mentioned above
     5. click commit to save your file edit
2. git clone & cd into repo on your local
3. cd into the /content/ directory? (not sure yet)
4. academic import --normalize --bibtex content/publication/MBON_publications.bib to run the python import script
5. git commit -a -m 'update pubs'
6. git push

Adding / editing a "product" listing

It is relatively easy to add a "MBON Data or Software Product" to the grid display. You may open an issue for help with this but the general steps are:

1. create a folder for the product in /content/product/. The next steps take place in this folder.
2. (optional) add an image named featured.png to use on the product "card grid" display
3. create a file index.md using markdown syntax. This must include a basic header section. See other product index.mds for examples.
4. (optional) use the "tags" list in the .md header section to set relevant tags. Tags can be anything but the most important ones are listed under "filter_button" in the widget file (/content/product/index_widget_product_grid.md). Below is a list of those tags (as of 2021-10):

• regarding product_type: An explaination of the three types:
  • a data product represents publication of scientific data to be used by others
  • an instance software product is something created to address the needs of a specific group and is uniquely tied to that user-story.
  • a tool software product is something that can be used help to create instance products. This includes frameworks, libraries, etc

Publications have their own section of the website and should not be put under products. The products page exists to help users find resources they can use, so a product must link out to one of:

• a publicly usable user interface or downloadable software binaries
• a place to download a public dataset
• source code

Editing the Nav Menu

Modify the ./config/_default/menus.toml entries to define menu items. To define sub-menu items use the parent attribute as explained in this issue.

Local Dev Workflow

Wowchemy is designed to leverage lots of free cloud tools to allow CMS & WYSiWYG editing with minimal technical knowledge, but sometimes digging deeper into things is helpful. The wowchemy "edit on your pc" page outlines how to get set up building the site on your local machine rather than relying on netlify (or github actions or travis CI or whatever). This is useful for editing without needing to do a commit - something that is especially valuable when making lots of small test changes (looking at you, CSS) or debugging build issues.

hugo layout/page/etc lookup chain

This is the order in which files are used. Files from earlier in the chain will override files later in the chain.

As an example: if a page is using layout=publication, marinebon/www_marinebon2/layouts/publication/ will be used if it exists, else /wowchemy/wowchemy-hugo-themes/modules/wowchemy/layouts/publication/ will be used.

A note on media content

We ran into issues setting up where to put media content (see #10). There are three options on where to put media:

1. /assets/media
2. /content/...
3. /static/media_content

Useful tools

• **Hugo Academic CLI: Automatically import publications from BibTeX
• prose.io markdown (+ more) editor: in-browser file editing alternative to github editor

Upstream Tech

This website is built starting from the Academic Template for Hugo.

Wowchemy

Wowchemy was used to set up this website. The site can be edited your site in Markdown, Jupyter, or RStudio (via Blogdown). Netlify is used to build the site with Hugo and deploy hosting on Netlify. A CMS is provided for editing the site using Netlify (or is this a Wowchemy tech?).

Associated wowchemy repositories:

1. wowchemy core functionality: wowchemy-hugo-modules
2. wowchemy template used: starter-hugo-academic
3. theme CLI tools: hugo-academic-cli
4. CMS: wowchemy/netlify-cms