/wdfn-blog

The blog of USGS Water Data for the Nation

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wdfn-blog

The blog for USGS Water Data For The Nation

Guidelines for submission

  1. Applicable/useful to a greater audience.
  2. Content provides additional information not available elsewhere.
  3. Relevant to USGS employees or USGS data users
  4. Showcases databases, applications, software, or common practices associated with USGS WMA or within the USGS WMA portfolio.

Submitting an update

  1. Fork repo and set up local development environment as needed (see sections below)
  2. Create a markdown file in (.md). This should be all lowercase and dashes (e.g. name-of-post)
  3. Add your markdown file to the content folder
  4. Include static images in static\name-of-post. Images must include alt and title text
  5. Add a header similar to:
---
author: Laura DeCicco
date: 2016-06-16
slug: plotFlowConc
draft: True
type: post
title: EGRET plotFlowConc using ggplot2
categories: Data Science
tags:
  - EGRET
  - R
image: static/plotFlowConc/unnamed-chunk-4-1.png
description: Using the R packages, ggplot and EGRET, a new function plotFlowConc        shows a new way to visualize the changes between flow and concentration.
keywords:
  - EGRET
  - ggplot2
  - data visualization
author_twitter: DeCiccoDonk
author_github: ldecicco-usgs
author_gs: jXd0feEAAAAJ
author_staff: laura-decicco
author_email: <ldecicco@usgs.gov>
author_researchgate: Laura_De_Cicco
  ---

Important notes about header:

  • Date format has to be "YYYY-MM-DD" for the updates to be organized properly.

  • Initial submission must include draft: True

  • slug slug will be the name of your url after waterdata.usgs.gov/blog/xxx

  • image is not required, but will improve the look of the main "blog" page. Without an image, a generic USGS image will be included.

  • categories is a small list of approved options, curated by the managing editor. They help build the overall site navigation structure.

  • tags are more specific words, and do not need to be on a pre-approved list, these will show up on the navigation of the post.

  • description will go into a "meta" tag that Google and other sites use

  • keywords (can be the same as tags), also go in a "meta" tag to be used by Google and others.

  • It's a good idea to direct people to github issues, emails, or other ways to communicate if they have questions/comments/etc.

  • You can also add single author attributes for the following: twitter handles (author_twitter), github (author_github), Google Scholor (author_gs), ResearchGate (author_researchgate), USGS staff profile (author_staff), and email (author_email)

  1. Commit locally and push as needed, then submit a pull request
  2. Wait for the pull request to get merged, it will then appear on the dev site.
  3. Submitter is responsible for getting 1 internal peer-review of content (interal reviews can be done on a Google Form). Send the reviewer a link to the dev site.
  4. A designated approver must sign off on content based on review response
  5. A designated web content manager will sign-off on if the page is generally fit to be published on a government website (verify the header follows the "Important notes" above, images contain alt/title tags)
  6. Once the content is approved, the draft status can be removed, and the content will appear on the QA site.
  7. Assuming all looks good, push to prod

Tips to writing content

  1. If you want to add an image to your content, use the figure shortcode. See < figure > shortcode, https://gohugo.io/content-management/shortcodes/#figure. There are a few required tags:
    • caption: The caption of the image. Will be displayed. Markdown within the caption will be rendered.
    • alt: alt text, for accessibility. Aim for text that actaully discribes in the image or gif, not just the caption text again.
    • src: path to the image that you want to display.
  2. You can use the class ".side-by" if you want your image to only take up 50% of the screen width or if you want to place two images side by side. You should wrap them in a
    tag with the class set to "grid-row". Example below:
<div class="grid-row">

{{< figure src="/static/nldi-intro/upstream.png" caption="caption, which can have markdown in it" alt="Description of the image" class="side-by-side" >}}
{{< figure src="/static/nldi-intro/downstream.png" caption="other caption, which can have markdown in it" alt="Description of the image" class="side-by-side" >}}

</div>
  1. For embedded r code make sure there is a blank line in the markdown between the code and the preceding content text.
  2. Use the following markup to implement the ability to Show/Hide code sections:
<button class="toggle-button" onclick="toggle_visibility(this, 'hideMe1')">Show Code</button>
<div id="hideMe1" style="display:none">

``` r
library(jsonlite) 
.
.
.

</div>

Simplified Local development in Windows

Developing without Docker can be simpler on a Windows workstation, particularly if that workstation has software restrictions imposed by an organization's I.T. department. There are several ways to make this work and here is one (relatively) simple example of setting up a development environment. Stick with us. This takes a bit of time and is something of a learning curve, but hang in there; soon you can be authoring articles and previewing the results on the your own Windows workstation with ease!

One-time installation steps:

Note that items marked with (ADMIN) require administrative privilieges, so if your computer is managed by an I.T. department, you will likely need to originate a service ticket that requests these steps to be done on your behalf.

  1. (ADMIN) Install Visual Studio Code

    • Visit the Visual Studio Code website and download and install the latest stable version. Launch VS Code to confirm install.
    • Optional: Install the Front Matter extension using the icon the left-hand bar that looks like a Tetris game.
      • Front Matter can make it easier to set up blog articles. It has some one-time configuration for the wdfn-blog website, which is beyond the scope of this document.

  2. (ADMIN) Install Git for Windows

    • This is required to use Git Bash for subsequent steps here.
    • Skip this step if your I.T. department already installed this for you. It's a common tool these days.

  3. (ADMIN) Install Node.js

    • This is required to compile code related to the blog's visual theme.
    • Select the latest LTS (long-term stable) installer for Windows. Install with default options. Decline additional complexities such as installing Choclatey.

  4. Clone the wdfn-blog repo

    • In VS Code, click the source control tab on the left side, select "clone repository"
    • Either paste in the repository URL ending in .git, or if working from wdfn-blog on Github:
      • Select "clone from GitHub" and you should conveniently see the wdfn-blog fork you have generated.
      • VS Code will ask you to select the folder to clone into.
      • In this tutorial, we clone to C:\sandbox\github-user, under which the cloning process will make the folder wdfn-blog\.
        • This tutorial recommends this new-root-folder-on-your-main-disk-drive approach, if you IT department allows you to create such things.
        • Pick whatever you like, including cloning to your Documents folder. However, if your Documents folder is under control of MS OneDrive, you may not have a positive experience.
        • You will need to create whatever folders needed for this new cloning destination.
      • Perform a one-time permissions granting step for GitHub.
        • You need a Github account for this. They're free.
        • NOTE!: If you receive a certificate error in this step, you likely are inside a corporate network, either hardwired or VPN. The simplest way around this is to temporarily log out of VPN when performing this step (you can log back in afterward). Resolving SSL certificate errors inside of corporate networks is beyond the scope of this document.
    • Open the wdfn-blog folder you just cloned using File->Open Folder
      • In this example, you'd select C:\sandbox\github-user\wdfn-blog
      • In the future, if you do nothing else to VS Code, this will always be the folder that opens in VS Code. Convenient!
      • Agree to trusting the content of this folder if asked.

  5. Compile the blog's static assets

    • Launch Git BASH
      • Note: You MUST use Git BASH. Windows Powershell or Command Prompt will not work because these steps require Linux-style command-line compatibility.
    • Use the cd command to change to the wdfn-blog directory of the cloned repo. In this example, it would be cd /c/sandbox/github-user/wdfn-blog
    • Note that, with cd (change directory) command, starting with a slash goes to the root of the filesystem. Not starting with a slash starts from the directory you already are in.
    • Use cd to move into the themes directory cd themes/wdfn_theme/
    • Install all packages needed to compile assets by typing npm ci
      • Note: This is better than running npm install, because npm ci does not change the package-lock.json file, which is a file that rarely needs to be altered.
      • After a some harmless text warnings, the process will complete and a large node_modules/ directory will have appeared. Cool.
    • Compile the blog assets by typine npm run build
      • A new directory called static/ will have appeared. Great job.
    • NOTE: This step is usually a one-time-only step, unless changes are made by you or someone else to code in this wdfn_theme directory.

  6. Download Hugo and place in path.

    • Visit Hugo Releases and download the latest proper Windows 64-bit Zipfile. For example hugo_0.89.2_Windows-64bit.zip is the proper file to download as of this writing in November 2021. Later versions should continue to work, as well.
    • Unzip the contents of the Zipfile and copy-and-paste this entire unzipped folder to somewhere convenient and near your cloned repo, such as c:\sandbox\
    • Add this folder to your path by right clicking on "This PC" in Windows explorer, selecting properties, searching for "envionment variables" for your account, editing the PATH variable, and adding a new entry. Paste the Hugo path here (you can copy it from the address bar in Windows file explorer if you navigate to the folder where you pasted it)
    • Confirm hugo works in the path by opening a new Git BASH terminal and typing hugo env and confirming it reports the Hugo version.
      • NOTE: You must launch a new Git BASH session after changing the path for it to honor the new path.

Now you are ready for development. A development cycle should look something like this:

  1. Launch Hugo server

    • Open a Git BASH terminal and use change directories to the wdfn-blog (e.g., cd /d/sandbox/github-user/wdfn-blog)
    • Launch Hugo server by typing hugo server --buildDrafts
      • This will start a local web server.
      • If a firewall issue is raised, contact your I.T. department for an exception.
      • Note the line that says "web server is available at..." for the next step.
      • Leave this window running, but in the background.

  2. Open the website in a browser

    • Launch your favorite web browser and navigate to the URL Hugo listed above. Usually it's http://localhost:1313

  3. In Github on your web browser, perform Fetch and Merge

    • This will obtain any changes other people have made to the blog since you forked your own copy.
    • You need to do this periodically, especially if there's any chance you'll be collaboratively editing articles with other people.

  4. Launch Visual Studio Code and pull the latest changes

    • Use File->Open Folder and select the wdfn-blog folder cloned from Git.
      • It may be open already because the cloning step added it as the active VS Code project.
    • Under the Source Control tab, select "Pull" to get the latest blog updates.
      • It may ask you if you'd like to periodically run Git Fetch. Yes is usually a good answer.
      • If you say no, remember to perform this Pull step anytime you have performed the previous "Fetch and Merge" step, so the latest blog files are on your Windows workstation.

  5. Make your edits and additions, view the results in that open web browser

    • See other parts of this README for how to do this. Modeling a new article based on a template of an already-published one is a good time saver.
    • Use the Front Matter extension if you'd like. It can be a more visually appealing way to manage the metadata for a blog post. It also supports blog-post templates to save time, but that is beyond the scope of this document.
    • When changes are saved, Hugo should detect them, rebuild the page, AND automatically refresh the web browser.
    • NOTE: Front Matter can be show this preview right in VS Code instead of you having to launch your own web browser, but that is beyond the scope of this document.

  6. Commit and push your changes to Github

    • After you push your changes to Github, continue with the other steps in this README related to creating a pull request.

Note: There are numerous other options for installing both Node and Hugo, through a package manager such as apt-get for Linux, Homebrew for MacOS, or Chocolatley for Windows. This tutorial bypasses a package manager because some I.T. departments may not approve of that form of software.

Local development without using Docker

To test without docker, you must have Hugo and node.js installed. You should install the latest HUGO and the latest LTS for node. There are numerous options for installing both Node and Hugo, though a package manager such as apt-get for Linux, Homebrew for MacOS, or Chocolatley for Windows is a good option. Then, from the terminal you can run:

cd themes/wdfn_theme/
rm -rf node_modules
npm install
npm run build

You will only need to do the previous steps, when you start a new branch or you have merged the latest changes from the canonical repo. Then in the home directory:

export HUGO_BASEURL="blog/"
hugo server --theme=wdfn_theme --buildDrafts

Local development with Docker

A Dockerfile and Docker Compose configuration is provided that is capable of running a development server and building the deployable static site.

Using docker-compose, you may run a development server on http://localhost:1313:

docker-compose up

The default server instance will include draft articles.

If the site on http://localhost:1313 is missing various static files, you may need to first run the following command to rebuild assets:

docker-compose run hugo build --buildDrafts

If you haven't set things up on the right cert bundle, it may be easier to run this command outside the USGS VPN.

Once that is done, you can use docker-compose up to start the development server again.

Debugging the container

If the need arises, you may run arbitrary commands in the container, such as a bash shell:

docker-compose run hugo bash -l

Build static site using Docker

Using docker-compose, the site may be built using the build command provided by the container:

docker-compose run hugo build

The base URL is specified with the HUGO_BASEURL environment variable:

docker-compose run -e HUGO_BASEURL=http://dev-owi.usgs.gov/blog/ hugo build

Additional arguments may be passed to the Hugo binary as the last argument:

docker-compose run hugo build --buildDrafts

Instructions for R users

Templates for R markdowns

remotes::install_github('usgs-r/USGSmarkdowntemplates')

This will add draft: True to the markdown header (not rmarkdown file). It is up to you to remove that AFTER the content has been reviewed.

Make sure to format your blog a .md file, not a .Rmd file (which is the deafult if using a package such as blogdown).There are some simple functions for converting between the two if using R.

When setting up a new project in RStudio, there are many ways to connect to the project. One is by starting a new project, then choose version control, select Git and use the URL "https://github.com/username/wdfn-blog.git". This should allow you to use Git push, pull, and merge code within RStudio.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

Reference herein to any specific commercial product, process, or service, or the use of any trade, firm or corporation name is for the information and convenience of the public, and does not constitute endorsement, recommendation, or favoring by the Department of the Interior.