Staging

README.md

@@ -1,4 +1,4 @@
-i[![Build Status](https://travis-ci.com/uvarc/rc-website.svg?branch=master)](https://travis-ci.com/uvarc/rc-website)
+<!-- [![Build Status](https://travis-ci.com/uvarc/rc-website.svg?branch=master)](https://travis-ci.com/uvarc/rc-website) -->
 
 # UVA Research Learning & Workshop Website
 
@@ -7,7 +7,6 @@ i[![Build Status](https://travis-ci.com/uvarc/rc-website.svg?branch=master)](htt
 | https://staging.learning.rc.virginia.edu | https://www.learning.rc.virginia.edu  |
 
   * [Developing](#developing)
-     * [Using Gitpod](#using-gitpod)
      * [Local Install](#local-install)
   * [Creating New Content](#creating-new-content)
      * [Methods for creating content](#two-methods-for-creating-content)
@@ -27,8 +26,8 @@ i[![Build Status](https://travis-ci.com/uvarc/rc-website.svg?branch=master)](htt
 
 ### Local Install
 
-* [Install](https://gohugo.io/overview/installing/) the HUGO binary on your local computer. This has been tested with version 0.74.x-extended. **You need the extended version.** Binaries for different operating systems can be downloaded from the Hugo GitHub repo: https://github.com/gohugoio/hugo/releases/tag/v0.74.3.
-* Clone this website repository: `git clone git@github.com:uvarc/rc-learning.git`.  The `master` branch is protected.  New content has to be pushed to the `staging` branch. Use this command to clone the staging branch only: `git clone --single-branch -b staging git@github.com:uvarc/rc-learning.git`.
+* [Install](https://gohugo.io/overview/installing/) the Hugo binary on your local computer. This has been tested with version 0.133.1-extended. **You need the extended version.** Binaries for different operating systems can be downloaded from the Hugo GitHub repo: https://github.com/gohugoio/hugo/releases/tag/v0.133.1
+* Clone this website repository: `git clone git@github.com:uvarc/rc-learning.git`.  The `main` branch is protected.  New content has to be pushed to the `staging` branch. Use this command to clone the staging branch only: `git clone --single-branch -b staging git@github.com:uvarc/rc-learning.git`.
 
 - - -
 
@@ -84,9 +83,9 @@ Using the `date` metadata smartly, you can forward date any post or article. [Au
 `hugo server` will bring up the local hugo server and give you a preview URL `http://localhost:1313/`. If making many changes, open another terminal to keep the `hugo server` running as you edit.
 
 ### Publish content
-Simply push `staging` back to GitHub. We're in the process of setting up the S3 buckets for hosting the content. 
+Simply push `staging` back to GitHub. 
 
-TravisCI will handle it from there and publish the content at the staging site, https://staging.learning.rc.virginia.edu. Pushing your content to the production website requires a PULL REQUEST.
+The CI will handle it from there and publish the content at the staging site, https://staging.learning.rc.virginia.edu. Pushing your content to the production website requires a PULL REQUEST.
 
 > Remember that after pushing your changes back to the `staging` branch, the https://staging.rc.virginia.edu/ website will be updated within 1-2 minutes. Hold down the SHIFT key when reloading your browser to refresh your local cache.
 

assets/js/academic-search.js

@@ -85,6 +85,7 @@ function searchAcademic(query, fuse) {
 function parseResults(query, results) {
   $.each( results, function(key, value) {
     let content_key = value.item.section;
+    let path = value.item.relpermalink;
     let content = "";
     let snippet = "";
     let snippetHighlights = [];
@@ -124,8 +125,11 @@ function parseResults(query, results) {
     // Parse template.
     let templateData = {
       key: key,
-      title: value.item.title,
+      title: value.item.title || "(no title)",
       type: content_key,
+      // turn relative path to breadcrumbs ("page1 > page2") format, removing the last part of the path (the result's page name)
+      // screen readers see a comma instead of "greater than sign", to allow for a pause in speech between each segment
+      pagepath: path.split('/').filter(item => item !== '').slice(0, -1).join('<span class="sr-only">,</span> <span aria-hidden=\"true\">&gt;</span> '),
       relpermalink: value.item.relpermalink,
       snippet: snippet
     };

assets/scss/custom.scss

@@ -75,6 +75,7 @@ h6 {
 
 html {
   scroll-behavior: smooth;
+  scroll-padding-top: 100px;
 }
 
 /* Change the colors for the "light" button */
@@ -173,7 +174,7 @@ html {
   color: #ab0728;
 }
 
-.alert-info {
+.alert-info, .alert-note {
   background-color: #fafafa;
   border-color: #209cee; // the same color as the info icon
 }
@@ -347,11 +348,19 @@ footer {
   .alert-warning {
     background-color: #550000;
     color: white;
+    code {
+      color: #8be9fd;
+    }
   }
 
-  .alert-info {
+  .alert-info, .alert-note {
     background-color: #12537e;
     color: white;
+    pre,
+    code {
+      color: white;
+      background-color: #44475aab;
+    }
   }
 
   .skip-to-main-content {
@@ -374,4 +383,9 @@ footer {
   .badge-light {
     color: white;
   }
+
+  .tag-cloud a:hover,
+  .tag-cloud a:focus {
+    color: hsl(231, 48%, 90%);
+  }
 }

config/_default/params.toml

@@ -58,7 +58,7 @@ description = ""
 # Enable source code highlighting? true/false
 # Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options
 highlight = true
-highlight_languages = ["awk","bash","cmake","c","c++","fortran","dockerfile","java","julia","makefile","matlab","mathematica","maxima","perl","python","r","sas","scala","tex"]  # Add support for highlighting additional languages
+highlight_languages = ["awk","bash","cmake","c","cpp","fortran","dockerfile","java","julia","latex","makefile","matlab","mathematica","maxima","perl","python","r","sas","scala"]  # Add support for highlighting additional languages
  highlight_style_light = "a11y-light"  # For supported styles, see https://cdnjs.com/libraries/highlight.js/
  highlight_style_dark = "a11y-dark"
 

content/courses/containers-for-hpc/building-apptainer.md

@@ -60,8 +60,10 @@ Inspect the runscript before running an image!
     The default cache directory is `~/.apptainer`. If you are an active container user it can quickly fill up your home. You can change it to scratch:
     {{< code-snippet >}}export APPTAINER_CACHEDIR=/scratch/$USER/.apptainer{{< /code-snippet >}}
     Otherwise, remember to clean up periodically.
-1. We have suppressed certain output from the `apptainer` command. To see the complete output, type `\apptainer`.
+1. Request an ijob
+    {{< code-snippet >}}ijob -A hpc_training -p interactive -c 1 -t 2:0:0{{< /code-snippet >}}
 1. Load the Apptainer module: `module load apptainer`
+1. We have suppressed certain output from the `apptainer` command. To see the complete output, type `\apptainer`.
 
 ## Definition File
 
@@ -487,7 +489,7 @@ Hints:
 
 {{< info >}}While PyTorch runs on a GPU, you do not need to build the container on a GPU.{{< /info >}}
 
-{{< info >}}You will likely run out of memory when building large containers (over a few GBs). Request an [interactive job](https://www.rc.virginia.edu/userinfo/rivanna/slurm/#submitting-an-interactive-job) to build on a compute node in the `largemem` partition.{{< /info >}}
+{{< info >}}You will likely run out of memory when building large containers (over a few GBs). Request an [interactive job](https://www.rc.virginia.edu/userinfo/rivanna/slurm/#submitting-an-interactive-job) with say `--mem=50G` to build on a compute node with 50 GB memory.{{< /info >}}
 
 ### R
 

content/courses/containers-for-hpc/building-docker.md

@@ -1,5 +1,5 @@
 ---
-date : "2024-6-03T00:00:00"
+date : "2024-06-03T00:00:00"
 title: Appendix 1 - Building Containers [Docker]
 toc: true
 type: book

content/courses/containers-for-hpc/minimal.md

@@ -1,5 +1,5 @@
 ---
-date : "2024-6-03T00:00:00-05:00"
+date : "2024-06-03T00:00:00-05:00"
 title: Appendix 2 - Minimal Containers [Docker]
 toc: true
 type: book

content/courses/containers-for-hpc/using.md

@@ -14,6 +14,8 @@ Log on to our HPC cluster
     - Make sure you have a few GBs of free space
 - Run `allocations`
     - Check if you have `hpc_training`
+- Request an interative job
+    {{< code-snippet >}}ijob -A hpc_training -p interactive -c 1 -t 2:0:0{{< /code-snippet >}}
 - Run `module load apptainer`
 
 ---

content/courses/cpp-introduction/building.md

@@ -32,9 +32,9 @@ An Integrated Development Environment (IDE) combines an editor and a way to comp
 A well-known IDE for Microsoft Windows is Visual Studio. This is available through the Microsoft Store; it is not free for individuals.
 macOS uses Xcode as its native IDE. Xcode includes some compilers, particularly for Swift, but it can manage several other languages.  Available at the App Store and free.
 
-A full-featured cross-platform IDE is [Eclipse] (http://www.eclipse.org/).  Free.
+A full-featured cross-platform IDE is [Eclipse](http://www.eclipse.org/).  Free.
 
-A lighter-weight IDE for Windows and Linux is [Code::Blocks] (http://www.codeblocks.org/).  Free.
+A lighter-weight IDE for Windows and Linux is [Code::Blocks](http://www.codeblocks.org/).  Free.
 
 Windows programmers using Intel's oneAPI distribution must also install [Visual Studio](https://visualstudio.microsoft.com/).  
 

content/courses/cpp-introduction/inheritance.md

@@ -46,7 +46,7 @@ class Mammal: public Animal {
 We could then derive Antelope from Mammal.  Further subdivisions would be possible (`class Ungulate` and so forth).
 Derived classes can continue like this in an _inheritance chain_ indefinitely, though it would be poor practice to set up more than a few links in the chain.   
 
-{{< diagram >}}
+{{< diagram alt="A diagram showing how classes are inherited. Animal is the parent of Reptile and Mammal, and Mammal is the parent of Antelope.">}}
 graph TD;
 A(Animal) --> B(Reptile)
 A(Animal) --> C(Mammal)

content/courses/cpp-introduction/linkers_libraries.md

@@ -101,4 +101,4 @@ If Geany is to run a multi-file executable then the main program file must be se
 
 The file ending in `.h` is called a _header file_. The best practice in C++ is to separate the _interface_ into a header file and the _implementation_ into the source file. We will discuss this, as well as the preprocessor commands, when we cover functions.
 
-This process becomes increasingly cumbersome as projects grow in number and complexity of files.  The most common way to manage projects is through the [make](courses/cpp-introduction/make.md) utility, which we will examine next.
+This process becomes increasingly cumbersome as projects grow in number and complexity of files.  The most common way to manage projects is through the [make](/courses/cpp-introduction/make.md) utility, which we will examine next.

content/courses/fiji-image-processing/fiji-omero/index.md

@@ -138,7 +138,7 @@ Let's create a new project and dataset through the OMERO web client.
 3. Click on the blue folder icon of your new project and take note of the `Project ID`. We will need this to direct Fiji where to load data from or save data to.  No right click on your blue project folder icon and create a new dataset.  Right-click on the dataset icon and take note of the `Dataset ID`.
 
 After the project is generated, your user interface should look like this:
-    ![](/courses/fiji-omero/fiji-omero-datasetid.png)
+    ![](/courses/fiji-image-processing/fiji-omero/fiji-omero-datasetid.png)
 
 ---
 
@@ -225,7 +225,7 @@ Before you begin, you need to know the dataset ID that the image should be linke
 
 3. Go to `File` > `Export` > `OMERO...`.  Enter the dataset ID you chose under step 1 and click `OK`.
 
-{{< figure src="/courses/fiji-omero/fiji-omero-blobs-export.png" >}}
+{{< figure src="/courses/fiji-image-processing/fiji-omero/fiji-omero-blobs-export.png" >}}
 
 4. Click on the `Results` table window and go to `File` > `Save As`.  Save the file as `Results.csv` on your computer.  Repeat the same for the `Summary` table.  
 
@@ -255,7 +255,7 @@ To follow along, you can download the Jython scripts presented in this tutorial
 
 We'll be using the built-in **Script Editor** in Fiji to run our scripts.  To start the script editor in Fiji go to menu `File` > `New` > `Script…`.
 
-{{< figure src="/courses/fiji-omero/fiji-script-editor.png" >}}
+{{< figure src="/courses/fiji-image-processing/fiji-omero/fiji-script-editor.png" >}}
 
 * The top pane provides the editor. Multiple scripts can be open at the same time and will show up as separate tabs.
 * The bottom pane shows output (e.g. produced by print statements) and any errors encountered during script execution.
@@ -589,7 +589,7 @@ Let's try to upload an image from Fiji to OMERO.
 
 ### Creating Key:Value Annotations
 
-{{< figure src="/courses/fiji-omero/fiji-omero-keyvalue.png" >}}
+{{< figure src="/courses/fiji-image-processing/fiji-omero/fiji-omero-keyvalue.png" >}}
 OMERO allows you to link other pieces of information to your Project, Dataset, Screen, Plate or Image objects. This additional information is displayed on the right side in the OMERO web client, labeled under the `General` tab as `Image Details`, `Tags`, `Key-Value Pairs`, `Tables`, `Attachments`, `Comments`, and `Ratings`. In addition, there is the `Acquisition` tab that provides metadata information that was automatically extracted from the image file headers during import.  
 
 For the remainder of this workshop, we will focus on `Key-Value` pairs and `Attachments`.  The key-value pairs are implemented as a dictionary (or HashMaps) that can be used to annotate individual images or whole datasets/project or plates/screens with additional information. Such information may include experimental conditions etc.. 
@@ -717,7 +717,7 @@ The example script, `Omero_Batch_Processing.py`, consists of five key functions:
 
 **Remember that the gateway connection needs to be closed at the end of the script**.
 
-{{< figure src="/courses/fiji-omero/fiji-omero-batchprocessing.png" >}}
+{{< figure src="/courses/fiji-image-processing/fiji-omero/fiji-omero-batchprocessing.png" >}}
 
 To test this and see the process in action we will process a set of four images that has been deposited in the OMERO database. The setup is as follows:
 

content/courses/fortran-introduction/_index.md

@@ -1,5 +1,5 @@
 ---
-date : "2021-04-5T00:00:00-05:00"
+date : "2021-04-05T00:00:00-05:00"
 title : "Programming in Modern Fortran"
 summary: "This short course is an introduction to programming in modern Fortran.  Experience programming in some other language is helpful but not required."
 authors: [kah]

content/courses/fortran-introduction/advanced_arrays.md

@@ -1,6 +1,6 @@
 ---
 title: "Advanced Array Usage"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 42

content/courses/fortran-introduction/advanced_file_io.md

@@ -1,6 +1,6 @@
 ---
 title: "Advanced File IO"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 55

content/courses/fortran-introduction/array_intrinsics.md

@@ -1,6 +1,6 @@
 ---
 title: "Array Intrinsics"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 43

content/courses/fortran-introduction/arrays.md

@@ -1,6 +1,6 @@
 ---
 title: "Introduction to Arrays"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 41

content/courses/fortran-introduction/building.md

@@ -1,6 +1,6 @@
 ---
 title: "Compilers and IDEs"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 11

content/courses/fortran-introduction/character_intrinsics.md

@@ -1,6 +1,6 @@
 ---
 title: "Character Intrinsics and Conditionals"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 44

content/courses/fortran-introduction/characters.md

@@ -1,6 +1,6 @@
 ---
 title: "Characters and Strings"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 43
@@ -62,7 +62,7 @@ An allocatable string may be deallocated if necessary with the usual `DEALLOCATE
 DEALLOCATE(str)
 ```
 
-Prior to Fortran 2003, the standard defined a module `iso_varying_string`.  Most compilers available now support the 2003 standard so will offer the standard variable string, but the iso_varying_string module provides a number of functions so may still be worthwhile.  We will discuss standardized modules [later](courses/fortran-introduction/standard_modules).
+Prior to Fortran 2003, the standard defined a module `iso_varying_string`.  Most compilers available now support the 2003 standard so will offer the standard variable string, but the iso_varying_string module provides a number of functions so may still be worthwhile.  We will discuss standardized modules [later](/courses/fortran-introduction/standard_modules).
 
 ## Substrings
 
@@ -103,7 +103,7 @@ Hello world          today
 
 ### String Length
 A useful string function, especially for variable-length strings, is `LEN(S)`.
-A fixed-length string will always occupy the specified number of characters. The default is to left-justify non-blank characters in the field.  This can be modified with [intrinsics](courses/fortran-introduction/character_intrinsics).
+A fixed-length string will always occupy the specified number of characters. The default is to left-justify non-blank characters in the field.  This can be modified with [intrinsics](/courses/fortran-introduction/character_intrinsics).
 
 **Exercises**
 * Declare character variables large enough to hold the indicated strings.  Make full_title at least 5 characters longer than you think necessary.

content/courses/fortran-introduction/classes.md

@@ -1,6 +1,6 @@
 ---
 title: "Classes"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 75

content/courses/fortran-introduction/conditionals.md

@@ -1,6 +1,6 @@
 ---
 title: "Conditionals"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 31

content/courses/fortran-introduction/console_io.md

@@ -1,6 +1,6 @@
 ---
 title: "Console Input/Output"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 51
@@ -72,7 +72,7 @@ In Fortran the PRINT statement always writes an end-of-line marker after all var
 
 Input values can be read from the command line.  This is usually accomplished in an IDE through an option to `Run`.
 
-We can read strings only.  You must convert if necessary to a numerical type using internal read/write.  See the discussion [earlier](courses/fortran-introduction/operators).
+We can read strings only.  You must convert if necessary to a numerical type using internal read/write.  See the discussion [earlier](/courses/fortran-introduction/operators).
 
 The COMMAND_ARGUMENT_COUNT intrinsic returns the number of command-line options.  For each one, we must call GET_COMMAND_ARGUMENT with its number and a character buffer variable.
 ```fortran

content/courses/fortran-introduction/declarations.md

@@ -1,6 +1,6 @@
 ---
 title: "Variable Declarations"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 22

content/courses/fortran-introduction/derived_types.md

@@ -1,6 +1,6 @@
 ---
 title: "Derived Types"
-date : "2021-04-5T00:00:00"
+date : "2021-04-05T00:00:00"
 toc: true
 type: book
 weight: 73

content/courses/fortran-introduction/file_io.md

@@ -1,6 +1,6 @@
 ---
 title: "File IO"
-date : "2021-04-5T00:00:00-05:00"
+date : "2021-04-05T00:00:00-05:00"
 toc: true
 type: book
 weight: 53

content/courses/fortran-introduction/formatted_io.md

@@ -1,6 +1,6 @@
 ---
 title: "Formatted Input/Output"
-date : "2021-04-5T00:00:00-05:00"
+date : "2021-04-05T00:00:00-05:00"
 toc: true
 type: book
 weight: 52

content/courses/fortran-introduction/getting_started.md

@@ -1,5 +1,5 @@
 ---
-date : "2021-04-5T00:00:00-05:00"
+date : "2021-04-05T00:00:00-05:00"
 title : "Starting with Fortran"
 toc: true
 type: book

content/courses/fortran-introduction/interfaces.md

@@ -1,6 +1,6 @@
 ---
 title: "Interfaces"
-date : "2021-04-5T00:00:00-05:00"
+date : "2021-04-05T00:00:00-05:00"
 toc: true
 type: book
 weight: 62