Merge pull request #64 from esciencecenter-digital-skills/titles_and_…

…image_updates Titles and image updates
esciencecenter-digital-skills · May 15, 2024 · 07996a9 · 07996a9
2 parents 12a2472 + 1b10f50
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diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -19,7 +19,7 @@ jobs:
       uses: actions/checkout@v4
       with:
           repository: esciencecenter-digital-skills/NEBULA
-          ref: v0.4.0
+          ref: v0.4.2
           path: ./NEBULA
 
     - name: Checkout content

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -12,8 +12,8 @@ jobs:
     with:
       content_organization: esciencecenter-digital-skills
       content_repository: research-software-support
-      content_ref: v0.1.1
+      content_ref: main
       base_url: research-software-support
-      nebula_ref: v0.4.1
+      nebula_ref: v0.4.2
 
 
diff --git a/modules/citation/citationcff.md b/modules/citation/citationcff.md
@@ -1,5 +1,5 @@
 ---
-title: The `CITATION.cff` file
+title: CITATION.cff file
 type: reading
 order: 4
 ---

diff --git a/modules/citation/create_citation_file.md b/modules/citation/create_citation_file.md
@@ -1,5 +1,5 @@
 ---
-title: Using cffinit to create `CITATION.cff`
+title: CFFinit tool
 type: exercise
 order: 5
 ---

diff --git a/modules/citation/ex_when_to_cite.md b/modules/citation/ex_when_to_cite.md
@@ -1,5 +1,5 @@
 ---
-title: Which software should I cite?
+title: What to cite?
 type: exercise
 order: 6
 ---

diff --git a/modules/citation/further_reading.md b/modules/citation/further_reading.md
@@ -1,5 +1,5 @@
 ---
-title: Reading material
+title: Further reading
 type: reading
 order: 7
 ---

diff --git a/modules/citation/index.md b/modules/citation/index.md
@@ -1,5 +1,5 @@
 ---
-id: 0
+id: 3
 trl: medium
 category: Publishing & Citing
 title: Software citation

diff --git a/modules/citation/principles.md b/modules/citation/principles.md
@@ -4,9 +4,8 @@ type: reading
 order: 3
 ---
 
-## The FORCE11 working group published the [Software Citation Principles](https://force11.org/info/software-citation-principles-published-2016/)
-
-### The principles
+### The software citation principles
+The FORCE11 working group published the [Software Citation Principles](https://force11.org/info/software-citation-principles-published-2016/)
 
 **Importance**: Software should be considered a legitimate and citable product of research. Software citations should be accorded the same importance in the scholarly record as citations of other research products, such as publications and data; they should be included in the metadata of the citing work, for example in the reference list of a journal article, and should not be omitted or separated. Software should be cited on the same basis as any other research product such as a paper or a book, that is, authors should cite the appropriate set of software products just as they cite the appropriate set of papers.
 

diff --git a/modules/fairsoftware/exercise1.md b/modules/fairsoftware/exercise1.md
@@ -4,9 +4,7 @@ type: exercise
 order: 2
 ---
 
-# Exercise 1
-
-## What is FAIR?
+## Exercise: What is FAIR?
 
 ### FAIR principles (15 minutes)
 

diff --git a/modules/fairsoftware/exercise2.md b/modules/fairsoftware/exercise2.md
@@ -4,9 +4,7 @@ type: exercise
 order: 3
 ---
 
-# Exercise 2
-
-## Mapping the principles
+## Exercise: Mapping the principles
 
 ### The FAIR4RS Principles are:
 
@@ -45,7 +43,7 @@ The following three examples of software have been described with statements tha
 
 #### Example 1: [Comet](https://doi.org/10.1002/pmic.201200439)
 
-Comet is a command-line tool and desktop application for tandem mass spectrometry sequence database search6.
+[Comet](https://doi.org/10.1002/pmic.201200439) is a command-line tool and desktop application for tandem mass spectrometry sequence database search6.
 
 - Comet is licensed under the Apache 2.0 open source licence.
 - Comet is registered in the bio.tools catalogue of bioinformatics tools, where it has a globally unique and persistent identifier, and rich metadata that includes the identifier and is searchable and indexable.
@@ -57,7 +55,7 @@ Comet is a command-line tool and desktop application for tandem mass spectrometr
 
 #### Example 2: [PureGoMe](https://doi.org/10.5281/zenodo.4337242)
 
-PuReGoMe is a project aimed at understanding Dutch public sentiment during the COVID-19 outbreak period by analysing real-time Twitter data. It provides a collection of Python scripts and Jupyter notebooks for this purpose.
+[PureGoMe](https://doi.org/10.5281/zenodo.4337242) is a project aimed at understanding Dutch public sentiment during the COVID-19 outbreak period by analysing real-time Twitter data. It provides a collection of Python scripts and Jupyter notebooks for this purpose.
 
 - PureGoMe can be downloaded from the project repository, while metadata is accessible independently from the registry.
 - PuReGoMe's GitHub repository has detailed records of the development history.
@@ -70,7 +68,7 @@ PuReGoMe is a project aimed at understanding Dutch public sentiment during the C
 
 #### Example 3: [gammaShiny](https://doi.org/10.5281/zenodo.4139005)
 
-gammaShiny is an application that provides enhanced graphical user interfaces for the R gamma package8. It is used to process in-situ gamma-ray spectrometry measurements for luminescence dating.
+[gammaShiny](https://doi.org/10.5281/zenodo.4139005) is an application that provides enhanced graphical user interfaces for the R gamma package8. It is used to process in-situ gamma-ray spectrometry measurements for luminescence dating.
 
 - gammaShiny has been deposited in the HAL French national archive and it has a persistent globally unique identifier, with the HAL identifier of the metadata record and a SWHID, identifying specifically the software artefact on the Software Heritage universal software source code archive.
 - Thanks to the HAL platform, where a licence is mandatory, gammaShiny is under a GNU General Public Licence v3.0.

diff --git a/modules/fairsoftware/exercise3.md b/modules/fairsoftware/exercise3.md
@@ -4,9 +4,7 @@ type: exercise
 order: 4
 ---
 
-# Exercise 3
-
-## FAIR in practice
+## Exercise: FAIR in practice
 
 Role playing exercise:
 One person presents the software, the other person gives feedback.

diff --git a/modules/fairsoftware/reading.md b/modules/fairsoftware/reading.md
@@ -1,5 +1,5 @@
 ---
-title: Reading material
+title: Further reading
 type: reading
 order: 5
 ---
@@ -11,4 +11,5 @@ Follow the links below to read about other resources related to FAIR research so
 
 ### FAIR Research Software Principles adoption
 The FAIR4RS Principles were [released in 2022](https://doi.org/10.15497/RDA00068), and since then there have been many efforts for adopting them.
+
 The blog post [The FAIR for Research Software Principles after two years: an adoption update](https://www.researchsoft.org/blog/2024-03/) contains a summary of these efforts.
diff --git a/modules/licenses/ex_choose_a_license.md b/modules/licenses/ex_choose_a_license.md
@@ -1,5 +1,5 @@
 ---
-title: Choose a license for or using your policy
+title: Choose a license
 type: exercise
 order: 5
 ---

diff --git a/modules/licenses/ex_have_licensing_policy.md b/modules/licenses/ex_have_licensing_policy.md
@@ -1,5 +1,5 @@
 ---
-title: Does your university have a software licensing policy?
+title: Is there a policy?
 type: exercise
 order: 6
 ---

diff --git a/modules/licenses/ex_licenses_in_use.md b/modules/licenses/ex_licenses_in_use.md
@@ -1,5 +1,5 @@
 ---
-title: What licenses do researchers at your university use?
+title: What's used?
 type: exercise
 order: 7
 ---

diff --git a/modules/licenses/university_policy.md b/modules/licenses/university_policy.md
@@ -1,5 +1,5 @@
 ---
-title: University software policies
+title: University Policies
 type: reading
 order: 3
 ---

diff --git a/modules/publication/automating_software_publication.md b/modules/publication/automating_software_publication.md
@@ -1,5 +1,5 @@
 ---
-title: Automating software publication
+title: Automating publication
 type: exercise
 order: 4
 ---

diff --git a/modules/publication/discussion.md b/modules/publication/discussion.md
@@ -1,12 +1,10 @@
 ---
-title: Discussion
-type: reading
+title: Before we dive in...
+type: exercise
 order: 1
 ---
 
-# Discussion
-
-## Before we dive in...
+## Discussion: Before we dive in...
 
 What do you already know about software publication? 
 

diff --git a/modules/publication/index.md b/modules/publication/index.md
@@ -1,5 +1,5 @@
 ---
-id: 8
+id: 1
 trl: medium
 category: Publishing & Citing
 title: Software publication

diff --git a/modules/publication/media/fair.png b/modules/publication/media/fair.png
diff --git a/modules/publication/reading.md b/modules/publication/reading.md
@@ -1,5 +1,5 @@
 ---
-title: Reading material
+title: Further reading
 type: reading
 order: 6
 ---

diff --git a/modules/publication/slides-publication.pmd b/modules/publication/slides-publication.pmd
@@ -31,15 +31,11 @@ The goal is to allow others to find and use your code, if they so wish, without
 
 ## Why Publish?
 
-### Major scientific considerations 
-* Citability
-* Reproducibility
-
-
-### FAIRness
-<center>
-<img src="/modules/fairsoftware/media/fair.png" width="40%">
-</center>
+* Major scientific considerations 
+    * Citability
+    * Reproducibility
+* FAIRness
+<img src="media/fair.png" width="30%">
 
 Note:
 

diff --git a/modules/publication/software_publication_pipeline.md b/modules/publication/software_publication_pipeline.md
@@ -1,5 +1,5 @@
 ---
-title: Software publication pipeline
+title: Publication pipeline
 type: reading
 order: 3
 ---

diff --git a/modules/researchsoftware/exercise-is-it-research-software.md b/modules/researchsoftware/exercise-is-it-research-software.md
@@ -1,7 +1,7 @@
 ---
-title: Is it research software?
+title: Research software?
 type: exercise
-order: 3
+order: 5
 ---
 
 ## Exercise: Is it research software?

diff --git a/modules/researchsoftware/exercise-research-life-cycle.md b/modules/researchsoftware/exercise-research-life-cycle.md
@@ -1,14 +1,14 @@
 ---
-title: Where does software fit in the research life cycle?
+title: Research life cycle
 type: exercise
-order: 4
+order: 6
 ---
 
 ## Exercise: Where does software fit in the research life cycle?
 
 Take a look at the research life cycle below.
 
-<img src="stories/_fairsoftware/researchcycle.png" alt="The Research Life Cycle" width="400"/>
+<img src="media/researchcycle.png" alt="The Research Life Cycle" width="400"/>
 
 Think of a piece of research software you have used or developed.
 

diff --git a/modules/researchsoftware/research-software.md b/modules/researchsoftware/research-software.md
@@ -1,7 +1,7 @@
 ---
-title: The role of research software
+title: Research software
 type: reading
-order: 5
+order: 4
 ---
 
 ## The role of research software (10 minutes)

diff --git a/modules/researchsoftware/slides-researchsoftware.pmd b/modules/researchsoftware/slides-researchsoftware.pmd
@@ -1,7 +1,7 @@
 ---
 title: Research Software
 type: slides
-order: 2
+order: 3
 ---
 
 <!-- .slide: data-state="title" -->
@@ -41,7 +41,7 @@ The data can be converted into an image using custom software.
 ## The research lifecycle
 
 <center>
-<img src="stories/_fairsoftware/researchcycle.png" alt="The Research Life Cycle" width="55%"/>
+<img src="media/researchcycle.png" alt="The Research Life Cycle" width="55%"/>
 </center>
 
 <small>Software is used all across the research lifecycle</small>
@@ -55,7 +55,7 @@ Software is used all across the research life cycle.
 <!-- .slide: data-state="standard" -->
 
 <center>
-<img src="stories/_fairsoftware/definition.png" width="55%">
+<img src="media/definition.png" width="55%">
 </center>
 
 <small>definition of Research Software from the FAIR4RS working group</small>

diff --git a/modules/researchsoftware/slides-software.pmd b/modules/researchsoftware/slides-software.pmd
@@ -16,9 +16,9 @@ order: 1
 
 ## Software is data
 
-Computer scientist: *"Software is just data"*
+Some data enthousiasts might say: *"Software is just data"*
 <center>
-<img src="stories/_researchsoftware/bits_heart.jpg" width="55%">
+<img src="media/bits_heart.jpg" width="55%">
 </center>
 
 <small>Photo by <a href="https://unsplash.com/@swimstaralex?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Alexander Sinn</a> on <a href="https://unsplash.com/photos/a-heart-is-shown-on-a-computer-screen-KgLtFCgfC28?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Unsplash</a>
@@ -53,12 +53,11 @@ Software is stored as bits and read from disk, loaded into memory and processed
 
 ## Software is <u>not</u> data
 
-Everyone but computer scientists: *"Software is not data"*
-
+Everyone but the data enthousiast: *"Software is not data"*
 
 
 <center>
-<img src="stories/_researchsoftware/tools.jpg" width="55%">
+<img src="media/tools.jpg" width="55%">
 </center>
 
 <small>Photo by <a href="https://unsplash.com/@barnimages?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Barn Images</a> on <a href="https://unsplash.com/photos/assorted-handheld-tools-in-tool-rack-t5YUoHW6zRo?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Unsplash</a>

diff --git a/modules/researchsoftware/software-and-data.md b/modules/researchsoftware/software-and-data.md
@@ -1,7 +1,7 @@
 ---
-title: Software is data
+title: Software and data
 type: reading
-order: 6
+order: 2
 ---
 
 ### Software is data (10 minutes, optional)
@@ -11,7 +11,7 @@ Read the following blogpost about why this concept is so powerful:
 https://www.blackliszt.com/2014/04/fundamental-concepts-of-computing-software-is-data.html
 
 
-### Software is a special type of data ()
+### Software is a special type of data (10 minutes, optional)
 However for most practical purposes in most domains of scientific research (except maybe the domain of computer science) it is useful to make a distinction between the data that is software and other data. From now on, when we use the word data, we mean the kind fo data which is not software and which we use to store more static information.
 
 - Software is executable, data is not.
@@ -27,5 +27,4 @@ https://doi.org/10.7287/peerj.preprints.2630v1
 
 ### Discussion
 
-- 
 - Can you think of examples where the line between software and data becomes fuzzy?
diff --git a/modules/smp/index.md → modules/softwaremanagementplans/index.md b/modules/smp/index.md → modules/softwaremanagementplans/index.md
diff --git a/modules/smp/info.md → modules/softwaremanagementplans/info.md b/modules/smp/info.md → modules/softwaremanagementplans/info.md
diff --git a/modules/smp/media/documentation.png → ...remanagementplans/media/documentation.png b/modules/smp/media/documentation.png → ...remanagementplans/media/documentation.png
diff --git a/modules/smp/media/engineering.png → ...waremanagementplans/media/engineering.png b/modules/smp/media/engineering.png → ...waremanagementplans/media/engineering.png
diff --git a/modules/smp/media/groupedrequirements.png → ...gementplans/media/groupedrequirements.png b/modules/smp/media/groupedrequirements.png → ...gementplans/media/groupedrequirements.png
diff --git a/modules/smp/media/maintenance.png → ...waremanagementplans/media/maintenance.png b/modules/smp/media/maintenance.png → ...waremanagementplans/media/maintenance.png
diff --git a/modules/smp/media/nlesc-dummy.png → ...waremanagementplans/media/nlesc-dummy.png b/modules/smp/media/nlesc-dummy.png → ...waremanagementplans/media/nlesc-dummy.png
diff --git a/modules/smp/media/projectmanagement.png → ...nagementplans/media/projectmanagement.png b/modules/smp/media/projectmanagement.png → ...nagementplans/media/projectmanagement.png
diff --git a/modules/smp/media/purpose.png → ...softwaremanagementplans/media/purpose.png b/modules/smp/media/purpose.png → ...softwaremanagementplans/media/purpose.png
diff --git a/modules/smp/media/researchcycle.png → ...remanagementplans/media/researchcycle.png b/modules/smp/media/researchcycle.png → ...remanagementplans/media/researchcycle.png
diff --git a/modules/smp/media/smpguide.png → ...oftwaremanagementplans/media/smpguide.png b/modules/smp/media/smpguide.png → ...oftwaremanagementplans/media/smpguide.png
diff --git a/modules/smp/media/softwarespectrum.png → ...anagementplans/media/softwarespectrum.png b/modules/smp/media/softwarespectrum.png → ...anagementplans/media/softwarespectrum.png
diff --git a/modules/smp/media/threelevels.png → ...waremanagementplans/media/threelevels.png b/modules/smp/media/threelevels.png → ...waremanagementplans/media/threelevels.png
diff --git a/modules/smp/media/thumbnail-smp.jpg → ...remanagementplans/media/thumbnail-smp.jpg b/modules/smp/media/thumbnail-smp.jpg → ...remanagementplans/media/thumbnail-smp.jpg
diff --git a/modules/smp/media/venn_fairsmp.png → ...aremanagementplans/media/venn_fairsmp.png b/modules/smp/media/venn_fairsmp.png → ...aremanagementplans/media/venn_fairsmp.png
diff --git a/modules/smp/media/viaappia.png → ...oftwaremanagementplans/media/viaappia.png b/modules/smp/media/viaappia.png → ...oftwaremanagementplans/media/viaappia.png
diff --git a/modules/smp/exercise1.md → ...softwaremanagementplans/practicalguide.md b/modules/smp/exercise1.md → ...softwaremanagementplans/practicalguide.md
@@ -1,12 +1,11 @@
 ---
-title: Exercise 1
-type: exercise
+title: Practical Guide
+type: reading
 order: 2
 ---
 
-# Exercise 1
 
-## Software Management Plans (10 minutes)
+## Practical Guide to Software Management Plans (15 minutes)
 
 Research software plays a crucial role in academic research and has become a key output of many research projects. A software management plan helps to implement best practices during software development and ensures that software is accessible and reusable in the short and longer term. It also contributes to the reproducibility of results and stimulates collaborative work on open-source software for research.
 

diff --git a/modules/smp/reading.md → modules/softwaremanagementplans/reading.md b/modules/smp/reading.md → modules/softwaremanagementplans/reading.md
diff --git a/modules/smp/slides-smp.pmd → ...es/softwaremanagementplans/slides-smp.pmd b/modules/smp/slides-smp.pmd → ...es/softwaremanagementplans/slides-smp.pmd
diff --git a/modules/smp/exercise3.md → modules/softwaremanagementplans/smpvsfair.md b/modules/smp/exercise3.md → modules/softwaremanagementplans/smpvsfair.md
@@ -1,11 +1,9 @@
 ---
-title: Exercise 3
+title: SMP vs FAIR
 type: exercise
 order: 4
 ---
 
-# Exercise 3
-
 ## SMP vs FAIR
 
 ### Why do we care?

diff --git a/modules/smp/exercise2.md → ...waremanagementplans/softwareassessment.md b/modules/smp/exercise2.md → ...waremanagementplans/softwareassessment.md
@@ -1,10 +1,10 @@
 ---
-title: Exercise 2
+title: Software Assessment
 type: exercise
 order: 3
 ---
 
-# Exercise 2
+# Assess your software
 
 *In a live setting, this exercise is done in groups.
 Each group will be assigned a software project.