Merge pull request #59 from alan-turing-institute/main

[pull] main from alan-turing-institute:main

.all-contributorsrc

@@ -599,7 +599,8 @@
       "avatar_url": "https://avatars3.githubusercontent.com/u/28339195?v=4",
       "profile": "https://github.com/jspickering",
       "contributions": [
-        "doc"
+        "doc",
+        "bug"
       ]
     },
     {
@@ -1685,7 +1686,8 @@
       "avatar_url": "https://avatars2.githubusercontent.com/u/1876667?v=4",
       "profile": "https://orcid.org/0000-0002-3127-5520",
       "contributions": [
-        "content"
+        "content",
+        "review"
       ]
     },
     {
@@ -4039,6 +4041,42 @@
       "contributions": [
         "content"
       ]
+    },
+    {
+      "login": "priyanshuone6",
+      "name": "Priyanshu Agarwal",
+      "avatar_url": "https://avatars.githubusercontent.com/u/64051212?v=4",
+      "profile": "http://git.io/priyanshu",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "pdurbin",
+      "name": "Philip Durbin",
+      "avatar_url": "https://avatars.githubusercontent.com/u/21006?v=4",
+      "profile": "http://greptilian.com",
+      "contributions": [
+        "content"
+      ]
+    },
+    {
+      "login": "sjDCC",
+      "name": "Sarah Jones",
+      "avatar_url": "https://avatars.githubusercontent.com/u/6169940?v=4",
+      "profile": "https://dmponline.dcc.ac.uk",
+      "contributions": [
+        "content"
+      ]
+    },
+    {
+      "login": "flavio2018",
+      "name": "Flavio Petruzzellis",
+      "avatar_url": "https://avatars.githubusercontent.com/u/39437769?v=4",
+      "profile": "http://flavio2018.github.io",
+      "contributions": [
+        "bug"
+      ]
     }
   ],
   "projectName": "the-turing-way",

.github/workflows/auto-compress-images.yaml

@@ -0,0 +1,27 @@
+name: Automatically compress image files
+
+on:
+  pull_request_target:
+    # Only trigger when images have changed
+    paths:
+      - '**.jpg'
+      - '**.jpeg'
+      - '**.png'
+      - '**.gif'
+
+jobs:
+  compress-images:
+    runs-on: ubuntu-latest
+    environment: compress-images
+    # Set permissions on GITHUB_TOKEN
+    permissions:
+      contents: write  # Make commits
+      pull-requests: write  # Post a comment on a PR
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: Compress images
+        uses: crush-pics/crush-pics-github-action@v1.0
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-key: ${{ secrets.CRUSHPICS_API_KEY }}

book/website/_bibliography/references.bib

@@ -1733,6 +1733,53 @@ @article{Kent2022change
 	pages = {e3001680}
 }
 
+@article{Henry2021RDM, 
+	title = {Data Management for Researchers: 8 Principles of Good Data Management},
+	url = {https://doi.org/10.31234/osf.io/5tmfe},
+	doi = {10.31234/osf.io/5tmfe},
+	author = {Henry, Teague R.},
+	year = {2021},
+	journal = {Open Science Framework}
+}
+
+@article{Borer2009RDM, 
+	title = {Some Simple Guidelines for Effective Data Management},
+	url = {https://doi.org/10.1890/0012-9623-90.2.205},
+	doi = {10.1890/0012-9623-90.2.205},
+	author = {Borer, Elizabeth T. and Seabloom, Eric W. and Jones, Matthew B. and Schildhauer, Mark},
+	year = {2009},
+	journal = {The Bulletin of the Ecological Society of America}
+}
+
+@misc{Larsen2021Documentation, 
+	title = {Dataset for "Quantification of Magnetic Resonance Spectroscopy data using a combined reference: Application in typically developing infants},
+	url = {https://doi.org/10.13012/B2IDB-3548139_V1},
+	doi = {10.13012/B2IDB-3548139_V1},
+	author = {Larsen, Ryan J. and Gagoski, Borjan and Morton, Sarah U. and Ou, Yangming and Vyas, Rutvi and Litt, Jonathanand Grant, P. Ellen and Sutton, Bradley P.},
+	year = {2021},
+	journal = {Illinois Data Bank}
+}
+
+@article{Wickham2014tidydata, 
+	title = {Tidy Data},
+	url = {https://doi.org/10.18637/jss.v059.i10},
+	doi = {10.18637/jss.v059.i10},
+	author = {Wickham, Hadley},
+	year = {2014},
+	journal = {Journal of Statistical Software}
+}
+
+@article{Borghi2022checklist, 
+	title = {Promoting Open Science Through Research Data Management},
+	volume = {4},
+	url = {https://doi.org/10.1162/99608f92.9497f68e},
+	doi = {10.1162/99608f92.9497f68e},
+	author = {Borghi, John and Van Gulick, Ana},
+	month = jul,
+	year = {2022},
+	journal = {Harvard Data Science Review},
+}
+
 @misc{anaconda2020sods,
   author = {Anaconda, Inc.},
   title = {2020 STATE OF DATA SCIENCE},
@@ -1758,3 +1805,12 @@ @article{mons2017fair
   month = {02},
   doi = {10.3233/ISU-170824}
 }
+
+@article{Levenstein2018sharing, 
+	title = {Data: Sharing Is Caring},
+	url = {https://doi.org/10.1177/2515245918758319},
+	doi = {10.1177/2515245918758319},
+	author = {Levenstein, Margaret C. and Lyle Jared A.},
+	year = {2018},
+	journal = {Advances in Methods and Practices in Psychological Science}
+}

book/website/collaboration/github-novice/github-novice-features.md

@@ -55,7 +55,7 @@ Annotated diagram of a collaborative project repository.
   - **1. Project:** This shows you the project boards for this repo.
   - **2. Issues:** All the tasks that have been raised on this repo.
   - **3. Files:** These are all the files in the repo.
-  - **4. Landing page or README.md file:** Your README.md file is automatically rendered as a landing page for your site.
+  - **4. Landing page or `README.md` file:** Your `README.md` file is automatically rendered as a landing page for your site.
 - Labels on the right-hand side of the image:
   - **5. Insights:** This shows you all the activity that has happened on your repo. 
   - **6. Edit repo details:** You can write a short description of your project and add labels.

book/website/collaboration/github-novice/github-novice-firststeps.md

@@ -34,7 +34,7 @@ Annotated diagram of repository after its basic creation, explaining the main fe
 - **3. Code:** this tab brings you back to your landing page. It shows you the folders that you have made in the repo.
 - **4. Main:** this is your default development branch or active branch of your repository.
 - **5. Branch:** parallel version(s) of your repository.
-- **6. README.md file:** this file contains basic information about your project (in this case it only has the project name: “trial-repo”. When we plan to make a website, this will be rendered as a landing (front) page for your site.
+- **6. `README.md` file:** this file contains basic information about your project (in this case it only has the project name: “trial-repo”. When we plan to make a website, this will be rendered as a landing (front) page for your site.
 
 On the right side of the webpage we have the following features:
 - **7. Green Code button:** click it to download your repository locally.
@@ -45,7 +45,7 @@ On the right side of the webpage we have the following features:
 - **12: Edit/Pencil symbol:** click this pencil symbol to edit your README.md file.
 ```
 
-## 3. Edit your README.md file
+## 3. Edit your `README.md` file
 
 Unless you have added any other files or included a license file during repo creation, you should have one file in your repository now - README.md.
 We'll need edit this file to add information about the repo.
@@ -54,13 +54,13 @@ This is where you start to use the Markdown formatting.
 Whatever you write in this file will be shown on the landing (front) page of your project on GitHub, so use it to tell people all about your project.
 
 ### Navigating the GitHub editing interface
-To edit your README.md file:
+To edit your `README.md` file:
 
 * You can click on the pencil symbol in the top right of the central box on your landing page.
 
 **Or**
 
-* Click on the README.md file and then click the pencil symbol.
+* Click on the `README.md` file and then click the pencil symbol.
 
 You can now edit the file.
 We'll talk about how to save your changes after some pointers on writing a good README.
@@ -101,18 +101,18 @@ Annotated diagram of README.md file in edit mode – before editing.
 * Tell people who you are and how you can be contacted.
 
 
-**NOTE: If you’re having trouble getting started, it’s a good idea to look at other peoples' README.md files.**
+**NOTE: If you’re having trouble getting started, it’s a good idea to look at other peoples' `README.md` files.**
 
 If you can’t get your raw markdown content to render in the way you want, it is also a good idea to find a file that has what you want and then look at the raw file.
-You can copy and paste other people’s raw file content into your README.md file and then edit it.
+You can copy and paste other people’s raw file content into your `README.md` file and then edit it.
 
-Here is an example of a really well formatted README.md file: [STEMM Role Models App](https://github.com/KirstieJane/STEMMRoleModels/blob/gh-pages/README.md)
+Here is an example of a really well formatted `README.md` file: [STEMM Role Models App](https://github.com/KirstieJane/STEMMRoleModels/blob/gh-pages/README.md)
 
-If you click the link above, it will take you to their README.file. You can use this as a template for your README.md file.
+If you click the link above, it will take you to their README file. You can use this as a template for your `README.md` file.
 
 * To look at the raw markdown file you need to click on the raw button (top right of the white box).
-* This takes you to the markdown raw file that is rendered into a nicely formatted README.md file on GitHub.
-* Now just copy and paste it into your README.md edit tab. You can now edit this for your project.
+* This takes you to the markdown raw file that is rendered into a nicely formatted `README.md` file on GitHub.
+* Now just copy and paste it into your `README.md` edit tab. You can now edit this for your project.
 * Remember to check what it looks like by clicking on the preview changes tab.
 * When you have finished editing, you need to scroll down to the bottom of the page and press the green commit changes button.
 
@@ -148,13 +148,13 @@ The standard licenses offered on GitHub are most approriate for software and won
 
 [Creative commons](https://creativecommons.org/licenses/) licenses are the best to use for this purpose, and the most open of these is the CC BY 4.0.
 
-To add a license to your repository, the first thing to do is create a LICENSE.md file:
+To add a license to your repository, the first thing to do is create a `LICENSE.md` file:
 
 * To do this, click on the Add file button, and click create file. This will give you a blank file.
-* Then, you need to name the file, so call it LICENSE.md. This makes it into a markdown file.
+* Then, you need to name the file, so call it `LICENSE.md`. This makes it into a markdown file.
 * You can find all the creative commons licenses in the link above so copy the text of the license you want and then paste it into this file.
 * Don’t forget to press the green commit new file button at the bottom and write a commit message to describe what you have done.
-* You can also add a link to the license to the bottom of your README.md file. Here is a link to a repository that you can copy to add in a [CC BY 4.0 license](https://github.com/santisoler/cc-licenses).
-It has a text file for your LICENSE.md file and also a shield (or badge) that you can put at the bottom of your README.md file.
+* You can also add a link to the license to the bottom of your `README.md` file. Here is a link to a repository that you can copy to add in a [CC BY 4.0 license](https://github.com/santisoler/cc-licenses).
+It has a text file for your `LICENSE.md` file and also a shield (or badge) that you can put at the bottom of your `README.md` file.
 
 You can find more information about licenses in the {ref}`rr-licensing` chapter of The Turing Way.

book/website/collaboration/research-infrastructure-roles/data-wrangler.md

@@ -3,6 +3,15 @@
 
 Data Wranglers can be viewed as a specialised type of data scientist, primarily working in the space between data generators and data analysts. There are many activities that a data scientist might undertake, for example, data collection, wrangling, analysis, modelling, visualisation and communication. How these activities map onto different job titles is domain specific and will vary on a project and organisational level.
 
+```{figure} ../../figures/data-wrangler.jpg
+---
+width: 500px
+name: data-wrangler
+alt: Hand-drawn illustration by Scriberia. A person representing a Data Wrangler is in a central bubble, on their left there are links to three clusters of connected shapes representing unstructured data. The Data Wrangler ‘unravels’ these clusters and re-structures them to form three distinct presents, labelled ‘Research Ready Data’, shown to the right of the central bubble. Attached to the central bubble there are smaller individual bubbles labelled ‘Connecting Specialists' (shown by a triangle of linked people), 'Data Privacy and Security’ (padlock) and 'Data Quality and Standards (sparkling diamond).
+---
+A Data Wrangler collaborates with multiple specialists to provide research-ready data whilst upholding data privacy and domain-specific standards. Created by Scriberia with The Turing Way community. Used under a CC-BY 4.0 licence. DOI: [10.5281/zenodo.3332807](https://doi.org/10.5281/zenodo.3332807).
+```
+
 (cl-infrastructure-data-wranglers-tasks)=
 ## What do Data Wranglers do?
 
@@ -78,7 +87,7 @@ Here are some examples of places that employ Data Wranglers in the UK:
 _Please get in touch if you know of other organisations that you would like to add to this list. This list, and this Data Wrangler page in general, is focused around Data Wrangler roles within an  academic research context, but they will also exist within an industry context._
 
 (cl-infrastructure-data-wranglers-summary)=
-# Data Wranglers: Summary
+## Data Wranglers: Summary
 
 A Data Wrangler position is becoming recognised as a crucial part of any project that involves large amounts of complex data, specifically in a research context.
 They will have a diverse set of technical and interpersonal skills.

book/website/communication/citable/citable-cite.md

@@ -7,7 +7,7 @@ A citation includes the following information:
 - Author
 - Title
 - Year of publication
-- Publisher (for data, this is often the data repository where it is housed),
+- Publisher (for data, this is often the data repository where it is housed)
 - Version (if indicated)
 - Access information (a URL or DOI)
 
@@ -23,8 +23,8 @@ See also [FORCE11 resource](https://www.force11.org/node/4771).
 
 (cm-citable-cite-data)=
 ## Citing Data
-When sharing a dataset, use the assigned DOI (from the data repository) and add this to your data availability statement at the end of the paper (similar to the acknowledgement section). It is important to also cite your dataset in the references themselves, as only the citations in the reference section will contribute to citation counts
-
+When sharing a dataset, use the assigned DOI (from the data repository) and add this to your data availability statement at the end of the paper (similar to the acknowledgement section). 
+It is important to also cite your dataset in the references themselves, as only the citations in the reference section will contribute to citation counts.
 
 You can find examples of these statements in the publishers' (research data) author policies.
 

book/website/community-handbook/presenting.md

@@ -1,6 +1,15 @@
 # Presenting About _The Turing Way_
 Talks are a great way to engage new communities, teach people about open and reproducible practices, and expand the reach of _The Turing Way_ by introducing the book and inviting new contributors. We encourage any Turing Way contributor to present on behalf of _The Turing Way_, and we ask that you use the guidelines detailed below to shape your talk and ensure consistency with _The Turing Way_ style. 
 
+```{figure} ../figures/giving-a-talk.*
+---
+height: 500px
+name: giving-a-talk
+alt: The image shows a female speaker with long dark hair standing in front of a large wall mounted screen giving a talk about the Turing Way. There are several audience members watching her. There is also an image of a head scarf wearing person sitting at their desk in front of a laptop running an online Turing Way workshop.
+---
+Giving a talk or workshop about _The Turing Way_. Illustration by Scriberia for _The Turing Way_ community, used under a CC-BY 4.0 licence. DOI: https://doi.org/10.5281/zenodo.3332807.
+```
+
 ## Planning a Talk
 Whether you are submitting an abstract to a conference or you have been invited to speak, a great thing to do is to engage _The Turing Way_ community for support and to publicize the event. Even if the talk is not open to all, you can work with other community members to refine your slides and give a practice talk. If you'd like, please post the details in Slack in the `#community` channel.