.github/workflows/README.md

@@ -2,7 +2,7 @@
 
 This directory contains workflows to be used for Lessons using the {sandpaper}
 lesson infrastructure. Two of these workflows require R (`sandpaper-main.yaml`
-and `pr-recieve.yaml`) and the rest are bots to handle pull request management.
+and `pr-receive.yaml`) and the rest are bots to handle pull request management.
 
 These workflows will likely change as {sandpaper} evolves, so it is important to
 keep them up-to-date. To do this in your lesson you can do the following in your
@@ -94,9 +94,9 @@ branch called `update/workflows` and a pull request is created. Maintainers are
 encouraged to review the changes and accept the pull request if the outputs
 are okay.
 
-This update is run ~~weekly or~~ on demand.
+This update is run weekly or on demand.
 
-### 03 Maintain: Update Pacakge Cache (update-cache.yaml)
+### 03 Maintain: Update Package Cache (update-cache.yaml)
 
 For lessons that have generated content, we use {renv} to ensure that the output
 is stable. This is controlled by a single lockfile which documents the packages
@@ -140,7 +140,7 @@ Once the checks are finished, a comment is issued to the pull request, which
 will allow maintainers to determine if it is safe to run the 
 "Receive Pull Request" workflow from new contributors.
 
-### Recieve Pull Request (pr-recieve.yaml)
+### Receive Pull Request (pr-receive.yaml)
 
 **Note of caution:** This workflow runs arbitrary code by anyone who creates a
 pull request. GitHub has safeguarded the token used in this workflow to have no
@@ -171,7 +171,7 @@ The artifacts produced are used by the next workflow.
 
 ### Comment on Pull Request (pr-comment.yaml)
 
-This workflow is triggered if the `pr-recieve.yaml` workflow is successful.
+This workflow is triggered if the `pr-receive.yaml` workflow is successful.
 The steps in this workflow are:
 
 1. Test if the workflow is valid and comment the validity of the workflow to the

.github/workflows/draft-pdf-paper.yml

@@ -0,0 +1,28 @@
+name: Draft PDF paper
+on:
+  push:
+    paths:
+      - paper/**
+      - .github/workflows/draft-pdf-paper.yml
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/pr-close-signal.yaml

@@ -8,16 +8,15 @@ on:
 jobs:
   send-close-signal:
     name: "Send closing signal"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ github.event.action == 'closed' }}
     steps:
       - name: "Create PRtifact"
         run: |
           mkdir -p ./pr
           printf ${{ github.event.number }} > ./pr/NUM
       - name: Upload Diff
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ./pr
-

.github/workflows/pr-comment.yaml

@@ -20,7 +20,7 @@ jobs:
   #  - no .github files were committed
   test-pr:
     name: "Test if pull request is valid"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
@@ -74,15 +74,15 @@ jobs:
   create-branch:
     name: "Create Git Branch"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
     permissions:
       contents: write
     steps:
       - name: 'Checkout md outputs'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: built
@@ -120,7 +120,7 @@ jobs:
   comment-pr:
     name: "Comment on Pull Request"
     needs: [test-pr, create-branch]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
@@ -150,7 +150,7 @@ jobs:
   comment-changed-workflow:
     name: "Comment if workflow files have changed"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ always() && needs.test-pr.outputs.is_valid == 'false' }}
     env:
       NR: ${{ github.event.workflow_run.pull_requests[0].number }}
@@ -182,4 +182,3 @@ jobs:
         with:
           pr: ${{ env.NR }}
           body: ${{ env.body }}
-

.github/workflows/pr-post-remove-branch.yaml

@@ -9,7 +9,7 @@ on:
 jobs:
   delete:
     name: "Delete branch from Pull Request"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'

.github/workflows/pr-preflight.yaml

@@ -11,7 +11,7 @@ jobs:
   test-pr:
     name: "Test if pull request is valid"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     permissions:

.github/workflows/pr-receive.yaml

@@ -13,7 +13,7 @@ jobs:
   test-pr:
     name: "Record PR number"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     steps:
@@ -25,7 +25,7 @@ jobs:
       - name: "Upload PR number"
         id: upload
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ${{ github.workspace }}/NR
@@ -48,7 +48,7 @@ jobs:
   build-md-source:
     name: "Build markdown source files if valid"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -58,10 +58,10 @@ jobs:
       MD: ${{ github.workspace }}/site/built
     steps:
       - name: "Check Out Main Branch"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Check Out Staging Branch"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: ${{ env.MD }}
@@ -107,20 +107,21 @@ jobs:
         shell: Rscript {0}
 
       - name: "Upload PR"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ${{ env.PR }}
+          overwrite: true
 
       - name: "Upload Diff"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: diff
           path: ${{ env.CHIVE }}
           retention-days: 1
 
       - name: "Upload Build"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: built
           path: ${{ env.MD }}

.github/workflows/sandpaper-main.yaml

@@ -21,7 +21,10 @@ on:
 jobs:
   full-build:
     name: "Build Full Site"
-    runs-on: ubuntu-latest
+
+    # 2024-10-01: ubuntu-latest is now 24.04 and R is not installed by default in the runner image
+    # pin to 22.04 for now
+    runs-on: ubuntu-22.04
     permissions:
       checks: write
       contents: write
@@ -32,7 +35,7 @@ jobs:
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

.github/workflows/sandpaper-version.txt

@@ -1 +1 @@
-0.12.0
+0.16.10

.github/workflows/update-cache.yaml

@@ -14,7 +14,7 @@ on:
 jobs:
   preflight:
     name: "Preflight Check"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       ok: ${{ steps.check.outputs.ok }}
     steps:
@@ -36,14 +36,14 @@ jobs:
 
   check_renv:
     name: "Check if We Need {renv}"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: preflight
     if: ${{ needs.preflight.outputs.ok == 'true'}}
     outputs:
       needed: ${{ steps.renv.outputs.exists }}
     steps:
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - id: renv
         run: |
           if [[ -d renv ]]; then
@@ -52,7 +52,7 @@ jobs:
 
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_renv
     if: ${{ needs.check_renv.outputs.needed == 'true' }}
     outputs:
@@ -69,14 +69,14 @@ jobs:
     name: "Update Package Cache"
     needs: check_token
     if: ${{ needs.check_token.outputs.repo== 'true' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

.github/workflows/update-workflows.yaml

@@ -18,7 +18,7 @@ on:
 jobs:
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       workflow: ${{ steps.validate.outputs.wf }}
       repo: ${{ steps.validate.outputs.repo }}
@@ -31,12 +31,12 @@ jobs:
 
   update_workflow:
     name: "Update Workflow"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_token
     if: ${{ needs.check_token.outputs.workflow == 'true' }}
     steps:
       - name: "Checkout Repository"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Update Workflows
         id: update

AUTHORS

@@ -10,3 +10,5 @@
 * Cunliang Geng <c.geng@esciencecenter.nl>
 * Pranav Chandramouli <p.chandramouli@esciencecenter.nl>
 * Carsten Schnober <c.schnober@esciencecenter.nl>
+* Ashwin Vishnu Mohanan <ashwin.mohanan@ri.se>
+* Yonglei Wang <yonglei@nsc.liu.se>

CITATION.cff

@@ -55,10 +55,19 @@ authors:
     email: c.schnober@esciencecenter.nl
   - given-names: Toby
     family-names: Hodges
+  - given-names: Ashwin Vishnu
+    family-names: Mohanan
+    orcid: https://orcid.org/0000-0002-2979-6327
+    email: ashwin.mohanan@ri.se 
+  - given-names: Yonglei
+    family-names: Wang
+    orcid: https://orcid.org/0000-0003-3393-7257
+    email: yonglei@nsc.liu.se
+
 repository-code: >-
-  https://github.com/carpentries-incubator/deep-learning-intro
+  https://github.com/carpentries-lab/deep-learning-intro
 url: >-
-  https://carpentries-incubator.github.io/deep-learning-intro/
+  https://carpentries-lab.github.io/deep-learning-intro/
 abstract: >-
   This course describes a hands-on introduction to the first
   steps in deep learning, 

README.md

@@ -1,6 +1,6 @@
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/carpentries-incubator/deep-learning-intro/scaffolds)
 [![DOI](https://zenodo.org/badge/163412836.svg)](https://zenodo.org/badge/latestdoi/163412836)
-
+[![The Carpentries Lab Review Status](http://badges.carpentries-lab.org/25_status.svg)](https://github.com/carpentries-lab/reviews/issues/25)
 
 # Introduction to deep learning
 This lesson gives an introduction to deep learning.
@@ -21,7 +21,7 @@ deep learning. In addition, we expect them to know basics of statistics and mach
 
 ## Lesson development sprints
 We regularly host lesson development sprints, in which we work together at the lesson.
-The next one is scheduled for the 22nd and 23rd of July 2024. We kickoff with an online meeting at 10:00 CEST.
+The next one is scheduled for the 13th and 14th of January 2025. We kickoff with an online meeting at 10:00 CEST.
 If you want to join (you are very welcome to join even if you have never contributed so far) send an email to deep-learning-lesson-dev@esciencecenter.nl .
 
 ## Contributing
@@ -70,12 +70,8 @@ See the [Carpentries Workbench usage instructions](https://carpentries.github.io
 ## Maintainer(s)
 
 Current maintainers of this lesson are
-* Peter Steinbach
-* Colin Sauze
-* Djura Smits
-* Sven van der Burg
-* Pranav Chandramouli
-* Carsten Schnober
+* Sven van der Burg (s.vanderburg@esciencecenter.nl)
+* Carsten Schnober (c.schnober@esciencecenter.nl)
 
 ## Citation and authors