Merge branch 'main' into update/workflows

Author: anenadic

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

@@ -16,7 +16,7 @@ jobs:
           mkdir -p ./pr
           printf ${{ github.event.number }} > ./pr/NUM
       - name: Upload Diff
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: pr
           path: ./pr

.github/workflows/pr-comment.yaml

@@ -127,8 +127,8 @@ jobs:
     permissions:
       contents: write
     steps:
-      - name: "Checkout md outputs"
-        uses: actions/checkout@v4
+      - name: 'Checkout md outputs'
+        uses: actions/checkout@v5
         with:
           ref: md-outputs
           path: built

.github/workflows/pr-receive.yaml

@@ -25,7 +25,7 @@ jobs:
       - name: "Upload PR number"
         id: upload
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: pr
           path: ${{ github.workspace }}/NR
@@ -58,10 +58,10 @@ jobs:
       MD: ${{ github.workspace }}/site/built
     steps:
       - name: "Check Out Main Branch"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: "Check Out Staging Branch"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: md-outputs
           path: ${{ env.MD }}
@@ -107,21 +107,21 @@ jobs:
         shell: Rscript {0}
 
       - name: "Upload PR"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: pr
           path: ${{ env.PR }}
           overwrite: true
 
       - name: "Upload Diff"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: diff
           path: ${{ env.CHIVE }}
           retention-days: 1
 
       - name: "Upload Build"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: built
           path: ${{ env.MD }}

.github/workflows/sandpaper-main.yaml

@@ -35,7 +35,7 @@ jobs:
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

.github/workflows/update-cache.yaml

@@ -63,7 +63,12 @@ jobs:
       renv-needed: ${{ steps.renv-check.outputs.renv-needed }}
     steps:
       - name: "Checkout Lesson"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
+      - id: renv
+        run: |
+          if [[ -d renv ]]; then
+            echo "exists=true" >> $GITHUB_OUTPUT
+          fi
 
       - name: "Is renv required?"
         id: renv-check
@@ -89,7 +94,7 @@ jobs:
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
       - name: "Checkout Lesson"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

.github/workflows/update-workflows.yaml

@@ -28,7 +28,7 @@ jobs:
       id-token: write
     steps:
       - name: "Checkout Repository"
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: "Validate Current Org and Workflow"
         id: validate-org-workflow

episodes/14-collaboration-using-git.md

@@ -123,7 +123,10 @@ SVG of the diagram can be downloaded from:
 https://mermaid.ink/svg/pako:eNqFksFuwyAMhl8FcemmdS_AodKm7rZe2sOkKRcXnAQNcEaMpqjquw-SZZtUReEE9vfbP5iL1GRQKtnjZ8KgcW-hieCrIPJ6o_hhQyP2NqJmisPjbvdwYmhK8CkiKNFYFmDMxP9PFfSVNDhxxI56W-TiOULQ7aTS5L3lSbgAlhpH9MS4VKRLfTuVWOJWfdTIul21cfMUqmg9xgbX-9-Kf8w7J-76liLrlI1Q_DOUT87RFxpxHsRvq5EBseEIeqx4Hnts7uVWZsCDNXmWl-Koktyix0qqvDVYQ3JcySpcMwqJ6TQELRXHhFuZOgM8j16qGlyfo2jKPQ7T_xi_yUy-jJlZ3UF4J5p112_HVM9r
 -->
 
-![Software development lifecycle with Git](fig/git-lifecycle.svg){alt='Development lifecycle with Git, containing Git commands add, commit, push, fetch, restore, merge and pull' .image-with-shadow width="600px"}
+![Software development lifecycle with Git](fig/git-lifecycle.svg){
+  alt='Development lifecycle with Git. Four parts of Git infrastructure are represented: working tree, staging area, local repository and remote repository, and alongside this various git commands. git add is shown moving files from working tree to staging area. git commit is shown moving files from staging area to local repository. git push is shown moving files from local repository to remote repository and git fetch from remote repository to local repository. git checkout and git merge are both shown as moving files from local repository to working tree. git pull, a shortcut for git fetch followed by git checkout / merge, is shown moving files from remote repository to working tree.' 
+  .image-with-shadow width="600px"
+}
 
 ## Checking-in Changes to Our Project
 
@@ -306,7 +309,7 @@ Collaborating with others involves
 managing these remote repositories and pushing and pulling information
 to and from them when you need to share work.
 
-![](fig/git-distributed.png){alt='git-distributed' .image-with-shadow width="400px"}
+![](fig/git-distributed.png){alt='Representation of Git\'s distributed version control system showing interactions between a central repository and two local repositories on developer machines, with arrows showing pushing from central repository to developer repositories, pulling from developer repositories to central repository. A self-connecting arrow on developer repository shows creating commits in local repository.' .image-with-shadow width="400px"}
 
 <p style="text-align: center;">Git - distributed version control system<br> From <a href="https://www.w3docs.com/learn-git/git-repository.html" target="_blank">W3Docs</a> (freely available)</p>
 
@@ -364,7 +367,7 @@ So, working on a separate branch for each feature you are adding is good for sev
 
 Branches are commonly used as part of a feature-branch workflow, shown in the diagram below.
 
-![](fig/git-feature-branch.svg){alt='Git feature branch workflow diagram' .image-with-shadow width="800px"}
+![](fig/git-feature-branch.svg){alt='Git commit tree showing four branches - Main, Develop, FeatureX and FeatureY. The Main branch shows three commits corresponding to release tags v0.1, v0.2 and v0.3. The Develop branch branches off from Main branch with intermediate commits between release tags which are then merged into Main branch. Short-lived feature branches FeatureX and FeatureY branch off from Develop branch, have a small number of additional commits and are then merged back in to Develop branch.' .image-with-shadow width="800px"}
 
 <p style="text-align: center;">Git feature branches<br>
 Adapted from <a href="https://sillevl.gitbooks.io/git/content/collaboration/workflows/gitflow/" target="_blank">Git Tutorial by sillevl</a> (Creative Commons Attribution 4.0 International License)</p>
@@ -496,7 +499,7 @@ However, as we have just created this branch locally,
 it still does not exist in our remote repository.
 You can check that in GitHub by listing all branches.
 
-![](fig/github-main-branch.png){alt="Software project's main branch" .image-with-shadow width="600px"}
+![Software project's main branch](fig/github-main-branch.png){alt="Code tab of GitHub web interface showing main branch of software project. Branch selector dropdown is shown with main (default) branch showing as currently selected and one other branch feature-std-dev showing as present." .image-with-shadow width="600px"}
 
 To push a new local branch remotely for the first time,
 you could use the `-u` flag and the name of the branch you are creating and pushing to:
@@ -526,7 +529,7 @@ From the `Code` tab in your repository in GitHub,
 click the branch dropdown menu (currently showing the default branch `main`).
 You should see your `develop` branch in the list too.
 
-![](fig/github-develop-branch.png){alt="Software project's develop branch" .image-with-shadow width="600px"}
+![Software project's develop branch](fig/github-develop-branch.png){alt="Code tab of GitHub web interface showing notification indicating develop branch had recent pushes. Branch selector dropdown is shown with main (default) branch showing as currently selected and two other branches develop and feature-std-dev showing as present, with develop highlighted." .image-with-shadow width="600px"}
 
 You may also have noticed GitHub's notification about the latest push to your `develop` branch just
 on top of the repository files and branches drop-down menu.

episodes/23-continuous-integration-automated-testing.md

@@ -190,10 +190,10 @@ jobs:
     # Next we need to checkout out repository, and set up Python
     # A 'name' is just an optional label shown in the log - helpful to clarify progress - and can be anything
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 
@@ -332,7 +332,7 @@ we can use a feature called **build matrices**
 which really shows the value of using CI to test at scale.
 
 Suppose the intended users of our software use either Ubuntu, Mac OS, or Windows,
-and have Python versions 3.10 through 3.12 installed,
+and have Python versions 3.11 through 3.13 installed,
 and we want to support all of these.
 Assuming we have a suitable test suite,
 it would take a considerable amount of time to set up testing platforms
@@ -363,7 +363,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     # Here we add the reference to the os matrix values
     runs-on: ${{ matrix.os }}
@@ -372,10 +372,10 @@ jobs:
     steps:
 
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         # Here we add the reference to the python-version matrix values
         python-version: ${{ matrix.python-version }}
@@ -391,7 +391,7 @@ jobs:
 
 The `{{ }}` are used
 as a means to reference configuration values from the matrix.
-This way, every possible permutation of Python versions 3.10 through 3.12
+This way, every possible permutation of Python versions 3.11 through 3.13
 with the latest versions of Ubuntu, Mac OS and Windows operating systems
 will be tested, and we can expect 9 build jobs in total.
 We can also use this in the `name` key of the step to accurately reflect what it is doing

episodes/34-code-refactoring.md

@@ -282,7 +282,7 @@ i.e. their tests are:
 ::: challenge
 ## Exercise: Testing a Pure Function
 
-Add tests for `compute_standard_deviation_by_data()` that check for situations
+Add tests for `compute_standard_deviation_by_day()` that check for situations
 when there is only one file with multiple rows,
 multiple files with one row, and any other cases you can think of that should be tested.
 
@@ -299,9 +299,9 @@ with more inputs and expected outputs:
 ],
 ids=['Two patients in same file', 'Two patients in different files', 'Two identical patients in two different files'])
 def test_compute_standard_deviation_by_day(data, expected_output):
-    from inflammation.compute_data import compute_standard_deviation_by_data
+    from inflammation.compute_data import compute_standard_deviation_by_day
 
-    result = compute_standard_deviation_by_data(data)
+    result = compute_standard_deviation_by_day(data)
     npt.assert_array_almost_equal(result, expected_output)
 ```
 

episodes/43-software-release.md

@@ -134,7 +134,7 @@ Version [0.1.0]: 1.0.0
 Description []:  Analyse patient inflammation data
 Author [None, n to skip]: James Graham <J.Graham@software.ac.uk>
 License []:  MIT
-Compatible Python versions [>=3.13]:  >=3.10
+Compatible Python versions [>=3.13]:  >=3.11
 
 Would you like to define your main dependencies interactively? (yes/no) [yes] no
 Would you like to define your development dependencies interactively? (yes/no) [yes] no
@@ -149,7 +149,7 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
 ]