Release: merge develop into master

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-41-g508666e
+_commit: v0.11.3
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/actions/download-artifact/action.yml

@@ -1,5 +1,5 @@
 name: 'Download artifact'
-description: 'Generic wrapper for actions/download-artifact'
+description: 'Wrapper for actions/download-artifact'
 inputs:
   name:
     description: 'Name of the artifact to download'
@@ -39,7 +39,7 @@ runs:
   using: 'composite'
   steps:
     - name: Download artifact
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v8
       with:
         name: ${{ inputs.name }}
         path: ${{ inputs.path }}

.github/actions/github-script/action.yml

@@ -13,7 +13,7 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - uses: actions/github-script@v8
+    - uses: actions/github-script@v9
       with:
         script: ${{ inputs.script }}
         github-token: ${{ inputs.github-token }}

.github/actions/setup-easyscience-bot/action.yml

@@ -22,9 +22,9 @@ runs:
   steps:
     - name: Create GitHub App installation token
       id: app-token
-      uses: actions/create-github-app-token@v2
+      uses: actions/create-github-app-token@v3
       with:
-        app-id: ${{ inputs.app-id }}
+        client-id: ${{ inputs.app-id }}
         private-key: ${{ inputs.private-key }}
         repositories: ${{ inputs.repositories }}
 

.github/actions/setup-pixi/action.yml

@@ -1,5 +1,5 @@
 name: 'Setup Pixi Environment'
-description: 'Sets up pixi with common configuration'
+description: 'Wrapper for prefix-dev/setup-pixi'
 inputs:
   environments:
     description: 'Pixi environments to setup'
@@ -33,7 +33,7 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - uses: prefix-dev/setup-pixi@v0.9.4
+    - uses: prefix-dev/setup-pixi@v0.9.5
       with:
         environments: ${{ inputs.environments }}
         activate-environment: ${{ inputs.activate-environment }}

.github/actions/upload-artifact/action.yml

@@ -1,5 +1,5 @@
 name: 'Upload artifact'
-description: 'Generic wrapper for actions/upload-artifact'
+description: 'Wrapper for actions/upload-artifact'
 inputs:
   name:
     description: 'Artifact name'
@@ -38,7 +38,7 @@ runs:
   using: 'composite'
   steps:
     - name: Upload artifact
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v7
       with:
         name: ${{ inputs.name }}
         path: ${{ inputs.path }}

.github/actions/upload-codecov/action.yml

@@ -1,5 +1,5 @@
 name: 'Upload coverage to Codecov'
-description: 'Generic wrapper for codecov/codecov-action@v5'
+description: 'Wrapper for codecov/codecov-action'
 
 inputs:
   name:
@@ -32,7 +32,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: codecov/codecov-action@v5
+    - uses: codecov/codecov-action@v6
       with:
         name: ${{ inputs.name }}
         flags: ${{ inputs.flags }}

.github/scripts/publish-dashboard.sh

@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+remote_repository="${DASHBOARD_REMOTE_REPOSITORY:?}"
+publish_branch="${DASHBOARD_PUBLISH_BRANCH:-master}"
+source_dir="${DASHBOARD_SOURCE_DIR:?}"
+token="${DASHBOARD_TOKEN:?}"
+git_user_name="${DASHBOARD_GIT_USER_NAME:-easyscience[bot]}"
+git_user_email="${DASHBOARD_GIT_USER_EMAIL:?}"
+commit_message="${DASHBOARD_COMMIT_MESSAGE:?}"
+max_attempts="${DASHBOARD_PUSH_ATTEMPTS:-3}"
+delay_seconds="${DASHBOARD_PUSH_DELAY_SECONDS:-15}"
+
+workspace_dir="$(mktemp -d)"
+repo_dir="${workspace_dir}/dashboard"
+remote_url="https://x-access-token:${token}@github.com/${remote_repository}.git"
+
+cleanup() {
+  rm -rf "${workspace_dir}"
+}
+
+prepare_worktree() {
+  if [[ ! -d "${repo_dir}/.git" ]]; then
+    git clone --branch "${publish_branch}" --depth 1 "${remote_url}" "${repo_dir}"
+  else
+    git -C "${repo_dir}" fetch origin "${publish_branch}"
+    git -C "${repo_dir}" checkout "${publish_branch}"
+    git -C "${repo_dir}" reset --hard "origin/${publish_branch}"
+    git -C "${repo_dir}" clean -fd
+  fi
+
+  git -C "${repo_dir}" config user.name "${git_user_name}"
+  git -C "${repo_dir}" config user.email "${git_user_email}"
+}
+
+sync_publish_dir() {
+  cp -R "${source_dir}/." "${repo_dir}/"
+  git -C "${repo_dir}" add .
+
+  if git -C "${repo_dir}" diff --cached --quiet; then
+    return 1
+  fi
+
+  git -C "${repo_dir}" commit -m "${commit_message}"
+}
+
+trap cleanup EXIT
+
+prepare_worktree
+
+if ! sync_publish_dir; then
+  echo "No dashboard changes to publish."
+  exit 0
+fi
+
+for ((attempt = 1; attempt <= max_attempts; attempt += 1)); do
+  if git -C "${repo_dir}" push origin "HEAD:${publish_branch}"; then
+    echo "Dashboard published on attempt ${attempt}."
+    exit 0
+  fi
+
+  if ((attempt == max_attempts)); then
+    echo "Dashboard publish failed after ${max_attempts} attempts." >&2
+    exit 1
+  fi
+
+  echo "Dashboard push attempt ${attempt} failed. Retrying in ${delay_seconds}s." >&2
+  sleep "${delay_seconds}"
+
+  prepare_worktree
+
+  if ! sync_publish_dir; then
+    echo "Dashboard changes already exist in the target repository."
+    exit 0
+  fi
+done

.github/workflows/backmerge.yml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout repository (for local actions)
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup easyscience[bot]
         id: bot
@@ -38,7 +38,7 @@ jobs:
           repositories: ${{ github.event.repository.name }}
 
       - name: Checkout repository (with bot token)
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           token: ${{ steps.bot.outputs.token }}

.github/workflows/cleanup.yml

@@ -15,11 +15,11 @@ on:
       days:
         description: 'Number of days.'
         required: true
-        default: 30
+        default: '30'
       minimum_runs:
         description: 'The minimum runs to keep for each workflow.'
         required: true
-        default: 6
+        default: '6'
       delete_workflow_pattern:
         description:
           'The name or filename of the workflow. if not set then it will target all

.github/workflows/coverage.yml

@@ -5,8 +5,6 @@ on:
   push:
     branches:
       - develop
-    # Do not run on version tags (those are handled by other workflows)
-    tags-ignore: ['v*']
   # Trigger the workflow on pull request
   pull_request:
   # Allows you to run this workflow manually from the Actions tab
@@ -34,7 +32,7 @@ jobs:
 
     steps:
       - name: Check-out repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
@@ -48,7 +46,7 @@ jobs:
 
     steps:
       - name: Check-out repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
@@ -71,7 +69,7 @@ jobs:
 
     steps:
       - name: Check-out repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi

.github/workflows/dashboard.yml

@@ -7,6 +7,10 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  group: dashboard-publish-${{ github.repository }}
+  cancel-in-progress: false
+
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
@@ -21,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -44,19 +48,18 @@ jobs:
 
             git worktree add ../$BRANCH origin/$BRANCH
             mkdir -p reports/$BRANCH
-            CODE_PATH="../$BRANCH/src"
 
             echo "Docstring coverage for branch $BRANCH"
-            pixi run interrogate -c pyproject.toml --fail-under=0 $CODE_PATH > reports/$BRANCH/coverage-docstring.txt
+            pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
 
             echo "Cyclomatic complexity for branch $BRANCH"
-            pixi run radon cc -s -j $CODE_PATH > reports/$BRANCH/cyclomatic-complexity.json
+            pixi run radon cc -s -j ../$BRANCH/src > reports/$BRANCH/cyclomatic-complexity.json
 
             echo "Maintainability index for branch $BRANCH"
-            pixi run radon mi -j $CODE_PATH > reports/$BRANCH/maintainability-index.json
+            pixi run radon mi -j ../$BRANCH/src > reports/$BRANCH/maintainability-index.json
 
             echo "Raw metrics for branch $BRANCH"
-            pixi run radon raw -s -j $CODE_PATH > reports/$BRANCH/raw-metrics.json
+            pixi run radon raw -s -j ../$BRANCH/src > reports/$BRANCH/raw-metrics.json
           done
 
       - name: Generate dashboard HTML
@@ -82,22 +85,25 @@ jobs:
             ${{ github.event.repository.name }}
             dashboard
 
-      # Publish to external dashboard repository with retry logic.
+      # Push to external dashboard repository with retry logic.
       # Retry is needed to handle transient GitHub API/authentication issues
       # that occasionally cause 403 errors when multiple workflows push concurrently.
       # Uses personal_token (not github_token) as GITHUB_TOKEN cannot access external repos.
-      - name: Publish to main branch of ${{ github.repository }}
-        uses: Wandalen/wretry.action@v3.8.0
-        with:
-          attempt_limit: 3
-          attempt_delay: 15000 # 15 seconds between retries
-          action: peaceiris/actions-gh-pages@v4
-          with: |
-            publish_dir: ./_dashboard_publish
-            keep_files: true
-            external_repository: ${{ env.REPO_OWNER }}/dashboard
-            publish_branch: master
-            personal_token: ${{ steps.bot.outputs.token }}
+      - name:
+          Push to ${{ env.REPO_OWNER }}/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH
+          }}
+        shell: bash
+        env:
+          DASHBOARD_COMMIT_MESSAGE: ${{ env.CI_BRANCH }}
+          DASHBOARD_GIT_USER_EMAIL:
+            ${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com
+          DASHBOARD_PUSH_ATTEMPTS: '3'
+          DASHBOARD_PUSH_DELAY_SECONDS: '15'
+          DASHBOARD_PUBLISH_BRANCH: master
+          DASHBOARD_REMOTE_REPOSITORY: ${{ env.REPO_OWNER }}/dashboard
+          DASHBOARD_SOURCE_DIR: ./_dashboard_publish
+          DASHBOARD_TOKEN: ${{ steps.bot.outputs.token }}
+        run: bash ./.github/scripts/publish-dashboard.sh
 
       - name: Add dashboard link to summary
         run: |

.github/workflows/docs.yml

@@ -27,12 +27,16 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# Allow only one concurrent deployment to gh-pages at a time.
-# All docs workflows share the same concurrency group to prevent race conditions
-# when multiple branches/tags trigger simultaneous deployments.
+# - Non-tagged pushes and pull requests all use `docs-dev` group, so
+#   they cancel each other.
+# - Tagged pushes use their own group like docs-v1.2.3, so they do not
+#   cancel non-tagged runs, and non-tagged runs do not cancel them.
 concurrency:
-  group: docs-gh-pages-deploy
-  cancel-in-progress: false
+  group: >-
+    ${{ startsWith(github.ref, 'refs/tags/v')
+      && format('docs-{0}', github.ref_name)
+      || 'docs-dev' }}
+  cancel-in-progress: true
 
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
@@ -83,7 +87,7 @@ jobs:
       # Check out the repository source code.
       # Note: The gh-pages branch is fetched separately later for mike deployment.
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       # Activate dark mode to create documentation with Plotly charts in dark mode
       # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher