Release: merge develop into master

.copier-answers.yml

@@ -1,14 +1,16 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.4.8
+_commit: v0.11.0-9-g7085ef7
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/peasy-app
-app_doi: 10.5281/zenodo.18163581
+app_doi: 10.5281/zenodo.18700888
 app_package_name: easypeasy_app
 app_python: '3.13'
 app_repo_name: peasy-app
+home_page_url: https://easyscience.github.io/peasy
+home_repo_name: peasy
 lib_docs_url: https://easyscience.github.io/peasy-lib
-lib_doi: 10.5281/zenodo.18163581
+lib_doi: 10.5281/zenodo.18700888
 lib_package_name: easypeasy
 lib_python_max: '3.13'
 lib_python_min: '3.11'
@@ -17,9 +19,7 @@ project_contact_email: support@easyscience.org
 project_copyright_years: 2025-2026
 project_extended_description: A software for performing imaginary calculations based
     on a imaginary model and refining its parameters against imaginary data
-project_homepage_url: https://easyscience.github.io/peasy
 project_name: EasyPeasy
-project_repo_name: peasy
 project_short_description: Imaginary data analysis
 project_shortcut: EP
 project_type: both

.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@v0.9.3
+    - uses: prefix-dev/setup-pixi@v0.9.4
       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/configs/pages-deployment.json

@@ -0,0 +1,6 @@
+{
+  "source": {
+    "branch": "gh-pages",
+    "path": "/"
+  }
+}

.github/configs/rulesets-develop.json

@@ -0,0 +1,37 @@
+{
+  "name": "develop branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/develop"],
+      "exclude": []
+    }
+  },
+  "bypass_actors": [
+    {
+      "actor_id": 2476259,
+      "actor_type": "Integration",
+      "bypass_mode": "always"
+    }
+  ],
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["squash"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}

.github/configs/rulesets-gh-pages.json

@@ -0,0 +1,19 @@
+{
+  "name": "gh-pages branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/gh-pages"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    }
+  ]
+}

.github/configs/rulesets-master.json

@@ -0,0 +1,30 @@
+{
+  "name": "master branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["~DEFAULT_BRANCH"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["merge"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}

.github/scripts/backmerge-conflict-issue.js

@@ -0,0 +1,69 @@
+module.exports = async ({ github, context, core }) => {
+  // Repo context
+  const owner = context.repo.owner
+  const repo = context.repo.repo
+
+  // Link to the exact workflow run that detected the conflict
+  const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}`
+
+  // We use a *stable title* so we can find/reuse the same "conflict tracker" issue
+  // instead of creating a new issue on every failed run.
+  const title = 'Backmerge conflict: master → develop'
+
+  // Comment/issue body includes the run URL so maintainers can jump straight to logs.
+  const body = [
+    'Automatic backmerge failed due to merge conflicts.',
+    '',
+    `Workflow run: ${runUrl}`,
+    '',
+    'Manual resolution required.',
+  ].join('\n')
+
+  // Label applied to the tracker issue (assumed to already exist in the repo).
+  const label = '[bot] backmerge'
+
+  // Search issues by title across *open and closed* issues.
+  // Why: if the conflict was resolved previously and the issue was closed,
+  // we prefer to reopen it and append a new comment instead of creating duplicates.
+  const q = `repo:${owner}/${repo} is:issue in:title "${title}"`
+  const search = await github.rest.search.issuesAndPullRequests({
+    q,
+    per_page: 10,
+  })
+
+  // Pick the first exact-title match (search can return partial matches).
+  const existing = search.data.items.find((i) => i.title === title)
+
+  if (existing) {
+    // If a tracker issue exists, reuse it:
+    // - reopen it if needed
+    // - add a comment with the new run URL
+    if (existing.state === 'closed') {
+      await github.rest.issues.update({
+        owner,
+        repo,
+        issue_number: existing.number,
+        state: 'open',
+      })
+    }
+
+    await github.rest.issues.createComment({
+      owner,
+      repo,
+      issue_number: existing.number,
+      body,
+    })
+
+    core.notice(`Conflict issue updated: #${existing.number}`)
+    return
+  }
+
+  // No tracker issue exists yet -> create the first one.
+  await github.rest.issues.create({
+    owner,
+    repo,
+    title,
+    body,
+    labels: [label],
+  })
+}

.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