easyscience 2.3.1__tar.gz → 2.4.0__tar.gz

easyscience-2.4.0/.codecov.yml

@@ -0,0 +1,26 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecov-yaml
+
+github_checks:
+  annotations: true
+
+comment:
+  layout: 'reach, diff, flags, files'
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        # Make project coverage informational (won't block PR)
+        informational: true
+    patch:
+      default:
+        target: auto
+        # Require patch coverage but with threshold
+        threshold: 1%

{easyscience-2.3.1 → easyscience-2.4.0}/.copier-answers.yml

@@ -1,11 +1,11 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.0
+_commit: v0.13.1
 _src_path: gh:easyscience/templates
 lib_docs_url: https://easyscience.github.io/core
 lib_doi: 10.5281/zenodo.18163581
 lib_package_name: easyscience
-lib_python_max: '3.13'
+lib_python_max: '3.14'
 lib_python_min: '3.11'
 lib_repo_name: core
 project_contact_email: support@easyscience.org

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}
 

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

easyscience-2.4.0/.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

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}

{easyscience-2.3.1 → easyscience-2.4.0}/.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

{easyscience-2.3.1 → easyscience-2.4.0}/.github/workflows/coverage.yml

@@ -1,10 +1,10 @@
 name: Coverage checks
 
 on:
-  # Trigger the workflow on push
+  # Trigger the workflow on push to develop
   push:
-    # Do not run on version tags (those are handled by other workflows)
-    tags-ignore: ['v*']
+    branches:
+      - develop
   # Trigger the workflow on pull request
   pull_request:
   # Allows you to run this workflow manually from the Actions tab
@@ -15,11 +15,11 @@ permissions:
   actions: write
   contents: read
 
-# Allow only one concurrent workflow, skipping runs queued between the run
-# in-progress and latest queued. And cancel in-progress runs.
+# Allow only one concurrent workflow per PR or branch ref.
+# Cancel in-progress runs only for pull requests, but let branch push runs finish.
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
@@ -32,7 +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
@@ -46,7 +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
@@ -63,32 +63,8 @@ jobs:
           files: ./coverage-unit.xml
           token: ${{ secrets.CODECOV_TOKEN }}
 
-  # Job 2: Run integration tests with coverage and upload to Codecov
-  integration-tests-coverage:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check-out repository
-        uses: actions/checkout@v5
-
-      - name: Set up pixi
-        uses: ./.github/actions/setup-pixi
-
-      - name: Run integration tests with coverage
-        run:
-          pixi run integration-tests-coverage --cov-report=xml:coverage-integration.xml
-
-      - name: Upload integration tests coverage to Codecov
-        if: ${{ !cancelled() }}
-        uses: ./.github/actions/upload-codecov
-        with:
-          name: integration-tests-job
-          flags: integration
-          files: ./coverage-integration.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
-    needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs
+    needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
     uses: ./.github/workflows/dashboard.yml
     secrets: inherit

{easyscience-2.3.1 → easyscience-2.4.0}/.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 }}
@@ -21,16 +25,20 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
 
+      # Install badgery into the active Pixi environment without modifying
+      # pixi.toml/pixi.lock. Using `pixi add` here re-solves the whole project
+      # and rebuilds the local editable package, which can cause intermittent
+      # Linux CI failures (`Text file busy`, os error 26).
       - name: Install badgery
         shell: bash
-        run: pixi add --pypi --git https://github.com/enhantica/badgery badgery
+        run: pixi run python -m pip install git+https://github.com/enhantica/badgery
 
       - name: Run docstring coverage and code complexity/maintainability checks
         run: |
@@ -81,22 +89,25 @@ 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: |

{easyscience-2.3.1 → easyscience-2.4.0}/.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
@@ -119,11 +123,14 @@ jobs:
 
       # Build the static files for the documentation site for local inspection
       # Input: docs/ directory containing the Markdown files
-      # Output: site/ directory containing the generated HTML files
+      # Output: docs/site/ directory containing the generated HTML files
+      # Also verifies that mkdocstrings generated docs/site/objects.inv.
       - name: Build site for local check
-        run: pixi run docs-build-local
+        run: |
+          pixi run docs-build-local
+          pixi run docs-inventory-check
 
-      # Upload the static files from the site/ directory to be used for
+      # Upload the static files from the docs/site/ directory to be used for
       # local check
       - name: Upload built site as artifact
         uses: ./.github/actions/upload-artifact

easyscience-2.4.0/.github/workflows/issues-labels.yml

@@ -0,0 +1,40 @@
+# Verifies if the current issue has at least one `[scope]` label and one
+# `[priority]` label. If either is missing, the workflow adds a reminder label.
+
+name: Issue labels check
+
+on:
+  issues:
+    types: [opened, labeled, unlabeled]
+
+permissions:
+  issues: write
+
+jobs:
+  check-labels:
+    runs-on: ubuntu-latest
+
+    concurrency:
+      group: issue-labels-${{ github.event.issue.number }}
+      cancel-in-progress: true
+
+    steps:
+      - name: Ensure [scope] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
+        with:
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[scope]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[scope] ⚠️ label needed'
+
+      - name: Ensure [priority] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
+        with:
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[priority]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[priority] ⚠️ label needed'

easyscience-2.4.0/.github/workflows/lint-format.yml

@@ -0,0 +1,124 @@
+# The workflow checks
+#  - the validity of pyproject.toml,
+#  - the presence and correctness of SPDX license headers,
+#  - linting and formatting of Python code,
+#  - linting and formatting of docstrings in Python code,
+#  - formatting of non-Python files (like markdown and toml).
+#  - linting of Python code in Jupyter notebooks (for library template).
+#
+# A summary of the checks is added to the GitHub Actions summary.
+
+name: Lint and format checks
+
+on:
+  # Trigger the workflow on push
+  push:
+    branches-ignore: [master, main] # Already verified in PR
+    # Do not run this workflow on creating a new tag starting with
+    # 'v', e.g. 'v1.0.3' (see publish-pypi.yml)
+    tags-ignore: ['v*']
+  # Trigger the workflow on pull request
+  pull_request:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Allow only one concurrent workflow, skipping runs queued between the run
+# in-progress and latest queued. And cancel in-progress runs.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+
+jobs:
+  lint-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Run post-install developer steps
+        run: pixi run post-install
+
+      - name: Check validity of pyproject.toml
+        id: pyproject
+        continue-on-error: true
+        shell: bash
+        run: pixi run pyproject-check
+
+      - name: Check SPDX license headers
+        id: license_headers
+        continue-on-error: true
+        shell: bash
+        run: pixi run license-check
+
+      - name: Check linting of Python code
+        id: py_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run py-lint-check
+
+      - name: Check formatting of Python code
+        id: py_format
+        continue-on-error: true
+        shell: bash
+        run: pixi run py-format-check
+
+      - name: Check linting of docstrings in Python code
+        id: docstring_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run docstring-lint-check
+
+      - name: Check formatting of non-Python files (md, toml, etc.)
+        id: nonpy_format
+        continue-on-error: true
+        shell: bash
+        run: pixi run nonpy-format-check
+
+      - name: Check linting of Python code in Jupyter notebooks (ipynb)
+        id: notebook_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run notebook-lint-check
+
+      # Add summary
+      - name: Add quality checks summary
+        if: always()
+        shell: bash
+        run: |
+          {
+            echo "## 🧪 Checks Summary"
+            echo ""
+            echo "| Check | Status |"
+            echo "|-------|--------|"
+            echo "| pyproject.toml   | ${{ steps.pyproject.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| license headers  | ${{ steps.license_headers.outcome == 'success' && '✅'  || '❌' }} |"
+            echo "| py lint          | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| py format        | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| docstring lint   | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| nonpy format     | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| notebooks lint   | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |"
+          } >> "$GITHUB_STEP_SUMMARY"
+
+      # Fail job if any check failed
+      - name: Fail job if any check failed
+        if: |
+          steps.pyproject.outcome == 'failure'
+          || steps.license_headers.outcome == 'failure'
+          || steps.py_lint.outcome == 'failure'
+          || steps.py_format.outcome == 'failure'
+          || steps.docstring_lint.outcome == 'failure'
+          || steps.nonpy_format.outcome == 'failure'
+          || steps.notebook_lint.outcome == 'failure'
+        shell: bash
+        run: exit 1

easyscience-2.4.0/.github/workflows/pr-labels.yml

@@ -0,0 +1,45 @@
+# Verifies if a pull request has at least one label from a set of valid
+# labels before it can be merged.
+#
+# The label validation is delegated to `mheap/github-action-required-labels`,
+# which checks the current PR labels via the GitHub API and can add or update a
+# PR comment when the required label set is missing.
+
+name: PR labels check
+
+on:
+  pull_request_target:
+    types: [opened, labeled, unlabeled, synchronize]
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  check-labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - uses: mheap/github-action-required-labels@v5
+        with:
+          token: ${{ steps.bot.outputs.token }}
+          add_comment: true
+          mode: minimum
+          count: 1
+          labels: |
+            [bot] release
+            [scope] bug
+            [scope] documentation
+            [scope] enhancement
+            [scope] maintenance
+            [scope] significant

{easyscience-2.3.1 → easyscience-2.4.0}/.github/workflows/pypi-publish.yml

@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Check-out repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0 # full history with tags to get the version number by versioningit