easyscience 2.1.0__tar.gz → 2.3.0__tar.gz

easyscience-2.3.0/.badgery.yaml

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+default_branch: master
+develop_branch: develop
+
+cards:
+  - group: Tests
+    type: gh_action
+    title: Code/package tests (GitHub)
+    file: test.yml
+    enabled: true
+  - group: Tests
+    type: gh_action
+    title: Tutorial tests (GitHub)
+    file: tutorial-tests.yml
+    enabled: true
+
+  - group: Tests
+    type: gh_action
+    title: Package tests (PyPI)
+    file: pypi-test.yml
+    enabled: true
+
+  - group: Code Quality
+    type: codefactor
+    title: Code quality (CodeFactor)
+    enabled: true
+
+  - group: Code Quality
+    type: radon_mi
+    title: Maintainability index (radon)
+    report: reports/{branch}/maintainability-index.json
+    enabled: true
+
+  - group: Code Quality
+    type: radon_cc
+    title: Cyclomatic complexity (radon)
+    report: reports/{branch}/cyclomatic-complexity.json
+    enabled: true
+
+  - group: Size
+    type: radon_loc
+    title: Source/Logical lines of code (radon)
+    report: reports/{branch}/raw-metrics.json
+    enabled: true
+
+  - group: Size
+    type: radon_ff
+    title: Functions/Files count (radon)
+    report: reports/{branch}/cyclomatic-complexity.json
+    enabled: true
+
+  - group: Coverage
+    type: codecov
+    title: Unit test coverage (Codecov)
+    flag: unittests
+    enabled: true
+
+  - group: Coverage
+    type: interrogate
+    title: Docstring coverage (interrogate)
+    report: reports/{branch}/coverage-docstring.txt
+    enabled: true
+  - group: Build & Release
+    type: gh_action
+    title: Publishing (PyPI)
+    workflow: pypi-publish.yml
+    enabled: true
+
+  - group: Build & Release
+    type: gh_action
+    title: Docs build/deployment
+    workflow: docs.yml
+    enabled: true

easyscience-2.3.0/.codecov.yml

@@ -0,0 +1,8 @@
+github_checks:
+  annotations: true
+comment:
+  layout: 'reach, diff, flags, files'
+  behavior: default
+  require_changes: false # if true: only post the comment if coverage changes
+  require_base: no # [yes :: must have a base report to post]
+  require_head: yes # [yes :: must have a head report to post]

easyscience-2.3.0/.copier-answers.yml

@@ -0,0 +1,20 @@
+# WARNING: Do not edit this file manually.
+# Any changes will be overwritten by Copier.
+_commit: v0.10.0
+_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_min: '3.11'
+lib_repo_name: core
+project_contact_email: support@easyscience.org
+project_copyright_years: 2021-2026
+project_extended_description: The foundation of the framework, providing reusable
+    building blocks for scientific libraries and applications aimed at making data
+    analysis easier
+project_name: EasyScience
+project_short_description: Core building blocks for EasyScience
+project_shortcut: ES
+project_type: lib
+template_type: lib

easyscience-2.3.0/.coveragerc

@@ -0,0 +1,3 @@
+[paths]
+source =
+    src/easyscience/

easyscience-2.3.0/.github/actions/download-artifact/action.yml

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+name: 'Download artifact'
+description: 'Generic wrapper for actions/download-artifact'
+inputs:
+  name:
+    description: 'Name of the artifact to download'
+    required: true
+
+  path:
+    description: 'Destination path'
+    required: false
+    default: '.'
+
+  pattern:
+    description: 'Glob pattern to match artifact names (optional)'
+    required: false
+    default: ''
+
+  merge-multiple:
+    description: 'Merge multiple artifacts into the same directory'
+    required: false
+    default: 'false'
+
+  github-token:
+    description: 'GitHub token for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  repository:
+    description: 'owner/repo for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  run-id:
+    description: 'Workflow run ID for cross-run download (optional)'
+    required: false
+    default: ''
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v4
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        pattern: ${{ inputs.pattern }}
+        merge-multiple: ${{ inputs.merge-multiple }}
+        github-token: ${{ inputs.github-token }}
+        repository: ${{ inputs.repository }}
+        run-id: ${{ inputs.run-id }}

easyscience-2.3.0/.github/actions/github-script/action.yml

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+name: 'GitHub Script'
+description: 'Wrapper for actions/github-script'
+inputs:
+  script:
+    description: 'JavaScript to run'
+    required: true
+
+  github-token:
+    description: 'GitHub token (defaults to github.token)'
+    required: false
+    default: ${{ github.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - uses: actions/github-script@v8
+      with:
+        script: ${{ inputs.script }}
+        github-token: ${{ inputs.github-token }}

easyscience-2.3.0/.github/actions/setup-easyscience-bot/action.yml

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+name: 'Setup EasyScience bot for pushing'
+description: 'Create GitHub App token and configure git identity + origin remote'
+inputs:
+  app-id:
+    description: 'GitHub App ID'
+    required: true
+  private-key:
+    description: 'GitHub App private key (PEM)'
+    required: true
+  repositories:
+    description: 'Additional repositories to grant access to (newline-separated)'
+    required: false
+    default: ''
+
+outputs:
+  token:
+    description: 'Installation access token'
+    value: ${{ steps.app-token.outputs.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Create GitHub App installation token
+      id: app-token
+      uses: actions/create-github-app-token@v2
+      with:
+        app-id: ${{ inputs.app-id }}
+        private-key: ${{ inputs.private-key }}
+        repositories: ${{ inputs.repositories }}
+
+    - name: Configure git for pushing
+      shell: bash
+      run: |
+        git config user.name "easyscience[bot]"
+        git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com"
+
+    - name: Configure origin remote to use the bot token
+      shell: bash
+      run: |
+        git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git

easyscience-2.3.0/.github/actions/setup-pixi/action.yml

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+name: 'Setup Pixi Environment'
+description: 'Sets up pixi with common configuration'
+inputs:
+  environments:
+    description: 'Pixi environments to setup'
+    required: false
+    default: 'default'
+  activate-environment:
+    description: 'Environment to activate'
+    required: false
+    default: 'default'
+  run-install:
+    description: 'Whether to run pixi install'
+    required: false
+    default: 'true'
+  locked:
+    description: 'Whether to run pixi install --locked'
+    required: false
+    default: 'false'
+  frozen:
+    description: 'Whether to run pixi install --frozen'
+    required: false
+    default: 'true'
+  cache:
+    description: 'Whether to use cache'
+    required: false
+    default: 'false'
+  post-cleanup:
+    description: 'Whether to run post cleanup'
+    required: false
+    default: 'false'
+
+runs:
+  using: 'composite'
+  steps:
+    - uses: prefix-dev/setup-pixi@v0.9.4
+      with:
+        environments: ${{ inputs.environments }}
+        activate-environment: ${{ inputs.activate-environment }}
+        run-install: ${{ inputs.run-install }}
+        locked: ${{ inputs.locked }}
+        frozen: ${{ inputs.frozen }}
+        cache: ${{ inputs.cache }}
+        post-cleanup: ${{ inputs.post-cleanup }}

easyscience-2.3.0/.github/actions/upload-artifact/action.yml

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+name: 'Upload artifact'
+description: 'Generic wrapper for actions/upload-artifact'
+inputs:
+  name:
+    description: 'Artifact name'
+    required: true
+
+  path:
+    description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)'
+    required: true
+
+  include-hidden-files:
+    description: 'Include hidden files'
+    required: false
+    default: 'true'
+
+  if-no-files-found:
+    description: 'warn | error | ignore'
+    required: false
+    default: 'error'
+
+  compression-level:
+    description: '0-9 (0 = no compression)'
+    required: false
+    default: '0'
+
+  retention-days:
+    description: 'Retention in days (optional)'
+    required: false
+    default: ''
+
+  overwrite:
+    description: 'Overwrite an existing artifact with the same name'
+    required: false
+    default: 'false'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Upload artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        include-hidden-files: ${{ inputs.include-hidden-files }}
+        if-no-files-found: ${{ inputs.if-no-files-found }}
+        compression-level: ${{ inputs.compression-level }}
+        retention-days: ${{ inputs.retention-days }}
+        overwrite: ${{ inputs.overwrite }}

easyscience-2.3.0/.github/actions/upload-codecov/action.yml

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+name: 'Upload coverage to Codecov'
+description: 'Generic wrapper for codecov/codecov-action@v5'
+
+inputs:
+  name:
+    description: 'Codecov upload name'
+    required: true
+
+  flags:
+    description: 'Codecov flags'
+    required: false
+    default: ''
+
+  files:
+    description: 'Coverage report files'
+    required: true
+
+  fail_ci_if_error:
+    description: 'Fail CI if upload fails'
+    required: false
+    default: 'true'
+
+  verbose:
+    description: 'Enable verbose output'
+    required: false
+    default: 'true'
+
+  token:
+    description: 'Codecov token'
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - uses: codecov/codecov-action@v5
+      with:
+        name: ${{ inputs.name }}
+        flags: ${{ inputs.flags }}
+        files: ${{ inputs.files }}
+        fail_ci_if_error: ${{ inputs.fail_ci_if_error }}
+        verbose: ${{ inputs.verbose }}
+        token: ${{ inputs.token }}

easyscience-2.3.0/.github/configs/pages-deployment.json

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

easyscience-2.3.0/.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
+      }
+    }
+  ]
+}

easyscience-2.3.0/.github/configs/rulesets-gh-pages.json

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

easyscience-2.3.0/.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
+      }
+    }
+  ]
+}

easyscience-2.3.0/.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],
+  })
+}

easyscience-2.3.0/.github/workflows/backmerge.yml

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+# This workflow automatically merges `master` into `develop` whenever a
+# new version release with a tag is published. It can also be triggered
+# manually via workflow_dispatch for cases where an automatic backmerge
+# is needed outside of the standard release process.
+# If a merge conflict occurs, the workflow creates an issue to notify
+# maintainers for manual resolution.
+
+name: Backmerge (master → develop)
+
+on:
+  release:
+    types: [published, prereleased]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  issues: write
+
+concurrency:
+  group: backmerge-master-into-develop
+  cancel-in-progress: false
+
+jobs:
+  backmerge:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - name: Checkout repository (for local actions)
+        uses: actions/checkout@v5
+
+      - 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 }}
+          repositories: ${{ github.event.repository.name }}
+
+      - name: Checkout repository (with bot token)
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          token: ${{ steps.bot.outputs.token }}
+
+      - name: Configure git identity
+        run: |
+          git config user.name "easyscience[bot]"
+          git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com"
+
+      - name: Set merge message
+        run: |
+          if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            MESSAGE="Backmerge: master into develop (manual) [skip ci]"
+          else
+            TAG="${{ github.event.release.tag_name }}"
+            MESSAGE="Backmerge: master (${TAG}) into develop [skip ci]"
+          fi
+
+          echo "MESSAGE=$MESSAGE" >> "$GITHUB_ENV"
+          echo "message=$MESSAGE" >> "$GITHUB_OUTPUT"
+          echo "📝 Merge message: $MESSAGE" | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Prepare branches
+        run: |
+          git fetch origin master develop
+          git checkout -B develop origin/develop
+
+      - name: Check if develop is already up-to-date
+        id: up_to_date
+        run: |
+          if git merge-base --is-ancestor origin/master develop; then
+            echo "value=true" >> "$GITHUB_OUTPUT"
+            echo "ℹ️ Develop is already up-to-date with master" | tee -a "$GITHUB_STEP_SUMMARY"
+          else
+            echo "value=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Try merge master into develop
+        id: merge
+        if: steps.up_to_date.outputs.value == 'false'
+        continue-on-error: true
+        run: |
+          if ! git merge origin/master --no-ff -m "${MESSAGE}"; then
+            echo "conflict=true" >> "$GITHUB_OUTPUT"
+            echo "❌ Backmerge conflict detected." | tee -a "$GITHUB_STEP_SUMMARY"
+            git status --porcelain || true
+            exit 0
+          fi
+
+          echo "conflict=false" >> "$GITHUB_OUTPUT"
+          echo "✅ Merge commit created." | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Push to develop (if merge succeeded)
+        if:
+          steps.up_to_date.outputs.value == 'false' && steps.merge.outputs.conflict ==
+          'false'
+        run: |
+          git push origin develop
+          echo "🚀 Backmerge successful: master → develop" | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Create issue (if merge failed with conflicts)
+        if: steps.merge.outputs.conflict == 'true'
+        uses: ./.github/actions/github-script
+        with:
+          github-token: ${{ steps.bot.outputs.token }}
+          script: |
+            const run = require('./.github/scripts/backmerge-conflict-issue.js')
+            await run({ github, context, core })