diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 00000000..d001c41d --- /dev/null +++ b/.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% diff --git a/.copier-answers.yml b/.copier-answers.yml index a8e73301..f177f9fd 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,6 +1,6 @@ # WARNING: Do not edit this file manually. # Any changes will be overwritten by Copier. -_commit: v0.11.0 +_commit: v0.13.1 _src_path: gh:easyscience/templates lib_docs_url: https://easyscience.github.io/gui-components lib_doi: 10.5281/zenodo.18163581 diff --git a/.github/actions/download-artifact/action.yml b/.github/actions/download-artifact/action.yml index e4fd62f5..d1fff1a0 100644 --- a/.github/actions/download-artifact/action.yml +++ b/.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 }} diff --git a/.github/actions/github-script/action.yml b/.github/actions/github-script/action.yml index ab32da56..50de89b7 100644 --- a/.github/actions/github-script/action.yml +++ b/.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 }} diff --git a/.github/actions/setup-easyscience-bot/action.yml b/.github/actions/setup-easyscience-bot/action.yml index 4b28eaf8..e51eb01a 100644 --- a/.github/actions/setup-easyscience-bot/action.yml +++ b/.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 }} diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml index 167ee623..dc3232c6 100644 --- a/.github/actions/setup-pixi/action.yml +++ b/.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 }} diff --git a/.github/actions/upload-artifact/action.yml b/.github/actions/upload-artifact/action.yml index 825ac396..fe8e4680 100644 --- a/.github/actions/upload-artifact/action.yml +++ b/.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 }} diff --git a/.github/actions/upload-codecov/action.yml b/.github/actions/upload-codecov/action.yml index 37d6298a..0cb15d1f 100644 --- a/.github/actions/upload-codecov/action.yml +++ b/.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: ${{ inputs.flags }} diff --git a/.github/scripts/publish-dashboard.sh b/.github/scripts/publish-dashboard.sh new file mode 100644 index 00000000..dcbd0b32 --- /dev/null +++ b/.github/scripts/publish-dashboard.sh @@ -0,0 +1,77 @@ +#!/usr/bin/env bash + +set -euo pipefail + +remote_repository="${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 \ No newline at end of file diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml index d8569f05..36ce6f54 100644 --- a/.github/workflows/backmerge.yml +++ b/.github/workflows/backmerge.yml @@ -20,11 +20,6 @@ concurrency: group: backmerge-master-into-develop cancel-in-progress: false -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: backmerge: runs-on: ubuntu-latest @@ -32,7 +27,7 @@ jobs: steps: - name: Checkout repository (for local actions) - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Setup easyscience[bot] id: bot @@ -43,7 +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 }} diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml index d3ebf3a2..21c72b38 100644 --- a/.github/workflows/cleanup.yml +++ b/.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 @@ -61,11 +61,6 @@ on: - 'false' - 'true' -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: del-runs: runs-on: ubuntu-latest diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 1ad93139..277d80f9 100644 --- a/.github/workflows/coverage.yml +++ b/.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 @@ -26,9 +24,6 @@ concurrency: # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: # Job 1: Run docstring coverage @@ -37,7 +32,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -51,7 +46,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -94,6 +89,6 @@ jobs: # Job 4: Build and publish dashboard (reusable workflow) run-reusable-workflows: - needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs + needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs uses: ./.github/workflows/dashboard.yml secrets: inherit diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml index 68513427..573e3086 100644 --- a/.github/workflows/dashboard.yml +++ b/.github/workflows/dashboard.yml @@ -7,6 +7,10 @@ on: permissions: contents: read +concurrency: + group: dashboard-publish-${{ 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 }} @@ -14,9 +18,6 @@ env: DEVELOP_BRANCH: develop REPO_OWNER: ${{ github.repository_owner }} REPO_NAME: ${{ github.event.repository.name }} - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: dashboard: @@ -24,16 +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: | @@ -84,22 +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: | diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4ab21da3..32c7aeac 100644 --- a/.github/workflows/docs.yml +++ b/.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: @@ -81,7 +85,7 @@ 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 @@ -107,11 +111,14 @@ 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 diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml index ed9d1c8b..4fbf4fab 100644 --- a/.github/workflows/issues-labels.yml +++ b/.github/workflows/issues-labels.yml @@ -1,6 +1,5 @@ -# Verifies if an issue has at least one of the `[scope]` and one of the -# `[priority]` labels. If not, the bot adds labels with a warning emoji -# to indicate that those labels need to be added. +# 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 @@ -11,15 +10,8 @@ on: permissions: issues: write -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: check-labels: - if: github.actor != 'easyscience[bot]' - runs-on: ubuntu-latest concurrency: @@ -27,30 +19,22 @@ jobs: cancel-in-progress: true steps: - - name: Checkout repository - uses: actions/checkout@v5 - - - name: Setup easyscience[bot] - id: bot - uses: ./.github/actions/setup-easyscience-bot + - name: Ensure [scope] label + uses: Rindrics/expect-label-prefix@v1.2.1 with: - app-id: ${{ vars.EASYSCIENCE_APP_ID }} - private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} - - - name: Check for required [scope] label - uses: trstringer/require-label-prefix@v1 - with: - secret: ${{ steps.bot.outputs.token }} - prefix: '[scope]' - labelSeparator: ' ' - addLabel: true - defaultLabel: '[scope] ⚠️ label needed' - - - name: Check for required [priority] label - uses: trstringer/require-label-prefix@v1 + 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: - secret: ${{ steps.bot.outputs.token }} - prefix: '[priority]' - labelSeparator: ' ' - addLabel: true - defaultLabel: '[priority] ⚠️ label needed' + repository_full_name: ${{ github.repository }} + token: ${{ github.token }} + label_prefix: '[priority]' + label_separator: ' ' + add_label: 'true' + default_label: '[priority] ⚠️ label needed' diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml index 7f2d7bba..8fb80763 100644 --- a/.github/workflows/lint-format.yml +++ b/.github/workflows/lint-format.yml @@ -34,9 +34,6 @@ permissions: # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: lint-format: @@ -44,7 +41,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi diff --git a/.github/workflows/pr-labels.yml b/.github/workflows/pr-labels.yml index 642cd318..fcb8a78c 100644 --- a/.github/workflows/pr-labels.yml +++ b/.github/workflows/pr-labels.yml @@ -1,14 +1,9 @@ # Verifies if a pull request has at least one label from a set of valid # labels before it can be merged. # -# NOTE: -# This workflow may be triggered twice in quick succession when a PR is -# created: -# 1) `opened` — when the pull request is initially created -# 2) `labeled` — if labels are added immediately after creation -# (e.g. by manual labeling, another workflow, or GitHub App). -# -# These are separate GitHub events, so two workflow runs can be started. +# The label validation is delegated to `mheap/github-action-required-labels`, +# which checks the current PR labels via the GitHub API and can add or update a +# PR comment when the required label set is missing. name: PR labels check @@ -17,40 +12,34 @@ on: types: [opened, labeled, unlabeled, synchronize] permissions: - pull-requests: read + issues: write + pull-requests: write jobs: check-labels: runs-on: ubuntu-latest steps: - - name: Check for valid labels - run: | - PR_LABELS=$(echo '${{ toJson(github.event.pull_request.labels.*.name) }}' | jq -r '.[]') - - echo "Current PR labels: $PR_LABELS" - VALID_LABELS=( - "[bot] release" - "[scope] bug" - "[scope] documentation" - "[scope] enhancement" - "[scope] maintenance" - "[scope] significant" - ) - - found=false - for label in "${VALID_LABELS[@]}"; do - if echo "$PR_LABELS" | grep -Fxq "$label"; then - echo "✅ Found valid label: $label" - found=true - break - fi - done - - if [ "$found" = false ]; then - echo "ERROR: PR must have at least one of the following labels:" - for label in "${VALID_LABELS[@]}"; do - echo " - $label" - done - exit 1 - fi + - 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 diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index b03a4859..378a6103 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -10,11 +10,6 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: pypi-publish: runs-on: ubuntu-latest @@ -25,7 +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 diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index 6c3cb94e..ef7fd726 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -20,9 +20,6 @@ permissions: env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: # Job 1: Test installation from PyPI on multiple OS @@ -35,7 +32,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -46,11 +43,15 @@ jobs: frozen: false - name: Init pixi project - run: pixi init EasyApplication + run: + pixi init --platform linux-64 --platform osx-arm64 --platform win-64 + EasyApplication - - name: Set the minimum system requirements + - name: Configure pixi platforms working-directory: EasyApplication - run: pixi project system-requirements add macos 14.0 + run: | + pixi workspace platform edit linux-64 --glibc 2.35 --no-install + pixi workspace platform edit osx-arm64 --macos 14.0 --no-install - name: Add Python 3.14 from Conda working-directory: EasyApplication diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml index cdc0330c..fa3a4317 100644 --- a/.github/workflows/release-notes.yml +++ b/.github/workflows/release-notes.yml @@ -10,11 +10,6 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: draft-release-notes: permissions: @@ -25,7 +20,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: fetch-depth: 0 # full history with tags to get the version number @@ -66,7 +61,7 @@ jobs: GITHUB_TOKEN: ${{ steps.bot.outputs.token }} - name: Create GitHub draft release - uses: softprops/action-gh-release@v2 + uses: softprops/action-gh-release@v3 with: draft: true tag_name: ${{ steps.draft.outputs.tag_name }} diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml index 5694a2a0..3fa073b9 100644 --- a/.github/workflows/release-pr.yml +++ b/.github/workflows/release-pr.yml @@ -24,16 +24,13 @@ permissions: env: DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }} - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: create-pull-request: runs-on: ubuntu-latest steps: - name: Checkout ${{ env.SOURCE_BRANCH }} branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: ${{ env.SOURCE_BRANCH }} @@ -51,7 +48,7 @@ jobs: gh pr create \ --base ${{ env.DEFAULT_BRANCH }} \ --head ${{ env.SOURCE_BRANCH }} \ - --title "Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \ + --title "🎉 Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \ --label "[bot] release" \ --body "This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from \`${{ env.SOURCE_BRANCH }}\` into \`${{ env.DEFAULT_BRANCH }}\`. diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml index a53e9afc..0f43db35 100644 --- a/.github/workflows/security.yml +++ b/.github/workflows/security.yml @@ -44,11 +44,6 @@ permissions: contents: read security-events: write -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: codeql: name: Code scanning @@ -66,13 +61,13 @@ jobs: # focused on the active dev branch. - name: Checkout repository (scheduled → develop) if: ${{ github.event_name == 'schedule' }} - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: develop - name: Checkout repository if: ${{ github.event_name != 'schedule' }} - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Initialize CodeQL uses: github/codeql-action/init@v4 diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml index f4a39e93..440bae3c 100644 --- a/.github/workflows/test-trigger.yml +++ b/.github/workflows/test-trigger.yml @@ -10,18 +10,13 @@ on: permissions: contents: read -# Opt into Node.js 24 for all JavaScript actions. -# Remove once all referenced actions natively target Node 24. -env: - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true - jobs: code-tests-trigger: runs-on: ubuntu-latest steps: - name: Checkout develop branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: develop diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 313d9552..d84a3cdf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -46,9 +46,6 @@ env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} PY_VERSIONS: '3.12 3.14' PIXI_ENVS: 'py-312-env py-314-env' - # Opt into Node.js 24 for all JavaScript actions. - # Remove once all referenced actions natively target Node 24. - FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true jobs: # Job 1: Set up environment variables @@ -83,7 +80,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -187,7 +184,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Download package (incl. extras) from previous job uses: ./.github/actions/download-artifact @@ -214,15 +211,16 @@ jobs: echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" echo "Initializing pixi project" - pixi init EasyApplication_py$py_ver + pixi init --platform linux-64 --platform osx-arm64 --platform win-64 EasyApplication_py$py_ver cd EasyApplication_py$py_ver + echo "Configure pixi platforms" + pixi workspace platform edit linux-64 --glibc 2.35 --no-install + pixi workspace platform edit osx-arm64 --macos 14.0 --no-install + echo "Adding Python $py_ver" pixi add "python=$py_ver" - echo "Setting macOS 14.0 as minimum required" - pixi project system-requirements add macos 14.0 - echo "Looking for wheel in ../dist/py$py_ver/" ls -l "../dist/py$py_ver/" @@ -232,10 +230,10 @@ jobs: exit 1 fi - whl_url="file://$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + whl_abs_path="$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" - echo "Adding EasyApplication from: $whl_url" - pixi add --pypi "EasyApplication[dev] @ ${whl_url}" + echo "Adding EasyApplication from: $whl_abs_path" + pixi add --pypi "EasyApplication[dev] @ ${whl_abs_path}" echo "Exiting pixi project directory" cd .. diff --git a/.prettierignore b/.prettierignore index 71d6c650..87c7d03d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -29,6 +29,9 @@ node_modules *.min.js *.min.css +# Tox +.tox + # Misc .benchmarks .cache diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0476c549..835f2d82 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -42,8 +42,7 @@ Please make sure you follow the EasyScience organization-wide If you are not planning to contribute code, you may want to: - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues) -- 🛡 Report a security issue — see - [Security Issues](#12-security-issues) +- 🛡 Report a security issue — see [Security Issues](#12-security-issues) - 💬 Ask a question or start a discussion at [Project Discussions](https://github.com/easyscience/gui-components/discussions) diff --git a/codecov.yml b/codecov.yml deleted file mode 100644 index f62b13ab..00000000 --- a/codecov.yml +++ /dev/null @@ -1,13 +0,0 @@ -# Codecov configuration -# https://docs.codecov.com/docs/codecovyml-reference - -coverage: - status: - project: - default: - # Make project coverage informational (won't block PR) - informational: true - patch: - default: - # Require patch coverage but with threshold - threshold: 1% diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css index a625be80..5bc1db12 100644 --- a/docs/docs/assets/stylesheets/extra.css +++ b/docs/docs/assets/stylesheets/extra.css @@ -200,7 +200,14 @@ label.md-nav__title[for="__drawer"] { /* Change the overall width of the page */ .md-grid { - max-width: 1280px; + max-width: 116em; +} + +/* Keep prose line length stable when sidebars are hidden at narrower widths */ +.md-main .md-content > .md-content__inner { + width: min(100%, 40.5em); + margin-left: auto !important; + margin-right: auto !important; } /* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */ diff --git a/examples/AdvancedPy/pyproject.toml b/examples/AdvancedPy/pyproject.toml index 21e4c9d9..76493208 100644 --- a/examples/AdvancedPy/pyproject.toml +++ b/examples/AdvancedPy/pyproject.toml @@ -25,4 +25,4 @@ homepage = 'https://github.com/EasyScience/EasyApp/tree/master/examples/Advanced [tool.hatch.build.targets.wheel] packages = ['src/AdvancedPy'] -#artifacts = ['*.py', '*.qml', 'qmldir'] +# artifacts = ['*.py', '*.qml', 'qmldir'] diff --git a/pixi.lock b/pixi.lock index b0365d96..3fbbc2ee 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,3424 +1,4008 @@ -version: 6 +version: 7 +platforms: +- name: p1 + subdir: linux-64 + virtual-packages: + - 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shiboken6==6.11.2 + - pyside6-essentials==6.11.2 + requires_python: '>=3.10,<3.15' diff --git a/pixi.toml b/pixi.toml index 490fcc43..ac0b93cd 100644 --- a/pixi.toml +++ b/pixi.toml @@ -1,94 +1,95 @@ -####################### -# ENVIRONMENT VARIABLES -####################### - -# Platform-independent - -[activation.env] -PYTHONIOENCODING = 'utf-8' - -# Platform-specific - -# Ensures the main package is used from the source code during -# development, even if main package is installed in editable mode -# via uv. This is important because `pixi update` might replace -# the installed version with the latest released version. - -# Unix/macOS -[target.unix.activation.env] -PYTHONPATH = "${PIXI_PROJECT_ROOT}/src${PYTHONPATH:+:${PYTHONPATH}}" - -# Windows -[target.win.activation.env] -PYTHONPATH = "${PIXI_PROJECT_ROOT}/src;%PYTHONPATH%" - ########### # WORKSPACE ########### [workspace] - # Supported platforms for the lock file (pixi.lock) -platforms = ['win-64', 'linux-64', 'osx-arm64'] +platforms = [ + 'win-64', + # Set minimum supported version for glibc to be 2.35 to ensure packages + # like `crysfml` that only have wheels for glibc 2.35+ + # (manylinux_2_35_x86_64) are used. + # libc = { family = 'glibc', version = '2.35' } + { platform = 'linux-64', glibc = '2.35' }, + # Set minimum supported version for macOS to be 14.0 to ensure packages + # like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64) + # are used instead of building from source. This is a workaround for + # Pixi, see https://github.com/prefix-dev/pixi/issues/5667 + { platform = 'osx-arm64', macos = '14.0' }, +] # Channels for fetching packages -channels = ['conda-forge'] - -##################### -# SYSTEM REQUIREMENTS -##################### - -[system-requirements] - -# Set minimum supported version for macOS to be 14.0 to ensure packages -# like `skipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64) -# are used instead of building from source. This is a workaround for -# Pixi, see https://github.com/prefix-dev/pixi/issues/5667 -macos = '14.0' +channels = ['nodefaults', 'conda-forge'] ########## # FEATURES ########## -# Default feature configuration +# Default features: -[dependencies] -nodejs = '*' # Required for Prettier (non-Python formatting) -jupyterlab = '*' # Jupyter notebooks -pixi-kernel = '*' # Pixi Jupyter kernel +[activation.env] +PYTHONIOENCODING = 'utf-8' -[pypi-dependencies] # == [feature.default.pypi-dependencies] -#pip = '*' # Native package installer -EasyApplication = { path = '.', editable = true, extras = ['dev'] } +# Non-default features: -# Specific features: Set specific Python versions +# Set specific Python versions to be used in CI testing. [feature.py-min.dependencies] python = '3.12.*' + [feature.py-max.dependencies] python = '3.14.*' +# Development dependencies for local development and testing with +# editable installations. + +[feature.dev.dependencies] +nodejs = '*' # Required for Prettier (non-Python formatting) +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel + +[feature.dev.pypi-dependencies] +pip = '*' +EasyApplication = { path = '.', editable = true, extras = ['dev'] } + +# User-like behavior for testing with pip-installed dependencies instead +# of editable installations. + +[feature.user.dependencies] +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel + +[feature.user.pypi-dependencies] +pip = '*' +EasyApplication = '*' + ############## # ENVIRONMENTS ############## [environments] - # The `default` feature is always included in all environments. # Additional features can be specified per environment. -py-312-env = { features = ['py-min'] } -py-314-env = { features = ['py-max'] } -# The `default` environment is always created and includes the `default` feature. -# It does not need to be specified explicitly unless non-default features are included. -default = { features = ['py-max'] } +# Specific environments for CI testing with different Python versions. +py-312-env = { features = ['py-min', 'dev'] } +py-314-env = { features = ['py-max', 'dev'] } + +# The `default` environment is developer-oriented for local development +# and testing with editable installation of the current package. +default = { features = ['py-max', 'dev'] } + +# The `user` environment allows testing with pip-installed dependencies +# instead of editable installation of the current package. +user = { features = ['py-max', 'user'] } ####### # TASKS ####### [tasks] - ################## # 🧪 Testing Tasks ################## @@ -169,8 +170,9 @@ docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml' docs-serve-dirty = 'pixi run docs-serve --dirty' docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml' docs-build-local = 'pixi run docs-build --no-directory-urls' +docs-inventory-check = 'python -c "from pathlib import Path; p = Path(\"docs/site/objects.inv\"); raise SystemExit(0 if p.is_file() and p.stat().st_size > 0 else \"missing or empty docs/site/objects.inv\")"' -docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect' +docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type copy' docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages' docs-update-assets = 'python tools/update_docs_assets.py' @@ -247,7 +249,7 @@ clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +" post-install = { depends-on = [ 'npm-config', 'prettier-install', - #'pre-commit-setup', + # 'pre-commit-setup', ] } ########################## diff --git a/prettierrc.toml b/prettierrc.toml index b98c86eb..101d110c 100644 --- a/prettierrc.toml +++ b/prettierrc.toml @@ -1,22 +1,26 @@ plugins = [ - "prettier-plugin-toml", # use the TOML plugin + 'prettier-plugin-toml', # use the TOML plugin ] -endOfLine = 'lf' # change line endings to LF -proseWrap = 'always' # change wrapping in Markdown files -semi = false # remove semicolons -singleQuote = true # use single quotes instead of double quotes -tabWidth = 2 # change tab width to 2 spaces -useTabs = false # use spaces instead of tabs +endOfLine = 'lf' # change line endings to LF +proseWrap = 'always' # change wrapping in Markdown files +semi = false # remove semicolons +singleQuote = true # use single quotes instead of double quotes +tabWidth = 2 # change tab width to 2 spaces +useTabs = false # use spaces instead of tabs -printWidth = 79 # wrap lines at 79 characters +printWidth = 79 # wrap lines at 79 characters +trailingCommentAlignment = true # align trailing comments in TOML files +trailingCommentSpaceWidth = 2 # use at least 2 spaces before trailing comments [[overrides]] -files = ["*.md"] +files = ['*.md'] + [overrides.options] -printWidth = 72 # wrap Markdown files at 72 characters +printWidth = 72 # wrap Markdown files at 72 characters [[overrides]] -files = ["*.yml", "*.yaml"] +files = ['*.yml', '*.yaml'] + [overrides.options] -printWidth = 88 # wrap YAML files at 88 characters +printWidth = 88 # wrap YAML files at 88 characters diff --git a/pyproject.toml b/pyproject.toml index 53298d15..3ba7953a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ [project] name = 'EasyApplication' -dynamic = ['version'] # Use versioningit to manage the version +dynamic = ['version'] # Use versioningit to manage the version description = 'Qt/QML components for building graphical applications' authors = [{ name = 'EasyScience contributors' }] readme = 'README.md' @@ -23,43 +23,43 @@ classifiers = [ ] requires-python = '>=3.12' dependencies = [ - 'numpy', # Scientific computing library - 'PySide6', # Qt for Python + 'numpy', # Scientific computing library + 'PySide6', # Qt for Python ] [project.optional-dependencies] dev = [ - 'GitPython', # Interact with Git repositories - 'build', # Building the package - 'pre-commit', # Pre-commit hooks - 'jinja2', # Templating - 'nbmake', # Building notebooks - 'nbstripout', # Strip output from notebooks - 'nbqa', # Linting and formatting notebooks - 'pytest', # Testing - 'pytest-cov', # Test coverage - 'pytest-xdist', # Enable parallel testing - 'ruff', # Linting and formatting code - 'radon', # Code complexity and maintainability - 'validate-pyproject[all]', # Validate pyproject.toml - 'versioningit', # Automatic versioning from git tags - 'jupytext', # Jupyter notebook text format support - 'jupyterquiz', # Quizzes in Jupyter notebooks - 'pydoclint', # Docstring linter - 'format-docstring', # Docstring formatter - 'docstripy', # Convert docstrings to other formats - 'interrogate', # Docstring coverage checker - 'copier', # Template management - 'mike', # MkDocs: Versioned documentation support - 'mkdocs', # Static site generator - 'mkdocs-material', # Documentation framework on top of MkDocs - 'mkdocs-autorefs', # MkDocs: Auto-references support - 'mkdocs-jupyter', # MkDocs: Jupyter notebook support - 'mkdocs-plugin-inline-svg', # MkDocs: Inline SVG support - 'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables - 'mkdocstrings-python', # MkDocs: Python docstring support - 'pyyaml', # YAML parser - 'spdx-headers', # SPDX license header validation + 'GitPython', # Interact with Git repositories + 'build', # Building the package + 'pre-commit', # Pre-commit hooks + 'jinja2', # Templating + 'nbmake', # Building notebooks + 'nbstripout', # Strip output from notebooks + 'nbqa', # Linting and formatting notebooks + 'pytest', # Testing + 'pytest-cov', # Test coverage + 'pytest-xdist', # Enable parallel testing + 'ruff', # Linting and formatting code + 'radon', # Code complexity and maintainability + 'validate-pyproject[all]', # Validate pyproject.toml + 'versioningit', # Automatic versioning from git tags + 'jupytext', # Jupyter notebook text format support + 'jupyterquiz', # Quizzes in Jupyter notebooks + 'pydoclint', # Docstring linter + 'format-docstring', # Docstring formatter + 'docstripy', # Convert docstrings to other formats + 'interrogate', # Docstring coverage checker + 'copier', # Template management + 'mike', # MkDocs: Versioned documentation support + 'mkdocs', # Static site generator + 'mkdocs-material', # Documentation framework on top of MkDocs + 'mkdocs-autorefs', # MkDocs: Auto-references support + 'mkdocs-jupyter', # MkDocs: Jupyter notebook support + 'mkdocs-plugin-inline-svg', # MkDocs: Inline SVG support + 'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables + 'mkdocstrings-python', # MkDocs: Python docstring support + 'pyyaml', # YAML parser + 'spdx-headers', # SPDX license header validation ] [project.urls] @@ -91,7 +91,7 @@ packages = ['src/EasyApplication'] allow-direct-references = true [tool.hatch.version] -source = 'versioningit' # Use versioningit to manage the version +source = 'versioningit' # Use versioningit to manage the version ################################ # Configuration for versioningit @@ -107,9 +107,9 @@ source = 'versioningit' # Use versioningit to manage the version # pixi.lock update without any changes to the source code. [tool.versioningit.format] -distance = '{base_version}+dev{distance}' # example: 1.2.3.post4+dev3 -dirty = '{base_version}+dirty{distance}' # example: 0.5.8+dirty3 -distance-dirty = '{base_version}+devdirty{distance}' # example: 0.5.8+devdirty3 +distance = '{base_version}+dev{distance}' # example: 1.2.3.post4+dev3 +dirty = '{base_version}+dirty{distance}' # example: 0.5.8+dirty3 +distance-dirty = '{base_version}+devdirty{distance}' # example: 0.5.8+devdirty3 # Configure how versioningit detects versions from Git # - 'match' ensures it only considers tags starting with 'v' @@ -127,9 +127,9 @@ default-tag = 'v999.0.0' # https://interrogate.readthedocs.io/en/latest/ [tool.interrogate] -fail-under = 0 # Minimum docstring coverage percentage to pass +fail-under = 0 # Minimum docstring coverage percentage to pass verbose = 1 -#exclude = ['src/**/__init__.py'] +# exclude = ['src/**/__init__.py'] ####################################### # Configuration for coverage/pytest-cov @@ -139,13 +139,13 @@ verbose = 1 # https://coverage.readthedocs.io/en/latest/ [tool.coverage.run] -branch = true # Measure branch coverage as well -source = ['src'] # Limit coverage to the source code directory +branch = true # Measure branch coverage as well +source = ['src'] # Limit coverage to the source code directory [tool.coverage.report] -show_missing = true # Show missing lines -skip_covered = false # Skip files with 100% coverage in the report -fail_under = 0 # Minimum coverage percentage to pass +show_missing = true # Show missing lines +skip_covered = false # Skip files with 100% coverage in the report +fail_under = 0 # Minimum coverage percentage to pass ########################## # Configuration for pytest @@ -169,104 +169,107 @@ testpaths = ['tests'] [tool.ruff] exclude = ['tmp'] indent-width = 4 -line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] -preview = true # Enable new rules that are not yet stable, like DOC +line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] +preview = true # Enable new rules that are not yet stable, like DOC # Formatting options for Ruff [tool.ruff.format] -docstring-code-format = true # Whether to format code snippets in docstrings -docstring-code-line-length = 72 # Line length for code snippets in docstrings -indent-style = 'space' # PEP 8 recommends using spaces over tabs -quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) +docstring-code-format = true # Whether to format code snippets in docstrings +docstring-code-line-length = 72 # Line length for code snippets in docstrings +indent-style = 'space' # PEP 8 recommends using spaces over tabs +quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) # Linting rules to use with Ruff [tool.ruff.lint] select = [ # Various rules - #'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90 - #'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d - 'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f - #'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly - #'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb - 'I', # https://docs.astral.sh/ruff/rules/#isort-i - #'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n - #'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy - #'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh - #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf - #'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf - #'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try - #'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up + # 'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90 + # 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f + # 'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly + # 'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb + 'I', # https://docs.astral.sh/ruff/rules/#isort-i + # 'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n + # 'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy + # 'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh + # 'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf + # 'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf + # 'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try + # 'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up # pycodestyle (E, W) rules - 'E', # https://docs.astral.sh/ruff/rules/#error-e - 'W', # https://docs.astral.sh/ruff/rules/#warning-w + 'E', # https://docs.astral.sh/ruff/rules/#error-e + 'W', # https://docs.astral.sh/ruff/rules/#warning-w # Pylint (PL) rules - #'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc - #'PLE', # https://docs.astral.sh/ruff/rules/#error-ple - #'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr - #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw + # 'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc + # 'PLE', # https://docs.astral.sh/ruff/rules/#error-ple + # 'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr + # 'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw # flake8 rules - #'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a - #'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann - #'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg - #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async - #'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b - #'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble - #'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 - #'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com - #'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz - #'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em - #'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa - #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt - #'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix - #'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g - #'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn - #'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp - #'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc - #'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log - #'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie - #'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt - #'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth - #'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi - #'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret - #'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse - 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s - #'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim - #'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf - #'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot - #'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20 - #'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc - #'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td - #'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid + # 'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + # 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + # 'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + # 'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async + # 'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + # 'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble + # 'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + # 'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com + # 'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + # 'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + # 'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa + # 'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt + # 'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix + # 'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + # 'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn + # 'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp + # 'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc + # 'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log + # 'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + # 'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + # 'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + # 'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi + # 'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret + # 'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + # 'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + # 'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf + # 'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot + # 'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20 + # 'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc + # 'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td + # 'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid ] # Exceptions to the linting rules # Ignore specific rules globally ignore = [ - 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ + 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] - 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout - 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ + 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ ] # Ignore specific rules in certain files or directories [tool.ruff.lint.per-file-ignores] '*/__init__.py' = [ - 'F401', # re-exports are intentional in __init__.py + 'F401', # re-exports are intentional in __init__.py ] 'tests/**' = [ - 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann - 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d - 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc - 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ - 'S101', # https://docs.astral.sh/ruff/rules/assert/ + 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'S101', # https://docs.astral.sh/ruff/rules/assert/ ] 'docs/**' = [ - 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ - 'T201', # https://docs.astral.sh/ruff/rules/print/ + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'T201', # https://docs.astral.sh/ruff/rules/print/ +] +'docs/docs/tutorials/**' = [ + 'E402', # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/ ] # Specific options for certain rules @@ -288,7 +291,7 @@ max-complexity = 10 # https://peps.python.org/pep-0008/#maximum-line-length # Use 99 characters as the project-wide maximum for regular code lines. # Use 72 characters for docstrings. -max-line-length = 99 # See also `line-length` in [tool.ruff] +max-line-length = 99 # See also `line-length` in [tool.ruff] max-doc-length = 72 [tool.ruff.lint.pydocstyle] @@ -315,7 +318,7 @@ max-positional-args = 6 # the parameter declarations in the code (in function's signature). [tool.pydoclint] -exclude = '\.' # Temporarily disable pydoclint until we are ready +exclude = '\.' # Temporarily disable pydoclint until we are ready style = 'numpy' check-style-mismatch = true check-arg-defaults = true @@ -329,7 +332,7 @@ allow-init-docstring = true # https://github.com/jsh9/format-docstring [tool.format_docstring] -exclude = '\.' # Temporarily disable format-docstring until we are ready +exclude = '\.' # Temporarily disable format-docstring until we are ready docstring_style = 'numpy' line_length = 72 fix_rst_backticks = true diff --git a/tools/test_scripts.py b/tools/test_scripts.py deleted file mode 100644 index e24b28e2..00000000 --- a/tools/test_scripts.py +++ /dev/null @@ -1,57 +0,0 @@ -# SPDX-FileCopyrightText: 2026 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause -"""Test runner for tutorial scripts in the 'tutorials' directory. - -This test discovers and executes all Python scripts located under the -'tutorials' directory to ensure they run without errors. - -Important: each script must be executed in a fresh Python process. -Running many tutorials in-process (e.g. via runpy) leaks global state -between scripts (notably cached calculator dictionaries keyed only by -model/experiment names), which can cause false failures. -""" - -import os -import subprocess # noqa: S404 -import sys -from pathlib import Path - -import pytest - -_repo_root = Path(__file__).resolve().parents[1] -_src_root = _repo_root / 'src' - -# Discover tutorial scripts, excluding temporary checkpoint files -TUTORIALS = [ - p for p in Path('docs/docs/tutorials').rglob('*.py') if '.ipynb_checkpoints' not in p.parts -] - - -@pytest.mark.parametrize('script_path', TUTORIALS) -def test_script_runs(script_path: Path): - """Execute a tutorial script and fail if it raises an exception. - - Each script is run in the context of __main__ to mimic standalone - execution. - """ - env = os.environ.copy() - if _src_root.exists(): - existing = env.get('PYTHONPATH', '') - env['PYTHONPATH'] = ( - str(_src_root) if not existing else str(_src_root) + os.pathsep + existing - ) - - # This is a test harness executing repo-local tutorial scripts. - # We intentionally use subprocess isolation to prevent cross-test - # global state leaks (e.g. calculator caches) that can cause false - # failures when running tutorials in a shared interpreter. - result = subprocess.run( # noqa: S603 - [sys.executable, str(script_path)], - cwd=str(_repo_root), - env=env, - capture_output=True, - text=True, - ) - if result.returncode != 0: - details = (result.stdout or '') + (result.stderr or '') - pytest.fail(f'{script_path}\n{details.strip()}')