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Merge branch 'main' into sort-elements
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‎.github/BENCHMARK_FAIL_TEMPLATE.md‎

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---
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title: "{{ env.TITLE }}"
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labels: [bug]
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---
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The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
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The most recent failing benchmark was on {{ env.PLATFORM }} py{{ env.PYTHON }} {{ env.BACKEND }}
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with commit: {{ sha }}
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Full run: https://github.com/scverse/napari-spatialdata/actions/runs/{{ env.RUN_ID }}
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(This post will be updated if another test fails, as long as this issue remains open.)

‎.github/dependabot.yml‎

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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "monthly"
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commit-message:
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prefix: "ci(dependabot):"
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labels:
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- "maintenance"
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groups:
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actions:
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patterns:
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- "*"

‎.github/workflows/benchmarks.yml‎

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# This CI configuration for relative benchmarks is based on the research done
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# for scikit-image's implementation available here:
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# https://github.com/scikit-image/scikit-image/blob/9bdd010a8/.github/workflows/benchmarks.yml#L1
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# Blog post with the rationale: https://labs.quansight.org/blog/2021/08/github-actions-benchmarks/
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name: Benchmarks
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on:
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pull_request:
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types: [labeled]
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schedule:
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- cron: "6 6 * * 0" # every sunday
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workflow_dispatch:
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inputs:
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base_ref:
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description: "Baseline commit or git reference"
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required: true
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contender_ref:
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description: "Contender commit or git reference"
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required: true
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# This is the main configuration section that needs to be fine tuned to napari's needs
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# All the *_THREADS options is just to make the benchmarks more robust by not using parallelism
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env:
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OPENBLAS_NUM_THREADS: "1"
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MKL_NUM_THREADS: "1"
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OMP_NUM_THREADS: "1"
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ASV_OPTIONS: "--split --show-stderr --factor 1.5 --attribute timeout=900"
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# --split -> split final reports in tables
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# --show-stderr -> print tracebacks if errors occur
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# --factor 1.5 -> report anomaly if tested timings are beyond 1.5x base timings
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# --attribute timeout=300 -> override timeout attribute (default=60s) to allow slow tests to run
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# see https://asv.readthedocs.io/en/stable/commands.html#asv-continuous for more details!
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jobs:
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benchmark:
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if: ${{ github.event.label.name == 'run-benchmarks' && github.event_name == 'pull_request' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' }}
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name: ${{ matrix.benchmark-name }}
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runs-on: ${{ matrix.runs-on }}
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permissions:
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contents: read
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issues: write
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strategy:
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fail-fast: false
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matrix:
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include:
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- benchmark-name: Qt
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asv-command: continuous
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selection-regex: "^benchmark_qt_.*"
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runs-on: macos-latest
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# Qt tests run on macOS to avoid using Xvfb business
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# xvfb makes everything run, but some tests segfault :shrug:
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# Fortunately, macOS graphics stack does not need xvfb!
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- benchmark-name: non-Qt
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asv-command: continuous
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selection-regex: "^benchmark_(?!qt_).*"
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runs-on: ubuntu-latest
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steps:
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# We need the full repo to avoid this issue
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# https://github.com/actions/checkout/issues/23
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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name: Install Python
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with:
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python-version: "3.11"
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cache-dependency-path: pyproject.toml
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- uses: tlambert03/setup-qt-libs@v1
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- name: Setup asv
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run: python -m pip install "asv[virtualenv]"
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env:
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PIP_CONSTRAINT: ${{ github.workspace }}/benchmarks/benchmark.txt
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- uses: octokit/request-action@v2.x
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id: latest_release
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with:
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route: GET /repos/{owner}/{repo}/releases/latest
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owner: scverse
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repo: napari-spatialdata
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Run ${{ matrix.benchmark-name }} benchmarks
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id: run_benchmark
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env:
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# asv will checkout commits, which might contain LFS artifacts; ignore those errors since
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# they are probably just documentation PNGs not needed here anyway
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GIT_LFS_SKIP_SMUDGE: 1
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HEAD_LABEL: ${{ github.event.pull_request.head.label }}
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PIP_CONSTRAINT: ${{ github.workspace }}/benchmarks/benchmark.txt
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run: |
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set -euxo pipefail
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read -ra cmd_options <<< "$ASV_OPTIONS"
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# ID this runner
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asv machine --yes
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if [[ $GITHUB_EVENT_NAME == pull_request ]]; then
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EVENT_NAME="PR #${{ github.event.pull_request.number }}"
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BASE_REF=${{ github.event.pull_request.base.sha }}
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CONTENDER_REF=${GITHUB_SHA}
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echo "Baseline: ${BASE_REF} (${{ github.event.pull_request.base.label }})"
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echo "Contender: ${CONTENDER_REF} ($HEAD_LABEL)"
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elif [[ $GITHUB_EVENT_NAME == schedule ]]; then
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EVENT_NAME="cronjob"
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BASE_REF="${{ fromJSON(steps.latest_release.outputs.data).target_commitish }}"
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CONTENDER_REF="${GITHUB_SHA}"
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echo "Baseline: ${BASE_REF} (${{ fromJSON(steps.latest_release.outputs.data).tag_name }})"
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echo "Contender: ${CONTENDER_REF} (current main)"
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elif [[ $GITHUB_EVENT_NAME == workflow_dispatch ]]; then
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EVENT_NAME="manual trigger"
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BASE_REF="${{ github.event.inputs.base_ref }}"
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CONTENDER_REF="${{ github.event.inputs.contender_ref }}"
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echo "Baseline: ${BASE_REF} (workflow input)"
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echo "Contender: ${CONTENDER_REF} (workflow input)"
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fi
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echo "EVENT_NAME=$EVENT_NAME" >> "$GITHUB_ENV"
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echo "BASE_REF=$BASE_REF" >> "$GITHUB_ENV"
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echo "CONTENDER_REF=$CONTENDER_REF" >> "$GITHUB_ENV"
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# Run benchmarks for current commit against base
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asv continuous "${cmd_options[@]}" -b "${{ matrix.selection-regex }}" "${BASE_REF}" "${CONTENDER_REF}" \
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| sed -E "/Traceback | failed$|PERFORMANCE DECREASED/ s/^/::error:: /" \
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| tee asv_continuous.log
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# Report and export results for subsequent steps
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if grep "Traceback \|failed\|PERFORMANCE DECREASED" asv_continuous.log > /dev/null ; then
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exit 1
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fi
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- name: Report Failures as Issue
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if: ${{ (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch') && failure() }}
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PLATFORM: ${{ matrix.runs-on }}
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PYTHON: "3.9"
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BACKEND: ${{ matrix.benchmark-name }}
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RUN_ID: ${{ github.run_id }}
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TITLE: "[test-bot] Benchmark tests failing"
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with:
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filename: .github/BENCHMARK_FAIL_TEMPLATE.md
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update_existing: true
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- name: Add more info to artifact
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if: always()
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run: |
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# Copy the full `asv continuous` log
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cp asv_continuous.log .asv/results/asv_continuous_${{ matrix.benchmark-name }}.log
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# ensure that even if this isn't a PR, the benchmark_report workflow can run without error
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touch .asv/results/message_${{ matrix.benchmark-name }}.txt
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# Add the message that might be posted as a comment on the PR
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# We delegate the actual comment to `benchmarks_report.yml` due to
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# potential token permissions issues
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if [[ $GITHUB_EVENT_NAME == pull_request ]]; then
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echo "${{ github.event.pull_request.number }}" > .asv/results/pr_number
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echo \
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"The ${{ matrix.benchmark-name }} benchmark run requested by $EVENT_NAME ($CONTENDER_REF vs $BASE_REF) has" \
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"finished with status '${{ steps.run_benchmark.outcome }}'. See the" \
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"[CI logs and artifacts](||BENCHMARK_CI_LOGS_URL||) for further details." \
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> .asv/results/message_${{ matrix.benchmark-name }}.txt
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fi
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- uses: actions/upload-artifact@v4
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if: always()
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with:
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name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}-${{ matrix.benchmark-name }}
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path: .asv/results
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combine-artifacts:
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runs-on: ubuntu-latest
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needs: benchmark
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if: always()
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steps:
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- name: Download artifact
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uses: actions/download-artifact@v4
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with:
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pattern: asv-benchmark-results*
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path: asv_result
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merge-multiple: true
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}
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path: asv_result

‎.github/workflows/benchmarks_report.yml‎

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# Report benchmark results to the PR
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# We need a dual workflow to make sure the token has the needed permissions to post comments
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# See https://stackoverflow.com/a/71683208 for more details
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# When this workflow is triggered, it pulls the latest version of this file on
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# the default branch. Changes to this file won't be reflected until after the
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# PR is merged.
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# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_run
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name: "Benchmarks - Report"
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on:
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workflow_run:
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workflows: [Benchmarks]
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types:
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- completed
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permissions:
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pull-requests: write
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issues: write
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jobs:
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download:
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runs-on: ubuntu-latest
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steps:
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- name: "Download artifact"
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uses: actions/github-script@v7
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with:
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script: |
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let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
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owner: context.repo.owner,
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repo: context.repo.repo,
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run_id: context.payload.workflow_run.id,
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});
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let artifactName = `asv-benchmark-results-${context.payload.workflow_run.id}-${context.payload.workflow_run.run_number}-${context.payload.workflow_run.run_attempt}`
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console.log(`Artifact name: ${artifactName}`);
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console.log(`All artifacts: ${JSON.stringify(allArtifacts.data.artifacts)}`);
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let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
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return artifact.name == artifactName
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})[0];
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if (matchArtifact === undefined) {
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throw TypeError('Build Artifact not found!');
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}
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let download = await github.rest.actions.downloadArtifact({
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owner: context.repo.owner,
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repo: context.repo.repo,
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artifact_id: matchArtifact.id,
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archive_format: 'zip',
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});
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let fs = require('fs');
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fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/asv_results.zip`, Buffer.from(download.data));
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- name: Unzip and prepare data
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run: |
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unzip asv_results.zip
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# combine the Qt and non-Qt messages
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cat message_Qt.txt message_non-Qt.txt > message.txt
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- name: Replace URLs
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run: |
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sed -i 's@||BENCHMARK_CI_LOGS_URL||@${{ github.event.workflow_run.html_url }}@g' message.txt
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- name: Collect PR number if available
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run: |
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if [[ -f pr_number ]]; then
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echo "PR_NUMBER=$(cat pr_number)" >> "$GITHUB_ENV"
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fi
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- name: "Comment on PR"
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if: env.PR_NUMBER != ''
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uses: actions/github-script@v7
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |
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let fs = require('fs');
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let issue_number = Number(process.env.PR_NUMBER);
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let body = fs.readFileSync('message.txt', 'utf8');
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await github.rest.issues.createComment({
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owner: context.repo.owner,
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repo: context.repo.repo,
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issue_number: issue_number,
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body: body,
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});
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- name: "Remove run-benchmarks label"
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if: env.PR_NUMBER != ''
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uses: actions/github-script@v7
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |
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let fs = require('fs');
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let issue_number = Number(process.env.PR_NUMBER);
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await github.rest.issues.removeLabel({
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owner: context.repo.owner,
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repo: context.repo.repo,
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issue_number: issue_number,
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name: 'run-benchmarks',
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});

‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [published]
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push:
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# Sequence of patterns matched against refs/tags
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tags:
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- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
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pull_request:
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paths:
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- .github/workflows/release.yml
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jobs:
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release:
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# requires that you have put your twine API key in your
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# github secrets (see readme for details)
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runs-on: ubuntu-latest
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if: contains(github.ref, 'tags')
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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- uses: actions/checkout@v4
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -U setuptools setuptools_scm wheel twine build
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- name: Build and publish
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
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fetch-depth: 0
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- uses: hynek/build-and-inspect-python-package@v2
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id: build_dist
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- name: determine tag
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run: echo "tag=${GITHUB_REF/refs\/tags\/v/}" >> "$GITHUB_ENV"
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- name: debug dist
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run: |
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git tag
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python -m build .
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twine upload dist/*
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set -x
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echo "dist=${{ steps.build_dist.outputs.dist }}"
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ls -l ${{ steps.build_dist.outputs.dist }}
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mkdir -p dist
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cp ${{ steps.build_dist.outputs.dist }}/*.whl ./dist/
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cp ${{ steps.build_dist.outputs.dist }}/*.gz ./dist/
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- name: Create Release
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uses: "softprops/action-gh-release@v2"
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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with:
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tag_name: ${{ github.ref }}
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name: ${{ env.tag }}
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draft: false
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prerelease: ${{ contains(env.tag, 'rc') || contains(env.tag, 'a') || contains(env.tag, 'b') }}
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target_commitish: ${{ github.sha }}
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files: dist/*
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- name: Publish PyPI Package
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.TWINE_API_KEY }}

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