Bechmark using ASV

.github/workflows/benchmarks.yml

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+name: benchmarks
+
+env:
+  TARDIS_VER: release-2023.06.18
+
+on:
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+      - "*"
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - labeled # benchmarks label required
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  build:
+    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Restore Atom Data
+        uses: actions/cache/restore@v3
+        id: atom-data-restore
+        with:
+          path: benchmarks/kurucz_cd23_chianti_H_He.h5
+          key: atom-data
+
+      - name: Download Atom Data
+        if: steps.atom-data-restore.outputs.cache-hit != 'true'
+        run: |
+          REPO_URL="https://dev.azure.com/tardis-sn/TARDIS/_apis/git/repositories/tardis-refdata"
+          wget -q "$REPO_URL/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&versionType=branch&version=master&resolveLfs=true" -O benchmarks/kurucz_cd23_chianti_H_He.h5
+
+      - name: Save Atom Data
+        uses: actions/cache/save@v3
+        if: ${{ steps.atom-data-restore.cache-hit != 'true'  && always() || false }}
+        id: atom-data-cache-save
+        with:
+          path: benchmarks/kurucz_cd23_chianti_H_He.h5
+          key: atom-data
+
+      - name: Install asv
+        run: pip install asv==0.5.*
+
+      - name: Accept all asv questions
+        run: asv machine --yes
+
+      - name: Download TARDIS dependencies
+        run: |
+          LOCK_URL="https://github.com/tardis-sn/tardis/raw/${{ env.TARDIS_VER }}/tardis_env3.yml"
+          wget -q "$LOCK_URL"
+
+      - name: Add TARDIS install command to asv config file
+        run: |
+          TARDIS_INSTALL_CMD="pip install git+https://github.com/tardis-sn/tardis.git@${{ env.TARDIS_VER }}"
+          cat <<< $(jq '.build_command |= [$TARDIS_INSTALL_CMD] + .' --arg TARDIS_INSTALL_CMD "${TARDIS_INSTALL_CMD}" asv.conf.json) > asv.conf.json
+
+      - name: Run benchmarks for last 5 commits if not PR
+        if: github.event_name != 'pull_request'
+        run: |
+          git log -n 5 --pretty=format:"%H" >> tag_commits.txt
+          asv run -v HASHFILE:tag_commits.txt | tee asv-output.log  
+          if grep -q failed asv-output.log; then 
+            echo "Some benchmarks have failed!"
+            exit 1
+          fi
+
+      - name: Generate Graphs and HTML
+        if: github.event_name != 'pull_request'
+        run: asv publish
+
+      - name: Delete env files
+        run: rm -r .asv/env
+
+      - name: Create results html on dest repo
+        if: github.event_name != 'pull_request'
+        continue-on-error: true
+        uses: cpina/github-action-push-to-another-repository@main
+        env:
+          API_TOKEN_GITHUB: ${{ secrets.BOT_TOKEN }}
+        with:
+          source-directory: ".asv/html"
+          destination-github-username: "tardis-sn"
+          destination-repository-name: "stardis-benchmarks"
+          user.email: [email protected]
+          target-branch: main
+
+      - name: Push misc data to dest repo
+        if: github.event_name != 'pull_request'
+        continue-on-error: true
+        uses: cpina/github-action-push-to-another-repository@main
+        env:
+          API_TOKEN_GITHUB: ${{ secrets.BOT_TOKEN }}
+        with:
+          source-directory: ".asv/results"
+          destination-github-username: "tardis-sn"
+          destination-repository-name: "stardis-benchmarks"
+          user.email: [email protected]
+          target-branch: main
+          target-directory: "misc"
+
+      - name: Compare HEAD with main if PR
+        if: github.event_name == 'pull_request'
+        continue-on-error: true # TODO: step failed sporadically while testing
+        run: |
+          asv continuous ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }}  | tee asv-cont-output.log  
+          if grep -q failed asv-cont-output.log; then 
+            echo "Some benchmarks have errors!"
+            exit 1
+          fi
+
+      - run: asv compare ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} | tee asv-compare-output.log
+      - run: asv compare ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} --only-changed | tee asv-compare-changed-output.log
+
+      - name: asv output 1
+        id: asv_pr_vs_main
+        uses: juliangruber/[email protected]
+        with:
+          path: asv-compare-output.log
+
+      - name: asv output 2
+        id: asv_pr_vs_main_changed
+        uses: juliangruber/[email protected]
+        with:
+          path: asv-compare-changed-output.log
+
+      - name: Find Comment
+        if: always() && github.event_name == 'pull_request'
+        uses: peter-evans/find-comment@v1
+        id: fc
+        with:
+          issue-number: ${{ github.event.number }}
+          comment-author: "tardis-bot"
+          body-includes: I ran benchmarks as you asked
+
+      - name: Post comment
+        if: github.event_name == 'pull_request'
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          token: ${{ secrets.BOT_TOKEN }}
+          issue-number: ${{ github.event.number }}
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            *\*beep\* \*bop\**
+            Hi human, 
+            I ran benchmarks as you asked comparing main (${{ github.event.pull_request.base.sha }}) and the latest commit (${{ github.event.pull_request.head.sha }}). 
+            Here are the logs produced by ASV.
+            Results can also be downloaded as artifacts [**here**](${{ env.URL }}). 
+            Significantly changed benchmarks:
+            <details>
+
+              ```diff
+              ${{ steps.asv_pr_vs_main_changed.outputs.content }}
+              ```
+
+            </details>
+
+            All benchmarks:
+            <details>
+
+              ```diff
+              ${{ steps.asv_pr_vs_main.outputs.content }}
+              ```
+              
+            </details>
+        env:
+          URL: https://github.com/${{ github.repository_owner }}/${{ github.event.repository.name }}/actions/runs/${{ github.run_id }}?check_suite_focus=true
+
+      - name: Save results artifact
+        uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: asv-benchmark-results-${{ runner.os }}
+          path: |
+            .asv/results
+            asv-cont-output.log  
+            asv-compare-output.log
+            asv-compare-changed-output.log

asv.conf.json

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+
+{
+    "version": 1,
+    "project": "stardis",
+    "project_url": "https://tardis-sn.github.io/tardis",
+    "repo": ".",
+    "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
+    "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
+    "build_command": [
+        "python setup.py build",
+        "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
+    ],
+    "branches": ["main"],
+    "environment_type": "conda",
+    "show_commit_url": "https://github.com/tardis-sn/stardis/commit",
+    "conda_environment_file": "tardis_env3.yml",
+    "benchmark_dir": "benchmarks",
+    "env_dir": ".asv/env",
+    "results_dir": ".asv/results",
+    "html_dir": ".asv/html"
+}

benchmarks/benchmark_config.yml

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+stardis_config_version: 1.0
+atom_data: kurucz_cd23_chianti_H_He.h5
+model:
+    type: marcs
+    fname: sun.mod
+    final_atomic_number: 30
+opacity:
+    file:
+        Hminus_bf: h_minus_cross_section_wbr.dat
+    bf:
+        H_I: {}
+    ff:
+        H_I: {}
+    disable_electron_scattering: False
+    line:
+        disable: False
+        broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]
+        min: 6500 AA
+        max: 6600 AA
+no_of_thetas: 20

benchmarks/h_minus_cross_section_wbr.dat

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+../docs/quickstart/h_minus_cross_section_wbr.dat

benchmarks/run_stardis.py

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+# Import necessary code
+
+import os
+import numpy as np
+from stardis.base import run_stardis
+from astropy import units as u
+
+
+class BenchmarkRunStardis:
+    """
+    Class to benchmark run_stardis function.
+    """
+
+    timeout = 1800  # Worst case timeout of 30 mins
+
+    def setup(self):
+        base_dir = os.path.abspath(os.path.dirname(__file__))
+        self.config = os.path.join(base_dir, "benchmark_config.yml")
+        self.tracing_lambdas = np.arange(6540, 6590, 0.01) * u.Angstrom
+        os.chdir(base_dir)
+
+    def time_run_stardis(self):
+        run_stardis(self.config, self.tracing_lambdas)

benchmarks/sun.mod

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+../docs/quickstart/sun.mod