From bf7c62e3bc0ef50a6a26bed9db307999e0267dc1 Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 24 Apr 2024 14:36:25 +0100 Subject: [PATCH 1/9] Comparing profiling implementations --- .../pyrealm_profiling_after_push.yaml | 79 +++++++++++++++++++ ...yaml => pyrealm_profiling_on_approve.yaml} | 27 ++++--- 2 files changed, 93 insertions(+), 13 deletions(-) create mode 100644 .github/workflows/pyrealm_profiling_after_push.yaml rename .github/workflows/{pyrealm_profiling.yaml => pyrealm_profiling_on_approve.yaml} (67%) diff --git a/.github/workflows/pyrealm_profiling_after_push.yaml b/.github/workflows/pyrealm_profiling_after_push.yaml new file mode 100644 index 00000000..69430b67 --- /dev/null +++ b/.github/workflows/pyrealm_profiling_after_push.yaml @@ -0,0 +1,79 @@ +name: Profiling + +# This runs when code is pushed to main or develop +on: + push: + branches: [main, develop] + +jobs: + test: + uses: ./.github/workflows/pyrealm_ci.yaml + secrets: inherit + + profiling: + needs: test + runs-on: ubuntu-latest + strategy: + fail-fast: false + + steps: + - uses: actions/checkout@v4 + with: + ref: ${{ github.head_ref }} + + - uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Install Poetry + uses: abatilo/actions-poetry@v2.1.6 + with: + poetry-version: 1.2.2 + + - name: Install dependencies and add env vars + run: | + poetry install + sudo apt-get install graphviz + calculatedSha=$(git rev-parse --short ${{ github.sha }}) + echo "COMMIT_SHORT_SHA=$calculatedSha" >> $GITHUB_ENV + + - name: Run the profiling test suite, using time to get peak memory usage + id: profiling + run: poetry run /usr/bin/time -v pytest -m "profiling" --profile-svg + + # This step only runs if the profiling succeeds + - name: Benchmark performance + id: benchmarking + if: ${{steps.profiling.outcome == 'success'}} + run: poetry run python profiling/run_benchmarking.py prof/combined.prof profiling/profiling-database.csv profiling/benchmark-fails.csv ${{ env.COMMIT_SHORT_SHA }} --update-on-pass --plot-path profiling/performance-plot.png + + # This step copies over the updated call graph + - name: Copy call graph + id: update-call-graph + if: always() && steps.benchmarking.outcome != 'skipped' + run: cp prof/combined.svg profiling/call-graph.svg + + # Creates a PR to update the profiling stats if the benchmark passes or fails and + # skips if the profiling step fails. + - name: Create pull request + id: cpr + if: always() && steps.benchmarking.outcome != 'skipped' + uses: peter-evans/create-pull-request@v6 + with: + commit-message: Updating profiling stats for ${{ env.COMMIT_SHORT_SHA }} + title: Updating profiling stats for ${{ env.COMMIT_SHORT_SHA }} + add-paths: profiling/* + body: | + Automatic update of profiling stats. + + - Profiling update for merge of ${{ env.COMMIT_SHORT_SHA }} into ${{ github.head_ref }} + - Updated call graph, benchmark plot and profiling stats database. + - Auto-generated by `pyrealm_profiling.yaml` workflow + + ${{ steps.benchmarking.outcome != 'passed' && 'Benchmarking passed' || 'Benchmarking **failed**: review failures.' }} + + - name: Check outputs + if: ${{ steps.cpr.outputs.pull-request-number }} + run: | + echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" + echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}" \ No newline at end of file diff --git a/.github/workflows/pyrealm_profiling.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml similarity index 67% rename from .github/workflows/pyrealm_profiling.yaml rename to .github/workflows/pyrealm_profiling_on_approve.yaml index b630f698..b8fa69c8 100644 --- a/.github/workflows/pyrealm_profiling.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -1,12 +1,13 @@ -name: Profiling +name: Profiling on approve -# This runs when code is pushed to main or develop +# This runs when a pull request is submitted on: - push: - branches: [main, develop] + pull_request_review: + types: [submitted] jobs: test: + if: github.event.review.state == 'APPROVED' uses: ./.github/workflows/pyrealm_ci.yaml secrets: inherit @@ -30,25 +31,25 @@ jobs: with: poetry-version: 1.2.2 - - name: Install dependencies - run: poetry install - - - name: Run the profiling test suite - id: profiling + - name: Install dependencies and add env vars run: | + poetry install sudo apt-get install graphviz - poetry run pytest -m "profiling" --profile-svg calculatedSha=$(git rev-parse --short ${{ github.sha }}) echo "COMMIT_SHORT_SHA=$calculatedSha" >> $GITHUB_ENV + - name: Run the profiling test suite, using time to get peak memory usage + id: profiling + run: poetry run /usr/bin/time -v pytest -m "profiling" --profile-svg + # This step only runs if the profiling succeeds - - name: Benchmark performance and copy call graph + - name: Benchmark performance id: benchmarking if: ${{steps.profiling.outcome == 'success'}} - run: poetry run /usr/bin/time -v python profiling/run_benchmarking.py prof/combined.prof profiling/profiling-database.csv profiling/benchmark-fails.csv ${{ env.COMMIT_SHORT_SHA }} --update-on-pass --plot-path profiling/performance-plot.png + run: poetry run python profiling/run_benchmarking.py prof/combined.prof profiling/profiling-database.csv profiling/benchmark-fails.csv ${{ env.COMMIT_SHORT_SHA }} --update-on-pass --plot-path profiling/performance-plot.png # This step copies over the updated call graph - - name: Benchmark performance and copy call graph + - name: Copy call graph id: update-call-graph if: always() && steps.benchmarking.outcome != 'skipped' run: cp prof/combined.svg profiling/call-graph.svg From cd90a2baedf9cf23177995ec7608e9f7d2d3272d Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 24 Apr 2024 18:32:18 +0100 Subject: [PATCH 2/9] Naming profile workflow more clearly --- .github/workflows/pyrealm_profiling_after_push.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pyrealm_profiling_after_push.yaml b/.github/workflows/pyrealm_profiling_after_push.yaml index 69430b67..7ea298bd 100644 --- a/.github/workflows/pyrealm_profiling_after_push.yaml +++ b/.github/workflows/pyrealm_profiling_after_push.yaml @@ -1,4 +1,4 @@ -name: Profiling +name: Profiling after push # This runs when code is pushed to main or develop on: From 3e79bb4adab7612c2a1a16819a20442154693176 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 30 Apr 2024 19:35:46 +0100 Subject: [PATCH 3/9] Update pyrealm_profiling_on_approve.yaml to fix ref --- .github/workflows/pyrealm_profiling_on_approve.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pyrealm_profiling_on_approve.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml index b8fa69c8..9ac8bfe6 100644 --- a/.github/workflows/pyrealm_profiling_on_approve.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -19,8 +19,8 @@ jobs: steps: - uses: actions/checkout@v4 - with: - ref: ${{ github.head_ref }} + # with: + # ref: ${{ github.head_ref }} - uses: actions/setup-python@v5 with: From ceed750daf99b39b6ac5df288865310b125d0e2f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 May 2024 17:45:48 +0000 Subject: [PATCH 4/9] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2) - [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0) - [github.com/igorshubovych/markdownlint-cli: v0.39.0 → v0.40.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.39.0...v0.40.0) --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 518b5157..2c4f12f3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: - id: isort additional_dependencies: [toml] - repo: https://github.com/psf/black - rev: "24.4.0" + rev: "24.4.2" hooks: - id: black - repo: https://github.com/PyCQA/flake8 @@ -24,14 +24,14 @@ repos: - id: flake8 additional_dependencies: [flake8-docstrings] - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.9.0" + rev: "v1.10.0" hooks: - id: mypy additional_dependencies: [numpy, types-tabulate, pandas-stubs] exclude: "pyrealm_build_data/splash/splash_py_version/.*\\.py" # https://stackoverflow.com/a/75447331/3401916 - repo: https://github.com/igorshubovych/markdownlint-cli - rev: v0.39.0 + rev: v0.40.0 hooks: - id: markdownlint From 099582d5bd65c1c522250c6e46a16601beb1130a Mon Sep 17 00:00:00 2001 From: Amy Pike Date: Tue, 7 May 2024 16:03:42 +0100 Subject: [PATCH 5/9] Attempted fix for profiling autocommit step failing. --- .github/workflows/pyrealm_profiling_on_approve.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pyrealm_profiling_on_approve.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml index b8fa69c8..1cb7442b 100644 --- a/.github/workflows/pyrealm_profiling_on_approve.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -61,3 +61,4 @@ jobs: with: commit_message: Auto-generated profiling results [skip actions] file_pattern: 'profiling/*' + branch: ${{ github.head_ref }} From 02e9af16445ddc2960e1c23fc0cc55af76a55997 Mon Sep 17 00:00:00 2001 From: Amy Pike Date: Tue, 7 May 2024 16:42:06 +0100 Subject: [PATCH 6/9] attempting fix on profiling autocommit step --- .github/workflows/pyrealm_profiling_on_approve.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pyrealm_profiling_on_approve.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml index 5bf3df71..f9e56821 100644 --- a/.github/workflows/pyrealm_profiling_on_approve.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -19,8 +19,8 @@ jobs: steps: - uses: actions/checkout@v4 - # with: - # ref: ${{ github.head_ref }} + with: + ref: ${{ github.ref }} - uses: actions/setup-python@v5 with: @@ -61,4 +61,4 @@ jobs: with: commit_message: Auto-generated profiling results [skip actions] file_pattern: 'profiling/*' - branch: ${{ github.head_ref }} + branch: ${{ github.ref }} From 6b2fc2a303b64a9a2ed90134ac8d79dafe3b0f0c Mon Sep 17 00:00:00 2001 From: Amy Pike Date: Tue, 7 May 2024 16:59:44 +0100 Subject: [PATCH 7/9] attempting fix on profiling autocommit step --- .github/workflows/pyrealm_profiling_on_approve.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pyrealm_profiling_on_approve.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml index f9e56821..e2b2d776 100644 --- a/.github/workflows/pyrealm_profiling_on_approve.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -61,4 +61,4 @@ jobs: with: commit_message: Auto-generated profiling results [skip actions] file_pattern: 'profiling/*' - branch: ${{ github.ref }} + branch: ${{ github.ref_name }} From f810269a964d241f3f8a7480e93cf27f9a589f62 Mon Sep 17 00:00:00 2001 From: Amy Pike Date: Tue, 7 May 2024 17:14:59 +0100 Subject: [PATCH 8/9] attempting fix on profiling autocommit step --- .github/workflows/pyrealm_profiling_on_approve.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pyrealm_profiling_on_approve.yaml b/.github/workflows/pyrealm_profiling_on_approve.yaml index e2b2d776..975dc7d9 100644 --- a/.github/workflows/pyrealm_profiling_on_approve.yaml +++ b/.github/workflows/pyrealm_profiling_on_approve.yaml @@ -61,4 +61,4 @@ jobs: with: commit_message: Auto-generated profiling results [skip actions] file_pattern: 'profiling/*' - branch: ${{ github.ref_name }} + branch: ${{ github.event.pull_request.head.ref }} From 359c9ce8ce02039b8fd4b84316960bbff08bd849 Mon Sep 17 00:00:00 2001 From: AmyOctoCat Date: Tue, 7 May 2024 16:26:28 +0000 Subject: [PATCH 9/9] Auto-generated profiling results [skip actions] --- profiling/call-graph.svg | 3518 +++++++++++++----------------- profiling/profiling-database.csv | 78 + 2 files changed, 1581 insertions(+), 2015 deletions(-) create mode 100644 profiling/profiling-database.csv diff --git a/profiling/call-graph.svg b/profiling/call-graph.svg index 7c605702..77248d40 100644 --- a/profiling/call-graph.svg +++ b/profiling/call-graph.svg @@ -4,2394 +4,1882 @@ - - + + %3 - - + + -1 - - -~:0:<built-in method builtins.exec> -0.63% -(0.12%) -30× +73 + + +utilities:113:summarize_attrs +6.55% +(0.71%) +6× - + -7 - - -~:0:<built-in method _operator.getitem> -1.01% -(0.92%) -31× +885 + + +nanfunctions:236:nanmin +1.07% +(0.00%) +47× - + + +73->885 + + +0.65% +38× + + -50 - - -utilities:52:check_input_shapes -0.58% -(0.48%) -2971× +886 + + +nanfunctions:952:nanmean +4.41% +(0.12%) +38× - + + +73->886 + + +4.41% +38× + + -51 - - -functions:257:calc_gammastar -0.79% -(0.33%) -3× +891 + + 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