Merge branch 'develop' into release/1.0.0

.github/workflows/pyrealm_profiling_after_push.yaml

@@ -0,0 +1,79 @@
+name: Profiling after push
+
+# 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: ${{ github.head_ref }}
+
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.10"
+
+ - name: Install Poetry
+ uses: abatilo/[email protected]
+ with:
+ poetry-version: 1.2.2
+
+ - name: Install dependencies and add env vars
+ run: |
+ poetry install
+ sudo apt-get install graphviz
+ calculatedSha=$(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 }}"

.github/workflows/pyrealm_profiling.yaml → .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
 
@@ -19,7 +20,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  with:
- ref: ${{ github.head_ref }}
+ ref: ${{ github.ref }}
 
  - uses: actions/setup-python@v5
  with:
@@ -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
@@ -60,3 +61,4 @@ jobs:
  with:
  commit_message: Auto-generated profiling results [skip actions]
  file_pattern: 'profiling/*'
+ branch: ${{ github.event.pull_request.head.ref }}

.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