Higher splitting for Github Actions and Cache venv (#1213)

Here is the description for this PR by @YigitElma 

- I created a new workflow that runs every 2 days and updates the
requirements and stores them in a venv that is cached
- Black, unit, regression, notebook and benchmark workflows use the
cached venv (which takes around 4-8seconds whereas installing
dependencies usually more than a minute)
- Increase the spitting of `unit`, `notebook`, and `benchmark`
workflows.
- For some reason I couldn't make the linting test faster using venv (so
set it back to old version which is fine), actually for some reason venv
made it way slower around 8 minutes?!!!?

### Other Fixes
- We stopped using Python 3.8 in our tests with #923 but we forgot to
remove them from weekly tests. Since then (I guess the dates check) the
weekly tests fail (for the last 3 months). I removed Python 3.8 from
weekly tests.

.github/workflows/benchmark.yml

@@ -22,6 +22,12 @@ concurrency:
 jobs:
   benchmark:
     runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
+    strategy:
+      matrix:
+        python-version: ['3.9']
+        group: [1, 2]
 
     steps:
       # Enable tmate debugging of manually-triggered workflows if the input option was provided
@@ -31,41 +37,68 @@ jobs:
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
-      - name: Set up Python 3.9
+
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-      - name: Install dependencies
+          python-version: ${{ matrix.python-version }}
+
+      - name: Restore Python environment cache
+        id: restore-env
+        uses: actions/cache/restore@v4
+        with:
+          path: .venv-${{ matrix.python-version }}
+          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env.outputs.cache-hit != 'true'
         run: |
+          gh cache list
+          python -m venv .venv-${{ matrix.python-version }}
+          source .venv-${{ matrix.python-version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
-      - name: Benchmark with pytest-benchmark
+
+      - name: Benchmark with pytest-benchmark (PR)
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='Latest_Commit' \
             --durations=0 \
-            --benchmark-save-data
+            --benchmark-save-data \
+            --splits 2 \
+            --group ${{ matrix.group }} \
+            --splitting-algorithm least_duration
+
       - name: Checkout current master
         uses: actions/checkout@v4
         with:
           ref: master
           clean: false
+
       - name: Checkout benchmarks from PR head
         run: git checkout ${{ github.event.pull_request.head.sha }} -- tests/benchmarks
-      - name: Benchmark with pytest-benchmark
+
+      - name: Benchmark with pytest-benchmark (MASTER)
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='master' \
             --durations=0 \
-            --benchmark-save-data
-      - name: put benchmark results in same folder
+            --benchmark-save-data \
+            --splits 2 \
+            --group ${{ matrix.group }} \
+            --splitting-algorithm least_duration
+
+      - name: Put benchmark results in same folder
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           cd tests/benchmarks
           find .benchmarks/ -type f -printf "%T@ %p\n" | sort -n | cut -d' ' -f 2- | tail -n 1 > temp1
@@ -75,22 +108,43 @@ jobs:
           mkdir compare_results
           cp $t1 compare_results
           cp $t2 compare_results
+
+      - name: Download artifact
+        if: always()
+        uses: actions/download-artifact@v4
+        with:
+          pattern: benchmark_artifact_*
+          path: tests/benchmarks
+
+      - name: Unzip artifacts if downloaded
+        run: |
+          cd tests/benchmarks
+          ls
+          if [ -f tests/benchmarks/benchmark_artifact_*.zip ]; then
+            unzip tests/benchmarks/benchmark_artifact_*.zip -d tests/benchmarks
+          else
+            echo "No benchmark artifact file found."
+          fi
+
       - name: Compare latest commit results to the master branch results
         run: |
-          pwd
+          source .venv-${{ matrix.python-version }}/bin/activate
           cd tests/benchmarks
+          pwd
           python compare_bench_results.py
           cat commit_msg.txt
-      - name: comment PR with the results
+
+      - name: Comment PR with the results
         uses: thollander/actions-comment-pull-request@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filePath: tests/benchmarks/commit_msg.txt
           comment_tag: benchmark
+
       - name: Upload benchmark data
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: benchmark_artifact
+          name: benchmark_artifact_${{ matrix.group }}
           path: tests/benchmarks/.benchmarks

.github/workflows/black.yml

@@ -6,26 +6,48 @@ jobs:
   black_format:
 
     runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.10
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-      - name: Install dependencies
+          python-version: ${{ matrix.python-version }}
+
+      - name: Restore Python environment cache
+        id: restore-env
+        uses: actions/cache/restore@v4
+        with:
+          path: .venv-${{ matrix.python-version }}
+          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env.outputs.cache-hit != 'true'
         run: |
+          gh cache list
+          python -m venv .venv-${{ matrix.python-version }}
+          source .venv-${{ matrix.python-version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
+
       - name: Check files using the black formatter
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
           black --version
           black --check desc/ tests/ || black_return_code=$?
           echo "BLACK_RETURN_CODE=$black_return_code" >> $GITHUB_ENV
           black desc/ tests/
+
       - name: Annotate diff changes using reviewdog
         uses: reviewdog/action-suggester@v1
         with:
           tool_name: blackfmt
+
       - name: Fail if not formatted
         run: |
           exit ${{ env.BLACK_RETURN_CODE }}

.github/workflows/cache_dependencies.yml

@@ -0,0 +1,55 @@
+name: Cache dependencies
+# This workflow is triggered every 2 days and updates the Python
+# and pip dependencies cache
+on:
+  schedule:
+    - cron: '30 4 */2 * *'  # This triggers the workflow at 4:30 AM every 2 days
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Delete old cached file with same python version
+        run: |
+          echo "Current Cached files list"
+          gh cache list
+          echo "Deleting cached files with pattern: ${{ runner.os }}-venv-${{ matrix.python-version }}-"
+          for cache_key in $(gh cache list --json key -q ".[] | select(.key | startswith(\"${{ runner.os }}-venv-${{ matrix.python-version }}-\")) | .key"); do
+            echo "Deleting cache with key: $cache_key"
+            gh cache delete "$cache_key"
+          done
+
+      - name: Set up virtual environment
+        run: |
+          python -m venv .venv-${{ matrix.python-version }}
+          source .venv-${{ matrix.python-version }}/bin/activate
+          python -m pip install --upgrade pip
+          pip install -r devtools/dev-requirements.txt
+
+      - name: Cache Python environment
+        id: cache-env
+        uses: actions/cache@v4
+        with:
+          path: .venv-${{ matrix.python-version }}
+          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Verify virtual environment activation
+        run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
+          python --version
+          pip --version
+          pip list

.github/workflows/linting.yml

@@ -5,17 +5,24 @@ on: [pull_request, workflow_dispatch]
 jobs:
   flake8_linting:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
     name: Linting
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.10
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: ${{ matrix.python-version }}
+
+      # For some reason, loading venv makes this way slower
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
+
       - name: flake8 Lint
         uses: reviewdog/action-flake8@v3
         with:

.github/workflows/nbtests.yml → .github/workflows/notebook_tests.yml

@@ -18,28 +18,46 @@ jobs:
   notebook_tests:
 
     runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
         python-version: ['3.10']
-        group: [1, 2]
+        group: [1, 2, 3]
 
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+
+      - name: Restore Python environment cache
+        id: restore-env
+        uses: actions/cache/restore@v4
+        with:
+          path: .venv-${{ matrix.python-version }}
+          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env.outputs.cache-hit != 'true'
         run: |
+          gh cache list
+          python -m venv .venv-${{ matrix.python-version }}
+          source .venv-${{ matrix.python-version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
+
       - name: Test notebooks with pytest and nbmake
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
           export PYTHONPATH=$(pwd)
           pytest -v --nbmake "./docs/notebooks" \
             --nbmake-timeout=2000 \
             --ignore=./docs/notebooks/zernike_eval.ipynb \
-            --splits 2 \
+            --splits 3 \
             --group ${{ matrix.group }} \
+            --splitting-algorithm least_duration

.github/workflows/regression_test.yml → .github/workflows/regression_tests.yml

@@ -18,6 +18,8 @@ jobs:
   regression_tests:
 
     runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
         python-version: ['3.10']
@@ -29,20 +31,36 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+
+      - name: Restore Python environment cache
+        id: restore-env
+        uses: actions/cache/restore@v4
+        with:
+          path: .venv-${{ matrix.python-version }}
+          key: ${{ runner.os }}-venv-${{ matrix.python-version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env.outputs.cache-hit != 'true'
         run: |
+          gh cache list
+          python -m venv .venv-${{ matrix.python-version }}
+          source .venv-${{ matrix.python-version }}/bin/activate
           python -m pip install --upgrade pip
           pip install -r devtools/dev-requirements.txt
           pip install matplotlib==3.7.2
+
       - name: Set Swap Space
         uses: pierotofy/set-swap-space@master
         with:
           swap-size-gb: 10
+
       - name: Test with pytest
         run: |
+          source .venv-${{ matrix.python-version }}/bin/activate
+          pip install matplotlib==3.7.2
           pwd
           lscpu
-          python -m pytest -v -m regression \
+          python -m pytest -v -m regression\
             --durations=0 \
             --cov-report xml:cov.xml \
             --cov-config=setup.cfg \
@@ -54,6 +72,7 @@ jobs:
             --group ${{ matrix.group }} \
             --splitting-algorithm least_duration \
             --db ./prof.db
+
       - name: save coverage file and plot comparison results
         if: always()
         uses: actions/upload-artifact@v4
@@ -63,6 +82,7 @@ jobs:
             ./cov.xml
             ./mpl_results.html
             ./prof.db
+
       - name: Upload coverage
         id : codecov
         uses: Wandalen/[email protected]