Misc ci updates

.github/scripts/average_test_durations.py

@@ -0,0 +1,84 @@
+# Description: This script averages the test durations from all the artifacts
+import glob
+import json
+import os
+import subprocess
+from collections import defaultdict
+
+
+# Function to collect test names using pytest
+def collect_tests_with_pytest():
+    # Run pytest with --collect-only to get the list of test cases
+    result = subprocess.run(["pytest", "--collect-only"], capture_output=True, text=True, check=False)
+
+    collected_tests = defaultdict(list)
+
+    # Parse the output to organize tests under their respective modules
+    for line in result.stdout.splitlines():
+        if line.startswith("tests/"):
+            collected_tests[line] = 0
+
+    return collected_tests
+
+
+# Consolidate durations from existing artifacts
+def consolidate_durations():
+    durations = defaultdict(lambda: {"total_duration": 0, "count": 0})
+
+    # Iterate over all downloaded duration artifacts
+    for folder in glob.glob("test-durations-*"):
+        # The path to the duration file in each directory
+        duration_file_path = os.path.join(folder, ".pytest-split-durations")
+
+        if os.path.isfile(duration_file_path):
+            with open(duration_file_path) as f:
+                data = json.load(f)
+                for test, duration in data.items():
+                    durations[test]["total_duration"] += duration
+                    durations[test]["count"] += 1
+
+    # Calculate the average duration for each test
+    return {test: info["total_duration"] / info["count"] for test, info in durations.items()}
+
+
+# Define the path to the consolidated durations file
+CONSOLIDATED_FILE = "tests/test_data/.pytest-split-durations"
+
+
+# Main script logic
+def main():
+    # Collect tests grouped by modules using pytest
+    collected_tests = collect_tests_with_pytest()
+
+    # Consolidate durations from artifacts
+    consolidated_durations = consolidate_durations()
+
+    # Merge and update with consolidated durations
+    updated_durations = {}
+    for test, duration in collected_tests.items():
+        # Update average test durations and exclude test which not exists (can happen on renaming or removing tests)
+        if test in consolidated_durations:
+            updated_durations[test] = consolidated_durations[test]
+
+    # Load the existing durations file if it exists
+    existing_durations = {}
+    if os.path.isfile(CONSOLIDATED_FILE):
+        with open(CONSOLIDATED_FILE) as f:
+            existing_durations = json.load(f)
+
+    # Sort the keys to compare the tests in both dictionaries
+    updated_durations_key = sorted(updated_durations.keys())
+    existing_durations_key = sorted(existing_durations.keys())
+
+    # Check if all keys in updated_durations are in existing_durations
+    if updated_durations_key == existing_durations_key:
+        print("No new tests detected; durations file remains unchanged.")
+    else:
+        # Write the updated durations to the consolidated file
+        with open(CONSOLIDATED_FILE, "w") as f:
+            json.dump(updated_durations, f, indent=4)
+        print("New tests detected; updated the durations file.")
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/docs.yml

@@ -15,8 +15,8 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
       - name: Install dependencies

.github/workflows/python-package.yml

@@ -9,11 +9,16 @@ on:
   pull_request:
     branches: [ main ]
 
+permissions:
+  contents: write
+  pull-requests: write
+
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
@@ -73,6 +78,14 @@ jobs:
         overwrite: false
         path: ./.coverage
 
+    - name: Upload test durations artifact
+      if: matrix.python-version == '3.10'
+      uses: actions/upload-artifact@v3
+      with:
+        name: test-durations-${{ matrix.python-version }}-${{ matrix.split }}
+        include-hidden-files: true
+        path: ./tests/test_data/.pytest-split-durations
+
   coverage:
       needs: test
       runs-on: ubuntu-latest
@@ -105,6 +118,50 @@ jobs:
             token: ${{ secrets.CODECOV_TOKEN }}
             slug: JaGeo/LobsterPy
 
+  commit-durations:
+    if: github.repository_owner == 'JaGeo' && github.ref == 'refs/heads/main'
+    needs: test
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+
+    steps:
+
+    - name: Check out repo
+      uses: actions/checkout@v4
+    - name: Set up micromamba
+      uses: mamba-org/setup-micromamba@main
+    - name: Create mamba environment
+      run: |
+          micromamba create -n lobpy_test python=3.10 --yes
+    - name: Install uv
+      run: micromamba run -n lobpy_test pip install uv
+    - name: Install lobsterpy and dependencies
+      run: |
+          micromamba activate lobpy_test
+          uv pip install --upgrade pip
+          uv pip install -e .[tests,featurizer]
+
+    - name: Download test duration artifacts
+      uses: actions/download-artifact@v4
+
+    - name: Compute average of test durations
+      run: |
+        micromamba activate lobpy_test
+        python3 .github/scripts/average_test_durations.py
+        rm -rf test-durations-*
+
+    - name: Create Pull Request to push consolidated test durations
+      uses: peter-evans/create-pull-request@v7
+      with:
+        commit-message: update test durations
+        title: Update test durations file
+        body: Auto updated test durations file
+        branch: update-test-durations
+        delete-branch: true
+        base: main
+
   docs:
     runs-on: ubuntu-latest
 

.github/workflows/python-publish.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v4
       with:

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|examples|tests/test_data)
+exclude: ^(docs|examples|tests|.github)
 
 ci:
   autoupdate_schedule: monthly