Automated comment on GitHub Pull Requests

.github/workflows/analyze.yml

@@ -0,0 +1,51 @@
+name: Analyze
+
+on: push
+
+jobs:
+  Analyze:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.9]
+        os: [ubuntu-latest]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[all]
+    - name: Pack test recipe
+      run: |
+        pack -r cellpack/tests/recipes/test_spheres.json -c cellpack/tests/packing-configs/test_config.json
+        analyze -a cellpack/tests/analysis-configs/PR_analysis_config.json
+    - name: Upload results
+      uses: actions/upload-artifact@v3
+      with:
+        name: results
+        path: cellpack/tests/outputs/test_spheres/
+  Comment:
+    runs-on: ubuntu-latest
+    needs: [Analyze]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Configure AWS credentials
+      uses: aws-actions/configure-aws-credentials@v1-node16
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-west-2
+    - uses: actions/download-artifact@v3
+    - name: Copy files to results bucket
+      run: aws s3 sync ./results s3://cellpack-results --delete
+    - uses: iterative/setup-cml@v1
+    - name: Update comment
+      env:
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: | 
+        cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --pr
+        cat ./results/analysis_report.md

.github/workflows/build-main.yml → .github/workflows/ci.yml

@@ -1,14 +1,24 @@
-name: Build Main
+name: Continuous Integration
 
 on:
   push:
     branches:
       - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
   schedule:
-    # <minute [0,59]> <hour [0,23]> <day of the month [1,31]> <month of the year [1,12]> <day of the week [0,6]>
+    # <minute [0,59]> <hour [0,23]> <day of the month [1,31]>
+    # <month of the year [1,12]> <day of the week [0,6]>
     # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
-    # Run every Monday at 18:00:00 UTC (Monday at 10:00:00 PST)
-    - cron: '0 18 * * 1'
+    # Run every Monday at 10:24:00 PST
+    # (Since these CRONs are used by a lot of people -
+    # let's be nice to the servers and schedule it _not_ on the hour)
+    - cron: "24 18 * * 1"
+  workflow_dispatch:
+
 
 jobs:
   test:
@@ -27,10 +37,10 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[all]
     - name: Test with pytest
       run: |
-        pytest --cov-report xml --cov=cellpack cellpack/tests/
+        pytest cellpack/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v1
 
@@ -55,7 +65,7 @@ jobs:
         black --check cellpack
 
   publish:
-    if: contains(github.event.head_commit.message, 'Bump version')
+    if: success() && startsWith(github.ref, 'refs/tags/')
     needs: [lint, test]
     runs-on: ubuntu-latest
 

.gitignore

@@ -46,6 +46,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+cellpack/tests/outputs/
 
 # Translations
 *.mo
@@ -119,4 +120,3 @@ cellpack/tests/outputs/
 # data
 data/
 **/converted/*
-

analysis-configs/gradient_analysis_config.json

@@ -0,0 +1,10 @@
+{
+    "version": "1.0.0",
+    "format_version": "1.0",
+    "input_path": "out/gradients_X/jitter/",
+    "output_path": "out/gradients_X/",
+    "ingredient_key" : "ext_A",
+    "run_similarity_analysis": true,
+    "save_plots": true,
+    "max_plots_to_save": 1
+}

cellpack/analysis-configs/peroxisomes_analysis_config.json → analysis-configs/peroxisomes_analysis_config.json

@@ -1,8 +1,8 @@
 {
     "version": "1.0.0",
     "format_version": "1.0",
-    "input_path": "out/analyze/peroxisomes_test/spheresSST/",
-    "output_path": "out/analyze/peroxisomes_test/spheresSST/",
+    "input_path": "out/analyze/peroxisomes_gradient/spheresSST/",
+    "output_path": "out/analyze/peroxisomes_gradient/",
     "ingredient_key" : "membrane_interior_peroxisome",
     "mesh_paths" : {
         "inner": "data/mean-nuc.obj",
@@ -11,6 +11,6 @@
     "run_similarity_analysis": true,
     "get_parametrized_representation": true,
     "save_plots": true,
-    "get_correlations": true,
-    "max_plots_to_save": 1
+    "get_correlations": false,
+    "max_plots_to_save": 5
 }