From a848020edf8594a544f46b89cf5821c134320d49 Mon Sep 17 00:00:00 2001
From: Saurabh Mogre <saurabh.mogre@alleninstitute.org>
Date: Thu, 17 Oct 2024 14:18:33 -0700
Subject: [PATCH] Run workflows through pdm

---
 .github/workflows/analyze.yml          | 5 ++---
 .github/workflows/ci.yml               | 6 +++---
 .github/workflows/cleanup-firebase.yml | 2 +-
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml
index 184e7239..3537043c 100644
--- a/.github/workflows/analyze.yml
+++ b/.github/workflows/analyze.yml
@@ -18,15 +18,14 @@ jobs:
             - uses: actions/checkout@v4
             - uses: ./.github/actions/dependencies
             - name: Pack test recipe
-              shell: bash
               run: |
-                  pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json
+                  pdm run pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json
             - name: Modify JSON with PR sub_directory path
               run: |
                   jq --arg branch_name "${{  github.ref_name  }}" '.create_report.output_image_location |= "https://cellpack-results.s3.us-west-2.amazonaws.com/\($branch_name)/spheresSST/figures"' cellpack/tests/analysis-configs/PR_analysis_config.json > cellpack/tests/analysis-configs/PR_analysis_config_temp.json
                   mv cellpack/tests/analysis-configs/PR_analysis_config_temp.json cellpack/tests/analysis-configs/PR_analysis_config.json
             - name: Run analysis code
-              run: analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST
+              run: pdm run analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST
             - name: Upload results
               uses: actions/upload-artifact@v4
               with:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cfbe2046..37fc88d5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
     - uses: ./.github/actions/dependencies
     - name: Test with pytest
       run: |
-        pytest --cov cellpack/tests/
+        pdm run pytest --cov cellpack/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v4
 
@@ -46,10 +46,10 @@ jobs:
     - uses: ./.github/actions/dependencies
     - name: Lint with flake8
       run: |
-        flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203
+        pdm run flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203
     - name: Check with black
       run: |
-        black --check cellpack
+        pdm run black --check cellpack
 
   publish:
     if: success() && startsWith(github.ref, 'refs/tags/')
diff --git a/.github/workflows/cleanup-firebase.yml b/.github/workflows/cleanup-firebase.yml
index 4bbebb94..4ba7a84d 100644
--- a/.github/workflows/cleanup-firebase.yml
+++ b/.github/workflows/cleanup-firebase.yml
@@ -19,4 +19,4 @@ jobs:
                     FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }}
                     FIREBASE_EMAIL: ${{ secrets.FIREBASE_EMAIL }}
                 run: |
-                    python cellpack/bin/cleanup_tasks.py
+                    pdm run python cellpack/bin/cleanup_tasks.py