ci: fix broken CI pipeline (#95)

* minor changes * pin pip version
elixir-cloud-aai · Jan 8, 2025 · 45ca5f4 · 45ca5f4
1 parent 6044d25
commit 45ca5f4
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -18,6 +18,9 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
+      - name: Pin pip version
+        run: |
+          python -m pip install --upgrade "pip<24.1"
       - name: Install requirements
         run: |
           pip install -r requirements_dev.txt
@@ -46,7 +49,7 @@ jobs:
         with:
           python-version: "3.10"
       - name: Deploy app
-        run: docker-compose up -d --build
+        run: docker compose up -d --build
       - name: Wait for app startup
         run: sleep 20
       - name: Probe endpoint

diff --git a/pro_wes/ga4gh/wes/workflow_runs.py b/pro_wes/ga4gh/wes/workflow_runs.py
@@ -482,7 +482,9 @@ def _validate_run_request(
         """
         dict_of_lists = form_data.to_dict(flat=False)
         # flatten single item lists
-        dict_atomic = {k: v[0] if len(v) == 1 else v for k, v in dict_of_lists.items()}
+        dict_atomic: dict = {
+            k: v[0] if len(v) == 1 else v for k, v in dict_of_lists.items()
+        }
         # remove 'workflow_attachment' field
         dict_atomic.pop("workflow_attachment", None)
         model_instance = RunRequest(**dict_atomic)

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
 connexion<3
 email-validator>=2.1.0,<3
-foca>=0.12.1
+foca==0.12.1
 gunicorn>=22