Chore/changes for uv

.github/workflows/integration_tests.yaml

@@ -15,7 +15,7 @@ permissions:
 jobs:
   integration_tests:
     name: Integration tests
-    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@chore/update_to_uv
     with:
       WORKING_DIR: gen3-integration-tests
     secrets:

.github/workflows/integration_tests_on_kind.yaml

@@ -17,7 +17,7 @@ permissions:
 jobs:
   integration_tests:
     name: Integration tests
-    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@chore/update_to_uv
     with:
       WORKING_DIR: gen3-integration-tests
       EXTERNAL_TO_CTDS: "true"

.github/workflows/nightly_run.yaml

@@ -13,7 +13,7 @@ on:
 jobs:
   nightly_run:
     name: Nightly run
-    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@chore/update_to_uv
     with:
       WORKING_DIR: gen3-integration-tests
       IS_NIGHTLY_RUN: "true"

.github/workflows/nightly_run_gen3ff.yaml

@@ -13,7 +13,7 @@ on:
 jobs:
   nightly_run_gen3ff:
     name: Nightly run Gen3FF
-    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@chore/update_to_uv
     with:
       WORKING_DIR: gen3-integration-tests
       IS_NIGHTLY_RUN: "true"

.github/workflows/run_tests_against_dev_env.yaml

@@ -97,11 +97,10 @@ jobs:
           if [[ "$REPO" == "gen3sdk-python" ]]; then
             sed -i "s|^gen3 = \".*\"|gen3 = { git = \"https://github.com/uc-cdis/gen3sdk-python\", rev = \"$BRANCH\" }|" pyproject.toml
           fi
-          pip install poetry
-          poetry lock
-          poetry install
-          poetry show
-          sudo apt update && poetry run playwright install-deps && poetry run playwright install --with-deps chromium
+          pip install uv
+          uv sync
+          uv pip list
+          sudo apt update && uv run playwright install-deps && uv run playwright install --with-deps chromium
           sudo apt install openjdk-11-jre -y
 
       - name: Configure AWS Credentials
@@ -133,7 +132,7 @@ jobs:
             mkdir $HOME/.gen3
             mkdir logs
             echo "****** Prepare CI Environment ******" > logs/gh_action_logs.txt
-            ./gen3_ci/scripts/generate_api_keys.sh test_data/test_setup/users.csv ${HOSTNAME} ${NAMESPACE} >> logs/gh_action_logs.txt 2>&1
+            ./gen3_ci/scripts/generate_api_keys.sh test_data/test_setup/users.csv ${HOSTNAME_PROTOCOL} ${HOSTNAME} ${NAMESPACE} >> logs/gh_action_logs.txt 2>&1
 
       - name: Get test labels
         id: get_test_labels
@@ -152,7 +151,7 @@ jobs:
         run: |
             echo -e "\n\n************ Run tests ************" >> logs/gh_action_logs.txt
             mkdir output
-            poetry run pytest --video=retain-on-failure -n logical -m "not wip" --alluredir allure-results --no-header --dist loadscope ${{ env.TEST_LABEL }} >> logs/gh_action_logs.txt 2>&1
+            uv run pytest --video=retain-on-failure -n logical -m "not wip" --alluredir allure-results --no-header --dist loadscope ${{ env.TEST_LABEL }} >> logs/gh_action_logs.txt 2>&1
             if [ $? -ne 0 ]; then
               echo "PR_ERROR_MSG=Test(s) failures encountered in PR" >> $GITHUB_ENV
             fi
@@ -265,7 +264,7 @@ jobs:
         id: generate_slack_report
         if: ${{ steps.upload_allure_report.outcome == 'success' || steps.upload_gh_action_logs.outcome == 'success' }}
         continue-on-error: true # if this fails, we still need to run clean-up steps
-        run: poetry run python -m gen3_ci.scripts.generate_slack_report
+        run: uv run python -m gen3_ci.scripts.generate_slack_report
 
       - name: Publish report to Slack
         id: slack_notify

.secrets.baseline

@@ -324,7 +324,7 @@
         "filename": "gen3-integration-tests/tests/test_oidc_client.py",
         "hashed_secret": "62bd0c4d3a6b445b13212d23500a7f0916757c3e",
         "is_verified": false,
-        "line_number": 143
+        "line_number": 144
       }
     ],
     "gen3-integration-tests/tests/test_presigned_url.py": [
@@ -394,5 +394,5 @@
       }
     ]
   },
-  "generated_at": "2026-06-23T15:10:45Z"
+  "generated_at": "2026-06-25T15:51:57Z"
 }

gen3-integration-tests/pyproject.toml

@@ -1,59 +1,47 @@
-[tool.poetry]
+[project]
 name = "gen3-integration-tests"
 version = "0.1.0"
-description = "Gen3 Integration Tests"
-authors = ["CTDS UChicago <cdis@uchicago.edu>"]
-license = "Apache-2.0"
+description = "Add your description here"
 readme = "README.md"
-repository = "https://github.com/uc-cdis/gen3-code-vigil"
-package-mode = false
-include = [
-  "NOTICE",
+authors = [
+    { name = "CTDS UChicago", email = "cdis@uchicago.edu" }
+]
+license = "Apache-2.0"
+requires-python = ">=3.13"
+dependencies = [
+    "allure-pytest>=2.16.0",
+    "boto3>=1.38.20",
+    "cdislogging<2",
+    "data-simulator",
+    "fastavro>=1.8.2",
+    "filelock<4",
+    "gen3>=4.28.1",
+    "langchain>=1.2.10",
+    "langchain-core>=1.2.14",
+    "langchain-mcp-adapters>=0.2.1",
+    "langchain-ollama>=1.0.1",
+    "nextflow>=26.4.4",
+    "nextflowpy>=0.13.1", # see https://github.com/goodwright/nextflow.py/issues/14
+    "packaging>=26.2",
+    "pandas<3",
+    "psutil>=5.9.8",
+    "pypfb>=0.5.29",
+    "pytest>=7.4.0",
+    "pytest-md-report>=0.5.0",
+    "pytest-playwright>=0.4.3",
+    "pytest-xdist>=3.3.1",
+    "python-dateutil>=2.9.0.post0",
+    "python-dotenv>=1.0.0",
+    "requests>=2.32.5",
 ]
 
-[tool.poetry.dependencies]
-python = "^3.13"
-cdislogging = "<2"
-data-simulator = {git = "https://github.com/uc-cdis/data-simulator", rev = "1.6.5"}
-filelock = "<4"
-gen3 = "*"
-pandas = "<3"
-pytest = "^7.4.0"
-pytest-md-report = "^0.5.0"
-pytest-playwright = "^0.4.3"
-pytest-xdist = "^3.3.1"
-python-dateutil = "*"
-python-dotenv = "^1.0.0"
-requests = "^2.32.5"
-pypfb = ">=0.5.29"
-fastavro = "^1.8.2"
-psutil = "^5.9.8"
-allure-pytest = "^2.16.0"
-boto3 = "^1.38.20"
-
-# We need to support the latest version of Nextflow.
-# DO NOT PIN THIS VERSION WITHOUT REPORTING THE ISSUE YOU ENCOUNTERED TO THE TEAM.
-nextflow = "*"
-nextflowpy = ">=0.13.1" # see https://github.com/goodwright/nextflow.py/issues/14
-
-# NOTE: NumPy version is pinned to <2.0.0
-# Without this, importing pandas throws the following error during CI:
-# ValueError: numpy.dtype size changed, may indicate binary incompatibility.
-# Expected 96 from C header, got 88 from PyObject
-# This is caused by a tertiary dependency conflict between newer versions of NumPy, Pandas, and Gen3.
-# numpy = "<2"
-langchain = "^1.2.10"
-langchain-ollama = "^1.0.1"
-langchain-mcp-adapters = "^0.2.1"
-langchain-core = "^1.2.14"
-packaging = "^26.2"
-
-[tool.poetry.group.dev.dependencies]
-pre-commit = "^3.8.0"
+[tool.uv.sources]
+data-simulator = { git = "https://github.com/uc-cdis/data-simulator.git", rev = "1.6.5" }
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[dependency-groups]
+dev = [
+    "pre-commit>=3.8.0",
+]
 
 [tool.pytest.ini_options]
 testpaths = ["tests/"]

gen3-integration-tests/tests/test_oidc_client.py

@@ -108,7 +108,8 @@ def test_oidc_client_rotation(self):
         logger.info(f"Getting client_id and client_secret for client {client_name} ...")
         client_id = pytest.clients[client_name]["client_id"]
         client_secret = pytest.clients[client_name]["client_secret"]
-        logger.info(client_id, client_secret)
+        logger.info(f"Client id: {client_id}")
+        logger.info(f"Client secret: {client_secret}")
 
         # Client is rotated as part of the setup, to enable test execution in parallel for this test suite.
         # Rotated client_id and client_secret are retrieved from pytest.rotated_clients.