Only run cleanup if tests ran, adds pytest marker config for slow tests

.github/pull_request_template.md

@@ -11,10 +11,10 @@
 - [ ]  Other (please describe):
 
 ### CI Pipeline Configuration
-Configure CI behavior by checking relevant boxes below. This will automatically apply labels.
+Configure CI behavior by applying the relevant labels:
 
-- [ ] [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests
-- [ ] [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest
+- [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests
+- [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest
 
 > [!NOTE]
 > By default, the notebooks validation tests are skipped unless explicitly enabled.

.github/workflows/unit-tests.yml

@@ -1,4 +1,4 @@
-name: "[Optional] BioNemo Image Build and Unit Tests"
+name: "BioNemo Image Build and Unit Tests"
 
 on:
   pull_request:
@@ -100,6 +100,12 @@ jobs:
           BIONEMO_DATA_SOURCE: ngc
         run: ./ci/scripts/run_pytest.sh --no-nbval --skip-slow
 
+      - name: Run notebook tests
+        if: ${{ contains(github.event.pull_request.labels.*.name, 'INCLUDE_NOTEBOOKS_TESTS') }}
+        env:
+          BIONEMO_DATA_SOURCE: ngc
+        run: pytest --nbval-lax -p no:python docs/ sub-packages/
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         with:
@@ -116,10 +122,9 @@ jobs:
   clean-up:
     needs: run-tests
     runs-on: self-hosted-nemo-gpus-1
-    if: ${{ always() }}
+    if: ${{ success() || failure() }}
     steps:
       - name: clean up image
         run: docker rmi nemoci.azurecr.io/bionemo:${{ github.run_id }}
-
 # TODO: exclude tests from base image; run tests from github workspace mounted in the image.
 # TODO: figure out way of cleaning up working directory (requires sudo or for us to fix file ownership from release container)

.secrets.baseline

@@ -139,9 +139,9 @@
         "filename": "pyproject.toml",
         "hashed_secret": "79670e9c9d1c7ea5b81a96a2053d81437712c78e",
         "is_verified": false,
-        "line_number": 47
+        "line_number": 43
       }
     ]
   },
-  "generated_at": "2024-11-01T22:26:03Z"
+  "generated_at": "2025-01-14T17:26:27Z"
 }

pyproject.toml

@@ -36,11 +36,7 @@ dependencies = [
 build = ['flash-attn', 'pip']
 
 [tool.uv.workspace]
-members = [
-    "3rdparty/*",
-    "sub-packages/bionemo-*/",
-    "internal/infra-bionemo/",
-]
+members = ["3rdparty/*", "internal/infra-bionemo/", "sub-packages/bionemo-*/"]
 
 [tool.uv.sources]
 # external
@@ -114,9 +110,10 @@ convention = "google"
 [tool.pytest.ini_options]
 norecursedirs = ["3rdparty"]
 addopts = ["--ignore=3rdparty"]
+markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 
 [tool.pyright]
-include = ["./scripts/", "./sub-packages/", "./internal/"]
+include = ["./internal/", "./scripts/", "./sub-packages/"]
 exclude = ["*/tests/"]
 executionEnvironments = [
     { "root" = ".", pythonVersion = "3.10", extraPaths = [