use changed-files, remove old uv stuff

Signed-off-by: Peter St. John <pstjohn@nvidia.com>

Author: pstjohn

.github/workflows/unit-tests.yml

@@ -20,18 +20,55 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  changed-files:
+    if: github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+    outputs:
+      any_changed: ${{ steps.changed-files.outputs.any_changed }}
+      docs_changed: ${{ steps.changed-files.outputs.docs_any_changed }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: step-security/changed-files@v46
+        id: changed-files
+        with:
+          base_sha: main
+          files_yaml: |
+            framework:
+              - '3rdparty/**'
+              - 'sub-packages/**'
+              - 'docker_build_patches/**'
+              - 'requirements-*.txt'
+              - 'Dockerfile'
+            docs:
+              - 'docs/**.ipynb'
+      - name: List all changed files
+        env:
+          ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
+        run: |
+          for file in ${ALL_CHANGED_FILES}; do
+            echo "$file was changed"
+          done
+
   pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          submodules: "recursive"
       - uses: actions/setup-python@v5
         with:
           python-version: "3.13"
           cache: "pip"
-      - run: pip install -r requirements-dev.txt
+      - name: Setup UV
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - run: |
+          uv tool install pre-commit --with pre-commit-uv --force-reinstall
+          uv tool install tach>=0.9.0
+          uv tool update-shell
       - run: ./ci/scripts/static_checks.sh
 
   # With copy-pr-bot, we need to get the PR labels from the PR API rather than from the event metadata.
@@ -65,8 +102,9 @@ jobs:
     needs:
       - pre-commit
       - get-pr-labels
+      - changed-files
     runs-on: linux-amd64-cpu16
-    if: ${{ !contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'SKIP_CI') }}
+    if: ${{ !contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'SKIP_CI') && (needs.changed-files.outputs.any_changed == 'true' || needs.changed-files.result == 'skipped') }}
     steps:
       - name: Login to Docker Hub
         uses: docker/login-action@v3
@@ -185,10 +223,12 @@ jobs:
     needs:
       - build-bionemo-image
       - get-pr-labels
+      - changed-files
     runs-on: linux-amd64-gpu-l4-latest-1
     if: |
       github.event_name == 'schedule' || github.event_name == 'merge_group' ||
-      contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'INCLUDE_NOTEBOOKS_TESTS')
+      contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'INCLUDE_NOTEBOOKS_TESTS') ||
+      needs.changed-files.outputs.docs_changed == 'true'
     container:
       image: svcbionemo023/bionemo-framework:${{ github.run_id }}
       credentials:

ci/docker/Dockerfile.uv

@@ -5,12 +5,6 @@ set -xueo pipefail
 REPOSITORY_ROOT=$(git rev-parse --show-toplevel)
 cd $REPOSITORY_ROOT
 
-echo "Running ruff checks"
-set +e
-ruff check scripts/ sub-packages/ docs/
-E_RUFF_CHECK="$?"
-set -e
-
 echo "Running tach checks"
 set +e
 tach check
@@ -19,7 +13,7 @@ set -e
 
 echo "Running pre-commit checks"
 set +e
-pre-commit run --all-files --show-diff-on-failure --color always
+pre-commit run --all-files --show-diff-on-failure --color always --verbose
 E_PRE_COMMIT="$?"
 set -e
 
@@ -29,10 +23,6 @@ if [[ "${E_PRE_COMMIT}" != "0" ]]; then
     ANY_FAILURE=1
     echo "ERROR: pre-commit hooks failed! (exit: ${E_PRE_COMMIT})"
 fi
-if [[ "${E_RUFF_CHECK}" != "0" ]]; then
-  ANY_FAILURE=1
-  echo "ERROR: ruff check failed! (exit: ${E_RUFF_CHECK})"
-fi
 if [[ "${E_TACH_CHECK}" != "0" ]]; then
   ANY_FAILURE=1
   echo "ERROR: tach check failed! (exit: ${E_TACH_CHECK})"