Merge branch 'main' into edawson/scdl-schema

Author: polinabinder1

.github/pull_request_template.md

@@ -20,7 +20,7 @@ Configure CI behavior by applying the relevant labels:
 - [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
 - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing
 
-> \[!NOTE\]
+> [!NOTE]
 > By default, the notebooks validation tests are skipped unless explicitly enabled.
 
 #### Authorizing CI Runs

.github/workflows/unit-tests.yml

@@ -29,7 +29,7 @@ jobs:
           submodules: "recursive"
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
       - run: pip install -r requirements-dev.txt
       - run: ./ci/scripts/static_checks.sh

.mdformat.toml

@@ -1 +1,4 @@
 number = true        # options: {false, true}
+exclude = [
+    "docs/docs/index.md",	# Exclude highly formatted index page
+]

.pre-commit-config.yaml

@@ -1,4 +1,13 @@
 repos:
+  - repo: local
+    hooks:
+      - id: license-header-check
+        name: Run license-check script
+        entry: ./ci/scripts/license_check.py
+        language: python
+        types_or: [python, rust]
+        pass_filenames: true
+        always_run: false
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
@@ -14,9 +23,10 @@ repos:
         args: ["--fix"]
       - id: ruff-format
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17             # Use the latest stable version
+    rev: 0.7.22             # Use the latest stable version
     hooks:
       - id: mdformat
+        language_version: python3.13
         additional_dependencies:
         - mdformat-tables
         - mdformat-gfm
@@ -32,12 +42,3 @@ repos:
       - id: detect-secrets
         name: detect-secrets (notebooks only)
         args: ['--baseline', '.secrets-nb.baseline', '--exclude-files', '^.(?!.*\.ipynb)', '--exclude-lines', '"(hash|id|image/\w+)":.*|<.*at 0x[0-9a-f]+>|object at 0x[0-9a-f]+', ]
-  - repo: local
-    hooks:
-      - id: license-header-check
-        name: Run license-check script
-        entry: python ci/scripts/license_check.py -c sub-packages -c docs -c ci --license-header ./license_header --modify
-        language: python
-        additional_dependencies: ["click==8.1.7"]
-        pass_filenames: false
-        always_run: true

README.md

@@ -82,7 +82,7 @@ We distribute a [development container](https://devcontainers.github.io/) config
 (`.devcontainer/devcontainer.json`) that simplifies the process of local testing and development. Opening the
 bionemo-framework folder with VSCode should prompt you to re-open the folder inside the devcontainer environment.
 
-> \[!NOTE\]
+> [!NOTE]
 > The first time you launch the devcontainer, it may take a long time to build the image. Building the image locally
 > (using the command shown above) will ensure that most of the layers are present in the local docker cache.