Merge branch 'main' into mvle/geneformer-unit-test

Author: dorotat-nv

.github/workflows/build-dashboard.yml

@@ -0,0 +1,24 @@
+name: Build Dashboard
+
+on:
+  workflow_dispatch:
+
+jobs:
+  trigger:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger GitLab dashboard pipeline
+        env:
+          GITLAB_TRIGGER_TOKEN: ${{ secrets.GITLAB_TRIGGER_TOKEN }}
+          GITLAB_PROJECT_ID_DASHBOARDS: "130554"
+        run: |
+          echo "Triggering GitLab dashboard pipeline (main)..."
+          if curl -fsS -X POST \
+              -F "token=${GITLAB_TRIGGER_TOKEN}" \
+              -F "ref=main" \
+              "https://gitlab-master.nvidia.com/api/v4/projects/${GITLAB_PROJECT_ID_DASHBOARDS}/trigger/pipeline" >/dev/null; then
+            echo "✓ Triggered GitLab dashboard pipeline."
+          else
+            echo "✗ Failed to trigger GitLab dashboard pipeline." >&2
+            exit 1
+          fi

.github/workflows/unit-tests-recipes.yml

@@ -131,6 +131,7 @@ jobs:
     if: ${{ needs.changed-dirs.outputs.dirs != '[]' }}
     container:
       image: ${{ matrix.recipe.image }}
+      options: --shm-size=16G
     strategy:
       matrix:
         recipe: ${{ fromJson(needs.changed-dirs.outputs.dirs) }}

LICENSE/third_party.txt

@@ -82,6 +82,8 @@ With a locally cloned repository and initialized submodules, build the BioNeMo c
 docker buildx build . -t my-container-tag
 ```
 
+If you see an error message like `No file descriptors available (os error 24)`, add the option `--ulimit nofile=65535:65535` to the docker build command.
+
 #### VSCode Devcontainer for Interactive Debugging
 
 We distribute a [development container](https://devcontainers.github.io/) configuration for vscode

README.md

@@ -2,21 +2,21 @@ line-length = 119
 target-version = "py312"
 
 [lint]
-ignore = ["D100", "E501", "N811", "N814"]
+ignore = ["C901", "D100", "E501", "N811", "N814"]
 select = [
-    "C",   # Pylint conventions
-    "D",   # Documentation formatting
-    "E",   # style stuff, whitespaces
-    "F",   # important pyflakes lints
-    "I",   # import sorting
-    "RUF", # Some Ruff-specific lints, unused noqas, etc.
-    "W",   # Pylint warnings
+    "C",    # Pylint conventions
+    "D",    # Documentation formatting
+    "E",    # style stuff, whitespaces
+    "F",    # important pyflakes lints
+    "FURB",
+    "I",    # import sorting
     "N",
     "NPY",
     "PERF",
     "PLE",
     "PLW",
-    "FURB",
+    "RUF",  # Some Ruff-specific lints, unused noqas, etc.
+    "W",    # Pylint warnings
 ]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
@@ -59,6 +59,7 @@ exclude = [
 [lint.isort]
 lines-after-imports = 2
 known-third-party = ["wandb"]
+known-first-party = ["esm"]
 
 [lint.pydocstyle]
 convention = "google"