Merge branch 'main' into Typo-correction-by-Harper

Amanda-dong · web-flow · commit 117e5cd336b1 · 2026-07-22T15:56:56.000+08:00
diff --git a/.github/workflows/code-quality.yml b/.github/workflows/code-quality.yml
@@ -18,14 +18,18 @@ jobs:
       - uses: actions/checkout@v7
 
       - name: Setup Node.js
-        uses: actions/setup-node@v6
+        uses: actions/setup-node@v7
         with:
           node-version: latest
 
       - name: Install pnpm
         uses: pnpm/action-setup@v6
         with:
-          version: latest
+          # Pinned below 11.12.0, whose self-install crashes with
+          # "Cannot use 'in' operator to search for 'integrity' in undefined".
+          # https://github.com/pnpm/action-setup/issues/276
+          # https://github.com/pnpm/pnpm/issues/12959
+          version: 11.11.0
 
       - name: Setup pnpm config
         run: |
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -20,7 +20,11 @@ jobs:
       - name: Install pnpm
         uses: pnpm/action-setup@v6
         with:
-          version: latest
+          # Pinned below 11.12.0, whose self-install crashes with
+          # "Cannot use 'in' operator to search for 'integrity' in undefined".
+          # https://github.com/pnpm/action-setup/issues/276
+          # https://github.com/pnpm/pnpm/issues/12959
+          version: 11.11.0
 
       - name: Install and Build
         run: |
diff --git a/.github/workflows/links.yaml b/.github/workflows/links.yaml
@@ -18,9 +18,14 @@ jobs:
       - name: Install pnpm
         uses: pnpm/action-setup@v6
         with:
-          version: latest
+          # Pinned below 11.12.0, whose self-install crashes with
+          # "Cannot use 'in' operator to search for 'integrity' in undefined".
+          # https://github.com/pnpm/action-setup/issues/276
+          # https://github.com/pnpm/pnpm/issues/12959
+          version: 11.11.0
+
       
-      - uses: actions/setup-node@v6
+      - uses: actions/setup-node@v7
         with:
           node-version: 22
 
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -25,13 +25,29 @@ jobs:
       - name: Install pnpm
         uses: pnpm/action-setup@v6
         with:
-          version: latest
+          # Pinned below 11.12.0, whose self-install crashes with
+          # "Cannot use 'in' operator to search for 'integrity' in undefined".
+          # https://github.com/pnpm/action-setup/issues/276
+          # https://github.com/pnpm/pnpm/issues/12959
+          version: 11.11.0
+
+      # npm (not pnpm) is intentional: remark-cli is installed globally by the
+      # action at /usr/local/lib/node_modules/. pnpm's global store is not on
+      # that resolution path, so remark-cli would fall back to resolving
+      # remark-mdx from the project's node_modules, where @mdx-js/react pulls
+      # in mdast-util-mdx-jsx@3 — incompatible with remark-cli@10's bundled
+      # unified v10 stack. npm -g puts remark-mdx@2 next to remark-cli so the
+      # versions stay compatible. install_deps: false prevents the action from
+      # running npm install and reintroducing the incompatible project deps.
+      - name: Install remark-mdx globally
+        run: npm install -g remark-mdx@2
 
       - name: remark-lint
         uses: reviewdog/action-remark-lint@v5
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          reporter: github-pr-check
+          reporter: github-pr-review
           fail_level: "warning"
           level: "warning"
-          remark_args: "--use=remark-preset-lint-recommended --use=remark-mdx"
+          install_deps: false
+          remark_args: "--use=remark-preset-lint-recommended --use=remark-mdx --ext .md,.mdx"
diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml
@@ -28,7 +28,11 @@ jobs:
       - name: Install pnpm
         uses: pnpm/action-setup@v6
         with:
-          version: latest
+          # Pinned below 11.12.0, whose self-install crashes with
+          # "Cannot use 'in' operator to search for 'integrity' in undefined".
+          # https://github.com/pnpm/action-setup/issues/276
+          # https://github.com/pnpm/pnpm/issues/12959
+          version: 11.11.0
 
       - run: echo "PREVIEW_PATH=pr-preview/pr-${{ github.event.number }}" >> "$GITHUB_ENV"
 
diff --git a/.github/workflows/spellcheck.yaml b/.github/workflows/spellcheck.yaml
@@ -17,6 +17,6 @@ jobs:
       uses: actions/checkout@v7
       
     - name: Spell Check Repo
-      uses: crate-ci/typos@v1.47.2
+      uses: crate-ci/typos@v1.48.0
       with:
         files: docs/**/**/*.md docs/**/**/*.mdx
diff --git a/.github/workflows/update-lockfiles.yml b/.github/workflows/update-lockfiles.yml
@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v7
       - name: Set up pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@v0.10.0
         with:
           run-install: false
 
diff --git a/.memsearch/.index-state.json b/.memsearch/.index-state.json
@@ -0,0 +1,16 @@
+{
+  "collection": "ms_rts_docs_f1cd2d40",
+  "failed_files": [],
+  "indexed_chunks": 1,
+  "indexed_files": 6,
+  "last_completed_at": "2026-07-21T18:32:57.171985Z",
+  "last_started_at": "2026-07-21T18:32:55.572924Z",
+  "last_success_at": "2026-07-21T18:32:57.171985Z",
+  "milvus_uri": "~/.memsearch/milvus.db",
+  "operation": "index",
+  "paths": ["/Users/ss19980/Documents/packages/rts-docs/.memsearch/memory"],
+  "schema_version": 1,
+  "status": "ok",
+  "total_files": 6,
+  "updated_at": "2026-07-21T18:32:57.171985Z"
+}
diff --git a/blog/2025-05-02-blog-post.mdx b/blog/2025-05-02-blog-post.mdx
@@ -7,6 +7,6 @@ tags: [pythia, genai]
 
 We are pleased to announce that `o4-mini` is now available via Pythia. Here is an overview of the model: https://platform.openai.com/docs/models/o4-mini
 
-<!-- truncate -->
+{/* truncate */}
 
 When compared to `o3-mini`, `o4-mini` adds support for images as inputs. It costs the same as o3-mini for regular usage, though the price is lower if you use cached inputs. Thus, this model will now be the default reasoning model we provide and the use of o3-mini is now deprecated.
diff --git a/blog/2025-09-10-blog-post.mdx b/blog/2025-09-10-blog-post.mdx
@@ -8,6 +8,6 @@ tags: [pythia, genai]
 We are pleased to announce that the `claude` (`4.0` and `3.7`) models are now available via Pythia. Here are the overviews for the models:
 https://www.anthropic.com/claude/sonnet, https://www.anthropic.com/claude/opus
 
-<!-- truncate -->
+{/* truncate */}
 
 With API keys to access Claude, you can also enable Claude API tools like Claude Code. Refer to this guide for more details: https://portkey.ai/docs/integrations/libraries/claude-code#2-integrate-portkey-with-claude-code
diff --git a/docs/hpc/01_getting_started/02_HPC_Accounts/01_getting_and_renewing_an_account.mdx b/docs/hpc/01_getting_started/02_HPC_Accounts/01_getting_and_renewing_an_account.mdx
@@ -85,14 +85,6 @@ HPC bulk accounts request is disabled for HPC sponsors.
 Accounts created for courses last until the end of the semester, rather than a full year.
 :::
 
-<!---
-## Getting an account with one of NYU partners
-
-\[NYU partners with many state and national facilities](**TODO:link to list**) with a variety of HPC systems and expertise. 
-
-[Contact us](email:hpc@nyu.edu) for assistance setting up a collaboration with any of these.
---->
-
 ## Non-NYU Researchers
 
 If you are collaborating with NYU researchers you will need to obtain **affiliate** status before applying for an NYU HPC account. A full-time NYU faculty member must sponsor a non-NYU collaborator for affiliate status.
diff --git a/docs/hpc/01_getting_started/03_Slurm_Accounts/04_requesting_an_allocation.mdx b/docs/hpc/01_getting_started/03_Slurm_Accounts/04_requesting_an_allocation.mdx
@@ -22,7 +22,7 @@ If you scroll down, you'll see "+Request Resource Allocation" button.
 
 After clicking "+Request Resource Allocation", you'll see a list of resources you can request. All projects can request access to Torch, which provides access to the cluster. However, depending on the school the project is affiliated with, high priority resources may be available.
 
-:::info Available resource for each school:
+:::info[Available resource for each school:]
 <Tabs>
   <TabItem value="tandon" label="Tandon">
     -   **tandon_advanced**: includes both A100, H100 and H200 GPUs
@@ -32,6 +32,7 @@ After clicking "+Request Resource Allocation", you'll see a list of resources yo
     -   **courant**: L40s and H200 GPUs 
     -   **lpinto**: stakeholder L40s GPUs
     -   **bpeher**: stakeholder H200 GPUs
+    -   **lzanna**: stakeholder RTXPro 6000 GPUs
   </TabItem>
   <TabItem value="cds" label="Center for Data Science">
     -   **cilvr**: A100 GPUs    
@@ -40,7 +41,10 @@ After clicking "+Request Resource Allocation", you'll see a list of resources yo
   </TabItem>
   <TabItem value="artscience" label="Arts & Science">
     -   **chemistry**: A100 GPUs for use by Chemistry Simmons Center PIs
-  </TabItem>
+    -   **humanities**: RTX Pro 6000 GPUs
+    -   **economics**: RTX Pro 6000 GPUs
+    -   **xwang**: stakeholder RTXPro 6000 GPUs
+    </TabItem>
 </Tabs>
 :::
 
diff --git a/docs/hpc/03_storage/02_data_transfers.md b/docs/hpc/03_storage/02_data_transfers.md
@@ -25,6 +25,7 @@ logout
 ## Tools for Data Transfer
 
 ### Linux & Mac Tools
+
 #### `scp` and `rsync`
 :::warning
 Please use Data Transfer Nodes (DTNs) with these tools. While one can transfer data while on login nodes, it is  considered a bad practice because it can degrade the node's performance.
diff --git a/docs/hpc/05_submitting_jobs/01_slurm_submitting_jobs.md b/docs/hpc/05_submitting_jobs/01_slurm_submitting_jobs.md
@@ -1,10 +1,10 @@
 # Submitting Jobs on Torch
 
-:::tip Beginner tutorial available
+:::tip[Beginner tutorial available]
 If you are new to using HPC resources and would like to learn about the principles of using the `SLURM` scheduler for submitting batch jobs, please refer to [this section](../13_tutorial_intro_hpc/04_scheduler_fundamentals.mdx). It focuses on the specifics of the Torch cluster and assumes familiarity with the tutorial.
 :::
 
-:::warning Active allocation in the HPC projects portal
+:::warning[Active allocation in the HPC projects portal]
 An active allocation in the HPC projects portal is needed to submit any jobs on Torch. For more information on how to get one, please refer to [this section](../../hpc/01_getting_started/03_Slurm_Accounts/02_hpc_project_management_portal.mdx). All job submissions must include the `--account` parameter. On Torch, you can list the SLURM accounts you have access to by running the command [`my_slurm_accounts`](https://services.rt.nyu.edu/docs/hpc/tools_and_software/utils/#my_slurm_accounts).
 ::: 
 
diff --git a/docs/hpc/07_containers/04_apptainer_with_uv.mdx b/docs/hpc/07_containers/04_apptainer_with_uv.mdx
@@ -0,0 +1,131 @@
+# Apptainer with `uv`
+
+## Overview
+
+This page describes a workflow for using `uv` with an Apptainer overlay on Torch. Rather than installing packages directly into the container image, both `uv` and the Python environment are stored inside the writable overlay (`/ext3`), allowing the environment to persist across container sessions while leaving the base container unchanged.
+
+This guide assumes you have already created an overlay and know how to launch it.
+
+## `uv` vs. `conda`
+
+`uv` is a fast replacement for pip that can install an environment entirely into the overlay without any base image modifications. `uv` manages both Python version installation and package dependencies in a standard `.venv` under `/ext3`, keeping the environment self-contained and reproducible via a lockfile. Prefer `conda` if your project requires `conda-forge` packages or is already defined by an `environment.yml`.
+
+## Install `uv`
+
+Launch an Apptainer container with your overlay mounted in read-write mode:
+
+```bash
+
+apptainer exec --fakeroot \
+
+    --overlay overlay-15GB-500K.ext3:rw \
+
+    /share/apps/images/ubuntu-22.04.2.sif \
+
+    /bin/bash
+
+```
+
+Inside the container, install `uv` into the overlay:
+
+```bash
+
+curl -LsSf https://astral.sh/uv/install.sh | \
+
+env UV_INSTALL_DIR="/ext3/.uv" sh
+
+```
+
+Load `uv` into the current shell:
+
+```bash
+
+source /ext3/.uv/env
+
+```
+
+Configure where `uv` should install Python versions:
+
+```bash
+
+export UV_PYTHON_INSTALL_DIR="/ext3/.uv/python"
+
+```
+
+## Configure the Environment
+
+Configure where the project virtual environment should be stored:
+
+```bash
+
+export UV_PROJECT_ENVIRONMENT="/ext3/.venv"
+
+```
+
+If your project already contains a `pyproject.toml` file, install the project dependencies:
+
+```bash
+
+uv sync
+
+```
+
+## Create an Activation Script
+
+Create `/ext3/env.sh`:
+
+```bash
+
+touch /ext3/env.sh
+
+nano /ext3/env.sh
+
+```
+
+Add the following:
+
+```bash
+
+#!/bin/bash
+
+unset -f which
+
+source /ext3/.uv/env
+
+export UV_PYTHON_INSTALL_DIR="/ext3/.uv/python"
+
+export UV_PROJECT_ENVIRONMENT="/ext3/.venv"
+
+source /ext3/.venv/bin/activate
+
+export PATH=/ext3/.venv/bin:$PATH
+
+export PYTHONPATH=/ext3/.venv/bin:$PATH
+
+```
+
+## Reusing the Environment
+
+The next time you start the same container with the same overlay:
+
+```bash
+
+apptainer exec --fakeroot \
+
+    --overlay overlay-15GB-500K.ext3:rw \
+
+    /share/apps/images/ubuntu-22.04.2.sif \
+
+    /bin/bash
+
+```
+
+Reactivate the environment:
+
+```bash
+
+source /ext3/env.sh
+
+```
+
+This workflow also works with Open OnDemand JupyterLab.
diff --git a/docusaurus.config.ts b/docusaurus.config.ts
@@ -209,7 +209,7 @@ const config: Config = {
 
   future: {
     v4: true, // opt-in to v4 to ease transition in the future
-    experimental_faster: {
+    faster: {
       rspackBundler: true, // required flag
       rspackPersistentCache: true, // new flag
     },
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -68,9 +68,7 @@ const eslintConfig = tseslint.config(
 
   {
     settings: {
-      react: {
-        version: "detect",
-      },
+      react: { version: "19" }, // Avoids auto-detection crash
     },
   },
 
diff --git a/package.json b/package.json
diff --git a/pixi.lock b/pixi.lock
diff --git a/pixi.toml b/pixi.toml
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
diff --git a/scripts/storage-finder-data-generator/config.ts b/scripts/storage-finder-data-generator/config.ts
diff --git a/src/pages/storage-finder.tsx b/src/pages/storage-finder.tsx
