NYU-RTS · s-sajid-ali · Sep 14, 2026 · Sep 9, 2026 · Sep 9, 2026 · Sep 9, 2026
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -16,56 +16,29 @@ jobs:
   remark-lint:
     name: runner / remark-lint
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v7
-        with:
-          fetch-depth: 0
 
-      - name: Install pnpm
-        uses: pnpm/action-setup@v6
+      # 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 the remark plugins next to remark-cli so
+      # the versions stay compatible.
+      #
+      # install_deps: false prevents the action from running npm install and
+      # reintroducing the incompatible project dependencies.
+      - name: Install remark plugins globally
+        run: npm install -g remark-mdx@2 remark-lint-no-undefined-references@4 remark-directive@3 remark-frontmatter@4
+
+      - name: remark-lint
+        uses: reviewdog/action-remark-lint@v5
         with:
-          # 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 remark plugins and reviewdog
-        run: |
-          npm install -g remark-cli@10 remark-lint@10 remark-preset-lint-recommended remark-mdx@2 remark-lint-no-undefined-references@4 remark-directive@3
-          curl -sfL https://raw.githubusercontent.com/reviewdog/reviewdog/master/install.sh | sh -s -- -b /tmp
-            # reviewdog/action-remark-lint runs remark against a directory, but this
-
-      # repository currently has existing repo-wide remark warnings. Because this
-      # workflow fails on warnings, running remark on the whole repository would
-      # fail PRs for warnings unrelated to the modified files.
-      # Until the existing repo-wide warnings are cleaned up, lint only Markdown/MDX
-      # files changed in the current PR and pipe the result to reviewdog manually.
-      # See the follow-up cleanup issue before reverting this back to
-      # reviewdog/action-remark-lint.
-
-      - name: Find changed Markdown files
-        id: changed_files
-        run: |
-          git fetch origin ${{ github.base_ref }}
-          git diff --name-only --diff-filter=ACMRT origin/${{ github.base_ref }}...HEAD -- '*.md' '*.mdx' > changed-markdown-files.txt
-
-          if [ -s changed-markdown-files.txt ]; then
-            echo "has_changed_files=true" >> "$GITHUB_OUTPUT"
-            cat changed-markdown-files.txt
-          else
-            echo "has_changed_files=false" >> "$GITHUB_OUTPUT"
-            echo "No changed Markdown files."
-          fi
-
-      - name: remark-lint changed files
-        if: steps.changed_files.outputs.has_changed_files == 'true'
-        run: |
-          remark $(cat changed-markdown-files.txt) --use=remark-preset-lint-recommended --use=remark-mdx --use=remark-directive --ext .md,.mdx 2>&1 \
-            | sed 's/\x1b\[[0-9;]*m//g' \
-            | /tmp/reviewdog -f=remark-lint \
-                -name="remark-lint" \
-                -reporter="github-pr-review" \
-                -filter-mode="nofilter" \
-                -fail-level="warning" \
-                -level="warning"
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          reporter: github-pr-review
+          fail_level: "warning"
+          level: "warning"
+          install_deps: false
+          remark_args: "--use=remark-preset-lint-recommended --use=remark-mdx --use=remark-directive --use=remark-frontmatter --ext .md,.mdx"
diff --git a/.memsearch/.index-state.json b/.memsearch/.index-state.json
diff --git a/docs/genai/01_getting_started/01_intro.mdx b/docs/genai/01_getting_started/01_intro.mdx
@@ -5,8 +5,8 @@ If you looking to access LLMs for non-research workflows, please reach out to th
 :::
 
 Welcome to Pythia, the generative AI platform for research workflows. As part of the Pythia platform, the following capabilities are offered:
-- [Access to externally hosted LLMs](../01_getting_started/02_llm_gateway.mdx)
-- [HPC resources for fine tuning LLMs](../../hpc/08_ml_ai_hpc/05_llm_fine_tuning.md)
+-   [Access to externally hosted LLMs](../01_getting_started/02_llm_gateway.mdx)
+-   [HPC resources for fine tuning LLMs](../../hpc/08_ml_ai_hpc/05_llm_fine_tuning.md)
 
 :::info[Personal use]
 If you want to access NYU provided LLMs for personal use, proceed to https://gemini.google.com/app with your NYU credentials. 

diff --git a/docs/genai/04_how_to_guides/02_embeddings.mdx b/docs/genai/04_how_to_guides/02_embeddings.mdx
@@ -43,9 +43,9 @@ and gives the following response:
 ## Applications of Embeddings
 
 Embeddings are typically used for:
--  retrieval-augmented generation
--  search
--  classification
+-   retrieval-augmented generation
+-   search
+-   classification
 
 :::info
 Embeddings are typically stored in a *vector* database which is designed for efficient storage and fast retrieval of vectors.

diff --git a/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx b/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx
@@ -5,8 +5,8 @@ For an in-depth overview of RAG and Jupyter notebook examples, please access the
 :::
 
 Large Language Models only know about the data they were trained upon and do not have the context needed to be effective at answering questions based on:
-- private datasets
-- newer knowledge past the cutoff date (i.e. the date at which data collection was frozen)
+-   private datasets
+-   newer knowledge past the cutoff date (i.e. the date at which data collection was frozen)
 
 To get around this issue, one of the most popular techniques is Retrieval-augmented generation, the most basic version of which is outlined below:
 

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
@@ -121,7 +121,7 @@ Linux clients are not officially supported, however we were able to successfully
       apt-get install openconnect
       sudo openconnect -b vpn.nyu.edu
       ```
-  - When prompted follow the instructions and provide your netID, password, and authenticate with ('push', 'phone1' or 'sms')
+  -   When prompted follow the instructions and provide your netID, password, and authenticate with ('push', 'phone1' or 'sms')
   This method was tested on few Linux distributions and settings however is not guaranteed to work in future.
   </TabItem>
 </Tabs>

diff --git a/docs/hpc/03_storage/08_sharing_data_on_hpc.mdx b/docs/hpc/03_storage/08_sharing_data_on_hpc.mdx
@@ -88,14 +88,14 @@ g-DEPT-LABNAME
 Once you have a group assigned, managers of the group can use the `ipa` commands to manage members via the login nodes.
 
 Relevant user commands include:
-- `ipa group-add-member`: Add members to a group.
-  - Example:
+-   `ipa group-add-member`: Add members to a group.
+    -   Example:
 `ipa group-add-member GROUP-NAME --users='NETID'`
-- `ipa group-add-member-manager`: Add users that can manage members of this group.
-  - Example:
+-   `ipa group-add-member-manager`: Add users that can manage members of this group.
+    -   Example:
 `ipa group-add-member-manager GROUP-NAME --users='NETID'`
-- `ipa group-find`: Search for groups.
-  - Example:
+-   `ipa group-find`: Search for groups.
+    -   Example:
 ```
 ipa group-find test
 ----------------
@@ -111,16 +111,16 @@ ipa group-find test
 Number of entries returned 2
 ----------------------------
 ```
-- `ipa group-remove-member`: Remove members from a group.
-  - Example:
+-   `ipa group-remove-member`: Remove members from a group.
+    -   Example:
 `ipa group-remove-member --users=NETID`
-- `ipa group-remove-member-manager`: Remove users that can manage members of this group.
-  - Example:
+-   `ipa group-remove-member-manager`: Remove users that can manage members of this group.
+    -   Example:
 `ipa group-remove-member-manager --users=NETID`
-- `ipa group-show`: Display information about a named group.
-  - Example:
+-   `ipa group-show`: Display information about a named group.
+    -   Example:
 `ipa group-show GROUP-NAME`
-  - Example:
+    -   Example:
 ```
 [mdw303@torch-login-1 ~]$ ipa group-show g-hpc-mdw303test
   Group name: g-hpc-mdw303test

diff --git a/docs/hpc/06_tools_and_software/05_r_packages_with_renv.mdx b/docs/hpc/06_tools_and_software/05_r_packages_with_renv.mdx
@@ -195,8 +195,8 @@ renv::init()
 
 ### What to save/publish/commit with Git
 In order to have your work reproducible by you and/or others:
-- save and/or commit your code in git
-- be sure to include `renv.lock` (which lists all packages and versions that you use including the version of R)
+-   save and/or commit your code in git
+-   be sure to include `renv.lock` (which lists all packages and versions that you use including the version of R)
 
 ### Migrating from Packrat
 The `renv` package has replaced the now deprecated `Packrat` package. The `renv::migrate()` function makes it possible to migrate projects from `Packrat` to `renv`. See the ?migrate documentation for more details. In essence, calling `renv::migrate("<project path>")` will be enough to migrate the `Packrat` library and lockfile such that they can then be used by `renv`.

diff --git a/docs/hpc/06_tools_and_software/09_vscode_remote_ssh_torch.mdx b/docs/hpc/06_tools_and_software/09_vscode_remote_ssh_torch.mdx
@@ -21,8 +21,8 @@ Ensure that you SSH client has been configured [as described here](../02_connect
 Install the VSCode Remote - SSH extension. 
 
 Configure Remote - SSH settings:
-1. Enable `Remote.SSH: Lockfiles In Tmp`
-2. Unable `Remote.SSH: Use Flock`
+1.  Enable `Remote.SSH: Lockfiles In Tmp`
+2.  Unable `Remote.SSH: Use Flock`
 
 Because Torch requires Microsoft device authentication during SSH login, VSCode may time out before you finish entering the device code. If this happens, search for Remote.SSH: Connect Timeout and set it to 120.
 

diff --git a/docs/hpc/09_ood/03_matlab_proxy.mdx b/docs/hpc/09_ood/03_matlab_proxy.mdx
@@ -19,10 +19,10 @@ Please be aware that when you run each version of Matlab for the first time, the
 Be careful not to go over your quota for `/home`.  You can find your current usage with the `myquota` command.  Please see our [Storage documentation](../03_storage/01_intro_and_data_management.mdx) for details about your storage options.
 :::
 Each time you start it up after that it will set its working directory to the last directory you were in.  If you'd like to change this behavior, so that you always start at the same directory:
-1.   click on `ENVIRONMENT` in your `Home` panel
-1.   select `Preferences`
-1.   select `Current Folder`
-1.   select `initial working folder preferences`
+1.  click on `ENVIRONMENT` in your `Home` panel
+1.  select `Preferences`
+1.  select `Current Folder`
+1.  select `initial working folder preferences`
 
 This will allow you to set the full path of the initial working folder you would prefer.  Be sure to hit the `Apply` button, so your changes are applied.
 ::::

diff --git a/docs/hpc/12_tutorial_intro_shell_hpc/03_moving_looking.mdx b/docs/hpc/12_tutorial_intro_shell_hpc/03_moving_looking.mdx
@@ -42,10 +42,10 @@ $ whoami
 
 More specifically, when we type `whoami` in the shell:
 
-1.   finds a program called whoami,
-1.   runs that program,
-1.   displays that program’s output, then
-1.   displays a new prompt to tell us that it’s ready for more commands.
+1.  finds a program called whoami,
+1.  runs that program,
+1.  displays that program’s output, then
+1.  displays a new prompt to tell us that it’s ready for more commands.
 
 Next, let’s find out where we are by running a command called `pwd` (which stands for “print working directory”). (“Directory” is another word for “folder”). At any moment, our current working directory (where we are) is the directory that the computer assumes we want to run commands in unless we explicitly specify something else. Here, the computer’s response is `/home/<NetID>`, which is `<NetID>`'s home directory. Note that the location of your home directory may differ from system to system.
 ```bash
@@ -64,7 +64,7 @@ $ ls
 <summary>
 :::info[**Differences between remote and local system**]
 Open a second terminal window on your local computer and run the `ls` command without logging in remotely. What differences do you see? <br />
-**[click to see the solution]**
+**\[click to see the solution\]**
 :::
 </summary>
 
@@ -236,7 +236,7 @@ Try 'ls --help' for more information.
 :::info[Looking at documentation]
 Looking at the man page for `ls` or using `ls --help`, what does the `-h` (`--human-readable`) option do?
 :::
-**[Click for Solution]**
+**\[Click for Solution\]**
 </summary>
 :::tip[Solution]
 When used with the `-l` option, use unit suffixes: Byte, Kilobyte, Megabyte, Gigabyte, Terabyte and Petabyte in order to reduce the number of digits to four or fewer using base 2 for sizes.  This option is not defined in IEEE Std 1003.1-2008 (“POSIX.1”).
@@ -248,28 +248,28 @@ When used with the `-l` option, use unit suffixes: Byte, Kilobyte, Megabyte, Gig
 :::info[Absolute vs Relative Paths]
 Starting from `/Users/amanda/data/`, which of the following commands could Amanda use to navigate to her home directory, which is `/Users/amanda`?
 
-1.   `cd .`
-1.   `cd /`
-1.   `cd /home/amanda`
-1.   `cd ../..`
-1.   `cd ~`
-1.   `cd home`
-1.   `cd ~/data/..`
-1.   `cd`
-1.   `cd ..`
+1.  `cd .`
+1.  `cd /`
+1.  `cd /home/amanda`
+1.  `cd ../..`
+1.  `cd ~`
+1.  `cd home`
+1.  `cd ~/data/..`
+1.  `cd`
+1.  `cd ..`
 :::
-**[Click for Solution]**
+**\[Click for Solution\]**
 </summary>
 :::tip[Solution]
-1.   No: `.` stands for the current directory.
-1.   No: `/` stands for the root directory.
-1.   No: Amanda’s home directory is `/Users/amanda`.
-1.   No: this goes up two levels, i.e. ends in `/Users`.
-1.   Yes: `~` stands for the user’s home directory, in this case `/Users/amanda`.
-1.   No: this would navigate into a directory home in the current directory if it exists.
-1.   Yes: unnecessarily complicated, but correct.
-1.   Yes: shortcut to go back to the user’s home directory.
-1.   Yes: goes up one level.
+1.  No: `.` stands for the current directory.
+1.  No: `/` stands for the root directory.
+1.  No: Amanda’s home directory is `/Users/amanda`.
+1.  No: this goes up two levels, i.e. ends in `/Users`.
+1.  Yes: `~` stands for the user’s home directory, in this case `/Users/amanda`.
+1.  No: this would navigate into a directory home in the current directory if it exists.
+1.  Yes: unnecessarily complicated, but correct.
+1.  Yes: shortcut to go back to the user’s home directory.
+1.  Yes: goes up one level.
 :::
 </details>
 
@@ -278,10 +278,10 @@ Starting from `/Users/amanda/data/`, which of the following commands could Amand
 :::info[Relative Path Resolution]
 Using the filesystem diagram below, if `pwd` displays `/Users/thing`, what will `ls -F ../backup` display?
 
-1.   `../backup: No such file or directory`
-1.   `2012-12-01 2013-01-08 2013-01-27`
-1.   `2012-12-01/ 2013-01-08/ 2013-01-27/`
-1.   `original/ pnas_final/ pnas_sub/`
+1.  `../backup: No such file or directory`
+1.  `2012-12-01 2013-01-08 2013-01-27`
+1.  `2012-12-01/ 2013-01-08/ 2013-01-27/`
+1.  `original/ pnas_final/ pnas_sub/`
 
 :::
 ```mermaid
@@ -305,13 +305,13 @@ block-beta
     d --> i
     d --> j
 ```
-**[Click for Solution]**
+**\[Click for Solution\]**
 </summary>
 :::tip[Solution]
-1.   No: there is a directory backup in `/Users`.
-1.   No: this is the content of `Users/thing/backup`, but with `..` we asked for one level further up.
-1.   No: see previous explanation.
-1.   Yes: `../backup/` refers to `/Users/backup/`.
+1.  No: there is a directory backup in `/Users`.
+1.  No: this is the content of `Users/thing/backup`, but with `..` we asked for one level further up.
+1.  No: see previous explanation.
+1.  Yes: `../backup/` refers to `/Users/backup/`.
 :::
 </details>
 
@@ -322,18 +322,18 @@ Assuming a directory structure as in the above figure, if `pwd` displays `/Users
 ::::info[Output]
 pnas_sub/ pnas_final/ original/
 ::::
-1.   `ls pwd`
-1.   `ls -r -F`
-1.   `ls -r -F /Users/backup`
-1.   Either #2 or #3 above, but not #1.
+1.  `ls pwd`
+1.  `ls -r -F`
+1.  `ls -r -F /Users/backup`
+1.  Either #2 or #3 above, but not #1.
 
-**[Click for Solution]**
+**\[Click for Solution\]**
 </summary>
 :::tip[Solution]
-1.   No: `pwd` is not the name of a directory.
-1.   Yes: `ls` without directory argument lists files and directories in the current directory.
-1.   Yes: uses the absolute path explicitly.
-1.   Correct: see explanations above.
+1.  No: `pwd` is not the name of a directory.
+1.  Yes: `ls` without directory argument lists files and directories in the current directory.
+1.  Yes: uses the absolute path explicitly.
+1.  Correct: see explanations above.
 :::
 </details>
 
@@ -343,7 +343,7 @@ pnas_sub/ pnas_final/ original/
 What does the command ls do when used with the `-l` and `-h` arguments?
 
 Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.
-<br />**[Click for Solution]**
+<br />**\[Click for Solution\]**
 :::
 </summary>
 :::tip[Solution]
@@ -360,7 +360,7 @@ The command `ls -t` lists things by time of last change, with most recently chan
 
 In what order does `ls -R -t` display things? **Hint:** `ls -l` uses a long listing format to view timestamps.
 :::
-**[Click for Solution]**
+**\[Click for Solution\]**
 </summary>
 :::tip[Solution]
 The directories are listed alphabetical at each level, the files/directories in each directory are sorted by time of last change.