Benjamin L. Stewart

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tagslinux, omarchy, guide
notes

6 min read

Set Up Obsidian on an Omarchy PC with Quartz Publishing

# Set Up Obsidian on an Omarchy PC with Quartz Publishing

This guide documents my working Obsidian setup on an Omarchy PC.

The setup uses:

- **Omarchy / Arch Linux**
- **Obsidian**
- An Obsidian vault stored on an external SanDisk drive
- GitHub for version control and publishing
- Quartz v5 for the public website
- Obsidian Shell Commands for one-key publishing

My public Quartz site is:

`https://bnleez1.github.io/PKM/`

---

# 1. Overall Setup

The publishing workflow is:

```text
Obsidian vault on SanDisk
        ↓
60 Public/Website
        ↓
~/Projects/PKM/content
        ↓
GitHub repository: bnleez1/PKM
        ↓
branch: v5
        ↓
GitHub Actions / Quartz
        ↓
https://bnleez1.github.io/PKM/

Only the following folder is published:

60 Public/Website

The rest of the Obsidian vault remains private.

2. Obsidian Vault Location

On the Office Omarchy PC, the vault is located at:

/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian

Set a temporary shell variable when needed:

VAULT="/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian"

Verify that the vault exists:

ls -ld "$VAULT"

Verify the public website folder:

ls -ld "$VAULT/60 Public/Website"

Both commands should return directory information without errors.

3. Open the Vault in Obsidian

Open Obsidian.

Choose:

Open folder as vault

Select:

/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian

Obsidian should now use the SanDisk vault directly.

Do not create a second copy of the vault on the internal drive unless intentionally changing the setup.

4. Verify Required Publishing Tools

Check the required tools:

git --version
gh --version
node --version
npm --version
rsync --version | head -n 1

The working Omarchy setup had:

Git
GitHub CLI
Node.js
npm
rsync

If needed, install the main tools with:

sudo pacman -S --needed git github-cli nodejs npm rsync

5. Authenticate GitHub

Check authentication:

gh auth status

If not authenticated:

gh auth login --web --git-protocol https

Follow the browser authentication procedure.

Then configure Git to use the GitHub CLI credentials:

gh auth setup-git

Verify:

gh auth status

The account should show:

bnleez1

6. Clone the Existing Quartz Repository

Do not create a new Quartz site.

The existing configured repository should be cloned instead.

Create the project directory:

mkdir -p "$HOME/Projects"

Clone the v5 branch:

git clone \
  --branch v5 \
  https://github.com/bnleez1/PKM.git \
  "$HOME/Projects/PKM"

Verify:

git -C "$HOME/Projects/PKM" status --short --branch

Expected:

## v5...origin/v5

Check the branch:

git -C "$HOME/Projects/PKM" branch --show-current

Expected:

v5

Check the remote:

git -C "$HOME/Projects/PKM" remote -v

It should point to:

https://github.com/bnleez1/PKM.git

7. Verify the Publishing Scripts

The Quartz repository already contains the required scripts:

~/Projects/PKM/scripts/publish-public.sh
~/Projects/PKM/scripts/sync-public.sh

Check them:

ls -lh "$HOME/Projects/PKM/scripts/"

They should be executable.

If necessary:

chmod +x \
  "$HOME/Projects/PKM/scripts/publish-public.sh" \
  "$HOME/Projects/PKM/scripts/sync-public.sh"

8. Create the Machine-Specific Publishing Configuration

The same publishing scripts can be used on different computers because the vault location is stored separately.

Create:

~/.config/pkm-publish.conf

Run:

mkdir -p "$HOME/.config"

cat > "$HOME/.config/pkm-publish.conf" <<'EOF'
VAULT="/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian"
PROJECT="$HOME/Projects/PKM"
BRANCH="v5"
REMOTE="origin"
EOF

Verify:

cat "$HOME/.config/pkm-publish.conf"

It should contain:

VAULT="/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian"
PROJECT="$HOME/Projects/PKM"
BRANCH="v5"
REMOTE="origin"

9. Verify All Paths

Run:

source "$HOME/.config/pkm-publish.conf"

test -d "$VAULT" \
  && echo "Vault: OK" \
  || echo "Vault: NOT FOUND"

test -d "$VAULT/60 Public/Website" \
  && echo "Public Website: OK" \
  || echo "Public Website: NOT FOUND"

test -d "$PROJECT/.git" \
  && echo "Quartz repo: OK" \
  || echo "Quartz repo: NOT FOUND"

Expected:

Vault: OK
Public Website: OK
Quartz repo: OK

10. How Publishing Works

The source content is:

$VAULT/60 Public/Website

The Quartz destination is:

~/Projects/PKM/content

The publishing scripts synchronize the public files into the Quartz repository.

They do not publish the entire Obsidian vault.

11. Test the Synchronization Script

Run:

cd "$HOME/Projects/PKM"

./scripts/sync-public.sh

The script can show the changes that will be made before synchronizing.

Review the proposed changes carefully.

This is especially useful after setting up a new machine.

12. Test Full Publishing from the Terminal

Run:

cd "$HOME/Projects/PKM"

./scripts/publish-public.sh

This should:

  1. Read the Office-PC vault location.
  2. Synchronize 60 Public/Website.
  3. Update the Quartz content folder.
  4. Commit changes when necessary.
  5. Push them to the v5 branch.
  6. Trigger the GitHub/Quartz publishing workflow.

Check recent GitHub Actions runs with:

gh run list \
  --repo bnleez1/PKM \
  --limit 5

The finished site should appear at:

https://bnleez1.github.io/PKM/

13. Configure Obsidian Shell Commands

Install or enable the Shell Commands community plugin in Obsidian.

Open:

Settings → Shell Commands

Create a command called:

Publish Website to GitHub

Use:

bash -lc "$HOME/Projects/PKM/scripts/publish-public.sh"

Assign the keyboard shortcut:

Ctrl + Alt + P

This makes publishing available directly from Obsidian.

14. Fix the Omarchy/Fcitx5 Preedit Conflict

Omarchy’s Fcitx5 input system also uses:

Ctrl + Alt + P

for toggling Preedit.

This can cause a popup such as:

Preedit
Preedit disabled

when trying to publish from Obsidian.

The solution is to move the Fcitx5 shortcut somewhere else.

Create or replace:

~/.config/fcitx5/config

with:

mkdir -p "$HOME/.config/fcitx5"

cat > "$HOME/.config/fcitx5/config" <<'EOF'
[Hotkey/TogglePreedit]
0=Control+Alt+Shift+F12
EOF

Verify:

cat "$HOME/.config/fcitx5/config"

Expected:

[Hotkey/TogglePreedit]
0=Control+Alt+Shift+F12

Restart Fcitx5:

pkill fcitx5
sleep 2
fcitx5 -d

The shortcuts are now:

Obsidian Publish
Ctrl + Alt + P

Fcitx5 Preedit
Ctrl + Alt + Shift + F12

15. Optional: Preview Quartz Locally

Move to the project:

cd "$HOME/Projects/PKM"

Install dependencies if this is the first setup:

npm ci

Then run:

npx quartz build --serve

Open:

http://localhost:8080

Stop the preview with:

Ctrl + C

16. Normal Daily Workflow

My normal workflow is now very simple.

Edit

Open Obsidian and work normally in the SanDisk vault.

Public material

Place material intended for the website somewhere under:

60 Public/Website

Publish

Press:

Ctrl + Alt + P

Obsidian runs:

Publish Website to GitHub

The publishing script handles the synchronization and GitHub push.

17. Important Rules

Do not run npx quartz create

The Quartz repository is already configured.

Creating a new Quartz installation can overwrite or conflict with the existing configuration.

Always clone:

https://github.com/bnleez1/PKM.git

and use branch:

v5

Do not publish the entire vault

Only:

60 Public/Website

belongs in Quartz content.

Private folders such as notes, people, research material, and other vault content should remain outside the public website tree.

Keep machine-specific paths out of GitHub

Different computers can use different vault locations.

Store the local path in:

~/.config/pkm-publish.conf

rather than hard-coding the external-drive path into the publishing scripts.

18. Quick Diagnostic

If publishing stops working, run:

echo "========== VAULT =========="
test -d "/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian" \
  && echo "Vault: OK" \
  || echo "Vault: NOT FOUND"

echo
echo "========== PUBLIC SOURCE =========="
test -d "/mnt/usb-SanDisk_Extreme_55AE_323432373153343031333038-0:0-part1/Obsidian/60 Public/Website" \
  && echo "Public Website: OK" \
  || echo "Public Website: NOT FOUND"

echo
echo "========== QUARTZ =========="
git -C "$HOME/Projects/PKM" status --short --branch

echo
echo "========== BRANCH =========="
git -C "$HOME/Projects/PKM" branch --show-current

echo
echo "========== REMOTE =========="
git -C "$HOME/Projects/PKM" remote -v

echo
echo "========== NODE =========="
node --version

echo
echo "========== GITHUB =========="
gh auth status

echo
echo "========== SCRIPTS =========="
ls -lh \
  "$HOME/Projects/PKM/scripts/sync-public.sh" \
  "$HOME/Projects/PKM/scripts/publish-public.sh"

echo
echo "========== CONFIG =========="
cat "$HOME/.config/pkm-publish.conf"

A healthy system should show:

Vault: OK
Public Website: OK
branch: v5
GitHub authenticated as bnleez1
publishing scripts present
pkm-publish.conf present

Final Setup

The completed Omarchy Obsidian system is:

SanDisk
└── Obsidian
    └── 60 Public
        └── Website
              │
              ▼
       sync-public.sh
              │
              ▼
~/Projects/PKM/content
              │
              ▼
     publish-public.sh
              │
              ▼
        GitHub / v5
              │
              ▼
          Quartz
              │
              ▼
https://bnleez1.github.io/PKM/

And publishing from Obsidian requires only:

Ctrl + Alt + P

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