SiYuan with Docker Compose

What SiYuan needs

Only figures SiYuan's own documentation publishes, each linked to the page it is on. Where the project gives no number, this page does not invent one.

On top of this, Caddy (the reverse proxy in the file) is a single small container.

Which hardware SiYuan has images for

Read from each image's manifest list in its registry (anonymous, read-only) when this page was built. An app counts for a CPU only if every one of its images lists it.

• x86-64 PC or NAS (linux/amd64): every image has a build.
• Raspberry Pi 4/5, 64-bit OS (linux/arm64): every image has a build.
• Raspberry Pi 3 or Zero 2 W, 32-bit OS (linux/arm/v7): every image has a build.

A manifest says an image exists for a CPU, not how well SiYuan runs on it: a build for arm64 or arm/v7 can still be too slow or need more memory than the board has. The RAM and disk SiYuan publishes are in the table above and, for a whole set of apps against a Raspberry Pi, on Will it run on my machine?. A tag like latest can move to a new digest after the date checked.

docker-compose.yml

This is exactly what the builder writes for SiYuan alone on example.org: the official definition with its published ports removed and Caddy added in front. The time zone is Etc/UTC here; the builder uses your browser's. Every ${VARIABLE} is defined in the .env below.

# docker-compose.yml built at dankhost.com for: SiYuan
# Each app block is its official compose definition. Only the names were prefixed with
# the app slug (services, containers, volumes, bind folders, .env variables) so any set of
# apps can share one file; other differences are listed under "Changed:" in each block.
# Only Caddy publishes ports. Secrets live in .env next to this file.

services:
  # ---- Caddy: the one reverse proxy, HTTPS certificates from Let's Encrypt ----
  # Source: https://caddyserver.com/docs/running (checked 2026-09-23)
  # Source: https://github.com/dani-garcia/vaultwarden/wiki/Using-Docker-Compose (checked 2026-09-23)
  # Caddyfile goes in ./caddy/Caddyfile. Fixed address 172.30.0.2 so apps can trust it exactly.
  caddy:
    image: "caddy:2"
    container_name: "caddy"
    restart: "unless-stopped"
    ports:
      - "80:80"
      - "443:443"
      - "443:443/udp"
    volumes:
      - "./caddy:/etc/caddy"
      - "caddy-data:/data"
      - "caddy-config:/config"
    networks:
      proxy:
        ipv4_address: "172.30.0.2"

  # ---- SiYuan (siyuan.example.org) ----
  # Source: https://github.com/siyuan-note/siyuan/blob/master/README.md (checked 2026-10-01)
  # Source: https://hub.docker.com/r/b3log/siyuan (checked 2026-10-01)
  # Changed: Removed the documented '6806:6806' port and the version: "3.9" line; Caddy reaches siyuan-main:6806 on the proxy network.
  #          The host folder /siyuan/workspace becomes ./workspace next to this file, mounted at the same /siyuan/workspace path the command's --workspace names.
  #          The README's ${AuthCode} (the lock screen password) is a generated value in .env, read as ${SIYUAN_ACCESS_AUTH_CODE}: the builder writes .env names in capitals with the app's prefix, and SIYUAN_ACCESS_AUTH_CODE is also the environment variable the README gives for the same password. ${YOUR_USER_PUID} and ${YOUR_USER_PGID} are 1000, the value the README says is used when they are not set, and ${YOUR_TIME_ZONE} is the time zone you pick in the builder.
  siyuan-main:
    image: "b3log/siyuan"
    container_name: "siyuan-main"
    command:
      - "serve"
      - "--workspace=/siyuan/workspace/"
      - "--accessAuthCode=${SIYUAN_ACCESS_AUTH_CODE}"
    volumes:
      - "./siyuan/workspace:/siyuan/workspace"
    restart: "unless-stopped"
    environment:
      TZ: "Etc/UTC"
      PUID: "${SIYUAN_YOUR_USER_PUID}"
      PGID: "${SIYUAN_YOUR_USER_PGID}"
    networks:
      proxy: {}

networks:
  # Pinned so the trusted-proxy address given to each app (172.30.0.2) is exact.
  # If "docker compose up" reports "Pool overlaps", change 172.30.0 here, in Caddy's
  # ipv4_address and in every trusted-proxy value to a free 172.x.0 range.
  proxy:
    ipam:
      config:
        - subnet: "172.30.0.0/24"
          ip_range: "172.30.0.128/25"
          gateway: "172.30.0.1"

volumes:
  caddy-data:
  caddy-config:

Caddyfile save as caddy/Caddyfile

Caddy gets and renews the HTTPS certificate for siyuan.example.org by itself once the DNS record points at your server and ports 80 and 443 reach it.

# Caddyfile built at dankhost.com. Save it as ./caddy/Caddyfile next to docker-compose.yml.
# Caddy gets and renews a Let's Encrypt certificate for each name below by itself,
# once the DNS records point at this server and ports 80 and 443 reach it.

# SiYuan
siyuan.example.org {
	reverse_proxy siyuan-main:6806
}

Already running nginx, Nginx Proxy Manager, Caddy or Traefik? The reverse-proxy settings SiYuan needs, for all four, each cited to SiYuan's own docs.

.env

The secret is left blank here on purpose: a password printed on a public page is the same for everyone who copies it. The builder fills it with random letters and digits made in your browser.

# .env for SiYuan, from dankhost.com/app/siyuan/. Fill the blank secret before starting.
# Keep this file private (chmod 600).

# SiYuan
# 24 random letters and digits: the builder fills this in your browser
SIYUAN_ACCESS_AUTH_CODE=
SIYUAN_YOUR_USER_PUID=1000
SIYUAN_YOUR_USER_PGID=1000

Changes from the official file

Besides prefixing every service, container, volume, folder and variable with siyuan (so any set of apps can share one file), these are all the differences from what the project documents:

• Removed the documented '6806:6806' port and the version: "3.9" line; Caddy reaches siyuan-main:6806 on the proxy network.
• The host folder /siyuan/workspace becomes ./workspace next to this file, mounted at the same /siyuan/workspace path the command's --workspace names.
• The README's ${AuthCode} (the lock screen password) is a generated value in .env, read as ${SIYUAN_ACCESS_AUTH_CODE}: the builder writes .env names in capitals with the app's prefix, and SIYUAN_ACCESS_AUTH_CODE is also the environment variable the README gives for the same password. ${YOUR_USER_PUID} and ${YOUR_USER_PGID} are 1000, the value the README says is used when they are not set, and ${YOUR_TIME_ZONE} is the time zone you pick in the builder.

Notes for SiYuan behind the proxy

• Open https://siyuan.example.org and unlock it with SIYUAN_ACCESS_AUTH_CODE from .env. The README asks you to be sure to change this password, "otherwise anyone can access your data".
• Before the first start: mkdir -p ./siyuan/workspace && sudo chown -R 1000:1000 ./siyuan/workspace. The README's User Permissions section: the workspace folder must belong to PUID:PGID.
• Served from Docker, SiYuan works in the browser only. The README lists what that leaves out: no desktop or mobile app connections, no export to PDF, HTML or Word, and no Markdown file import.
• The README asks a reverse proxy to pass the WebSocket at /ws and to keep the original Host header. Caddy and Traefik do both without extra settings.
• The README's compose names b3log/siyuan with no tag, which is 'latest'.

Back it up

SiYuan publishes no backup procedure for Docker. Everything it keeps is in the workspace folder; the README's note is to "be sure to confirm the correctness of the mounted volume, otherwise the data will be lost after the container is deleted".

Below is the BACKUP.md the builder writes next to the compose file above: which of its folders and volumes hold data, what to copy with which container stopped, and a restore check. Pick more apps in the builder and it covers them all in one file.

# BACKUP.md built at dankhost.com for: SiYuan

What to copy from the docker-compose.yml built with this file, the database dump each project documents (rewritten for the service names in that file), what to copy with which container stopped, and how to check the result. Run every command in the folder that holds docker-compose.yml.

The folders are owned by the containers' users: put sudo in front of tar if it says "Permission denied". Named volumes live under /var/lib/docker/volumes, not next to the compose file, so they are copied through a throwaway ubuntu container (Docker's documented --volumes-from method). tar makes a full copy each run; for large folders an incremental tool (restic, borg, rsync) saves time and space.

Never run "docker compose down -v" on this file: it deletes the named volumes of every app in it.

## Before you start

    BACKUP=/mnt/backup/selfhost   # change this: a disk or machine other than this server's system disk
    mkdir -p "$BACKUP"

## Every time: the three stack files

    tar czf "$BACKUP/stack-files.tar.gz" docker-compose.yml .env caddy

.env holds the database passwords and secret keys the apps were set up with; keep this archive as private as the data.

## Caddy (the reverse proxy)

Caddy's docs: 'The data directory must not be treated as a cache.' It holds the TLS certificates and their private keys; without it Caddy has to ask Let's Encrypt for every certificate again.

- caddy-data (named volume, /data in caddy)
  BACK UP: TLS certificates, private keys, OCSP staples.
- caddy-config (named volume, /config in caddy)
  SKIP: the last active configuration, kept for 'caddy run --resume', which this setup does not use: it starts from the Caddyfile.
- ./caddy (/etc/caddy in caddy)
  IN stack-files.tar.gz: the Caddyfile, copied with the stack files above.

Copy (Caddy keeps serving while you copy):

    docker run --rm --volumes-from caddy -v "$BACKUP":/backup ubuntu tar cvf /backup/caddy-data.tar /data

Restore check:

    tar tf "$BACKUP/caddy-data.tar" > /dev/null && echo OK
    docker run --rm --volumes-from caddy -v "$BACKUP":/backup ubuntu bash -c "cd /data && tar xvf /backup/caddy-data.tar --strip 1"

Sources:
- Caddy docs: Conventions, Data directory: https://caddyserver.com/docs/conventions#data-directory (checked 2026-09-24)
- Docker docs: Volumes, Back up, restore, or migrate data volumes: https://docs.docker.com/engine/storage/volumes/#back-up-restore-or-migrate-data-volumes (checked 2026-09-24)

## SiYuan

SiYuan publishes no backup procedure for Docker. Everything it keeps is in the workspace folder; the README's note is to "be sure to confirm the correctness of the mounted volume, otherwise the data will be lost after the container is deleted".

What this compose mounts:
- ./siyuan/workspace (/siyuan/workspace in siyuan-main)
  BACK UP: the whole workspace: notes (.sy files), assets, the search index and settings.

1. Stop siyuan-main. SiYuan writes its index database while it runs; stopping it keeps the copy in step with the notes.

    docker compose stop siyuan-main

2. Copy while siyuan-main is stopped:

    tar czf "$BACKUP/siyuan-workspace.tar.gz" ./siyuan/workspace

3. Start it again:

    docker compose start siyuan-main

Restore check:

    tar tzf "$BACKUP/siyuan-workspace.tar.gz" > /dev/null && echo OK

Put a copy back (with siyuan-main stopped):

    tar xzf "$BACKUP/siyuan-workspace.tar.gz"   # recreates ./siyuan/workspace; move the old folder aside first

Put ./siyuan/workspace back, owned by 1000:1000 (sudo chown -R 1000:1000 ./siyuan/workspace), and run docker compose up -d.

Sources:
- SiYuan README: Docker Hosting (Docker Compose, PUID/PGID, lock screen password, hidden port, limitations): https://github.com/siyuan-note/siyuan/blob/master/README.md (checked 2026-10-01)
- Docker docs: Volumes, Back up, restore, or migrate data volumes: https://docs.docker.com/engine/storage/volumes/#back-up-restore-or-migrate-data-volumes (checked 2026-10-01)

Update it

What docker compose pull does depends only on how each image line in the compose file above is tagged. For SiYuan as this page writes it:

What SiYuan's docs say about updating

SiYuan publishes no update procedure for this setup; the steps below are Docker's generic method.

The steps

1. Back up first, as in Back it up above. An update can migrate SiYuan's data on its first start; the copy is the way back.
2. Download the new images. Running containers are not touched yet:

   docker compose pull

3. Recreate the containers whose image changed. Volumes and bind-mounted folders stay as they are:

   docker compose up -d

4. Watch SiYuan start (Ctrl+C stops following the log, not the app):

   docker compose logs -f siyuan-main

5. Optional: remove the old images the pull left without a tag. This covers every stack on the machine, not only this one:

   docker image prune

Docker's reference for these commands: Docker docs: docker compose pull checked 2026-09-30; Docker docs: docker compose up (recreates changed containers, keeps volumes) checked 2026-09-30; Docker docs: docker image prune checked 2026-09-30

Sources

Every page below was fetched on the date shown.

• SiYuan on GitHub (repository description) checked 2026-10-01 (what it does)
• SiYuan README: Docker Hosting (Docker Compose, PUID/PGID, lock screen password, hidden port, limitations) checked 2026-10-01 (compose definition and proxy settings, backup plan)
• Docker Hub: b3log/siyuan (the README's image) checked 2026-10-01 (compose definition and proxy settings)
• Caddy docs: Keep Caddy running (Docker Compose section) checked 2026-09-23 (Caddy)
• Vaultwarden wiki: Caddy with HTTP challenge (uses the caddy:2 image) checked 2026-09-23 (Caddy)
• Docker docs: Volumes, Back up, restore, or migrate data volumes checked 2026-10-01 (backup plan)
• Caddy docs: Conventions, Data directory checked 2026-09-24 (backup plan)
• Docker docs: docker compose pull checked 2026-09-30 (update steps)
• Docker docs: docker compose up (recreates changed containers, keeps volumes) checked 2026-09-30 (update steps)
• Docker docs: docker image prune checked 2026-09-30 (update steps)

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