zotero-obsidian-codex-setup

name

zotero-obsidian-codex-setup

description

Windows setup and light customization of this cloned Zotero-Obsidian-Codex workflow template. Use when Codex needs to initialize the repo root as an Obsidian vault, verify Obsidian/Zotero/Better BibTeX/community-plugin prerequisites, write the expected Zotero Integration config, create the default `Research vault/references.bib/library.bib`, or hand the user off to `Research vault/` for daily literature work. Do not use for normal literature reading or writing tasks inside `Research vault/`.

Zotero Obsidian Codex Setup

Initialize this cloned repository on Windows so the repo root works as the Obsidian vault root and Research vault/ works as the daily Codex literature workspace.

Prefer the bundled setup script over hand-editing data.json.

The setup flow has two scripts:

• scripts/check_windows_setup.py: non-mutating readiness check
• scripts/apply_windows_setup.py: apply the repo-standard vault configuration

Workflow

1. Confirm you are at the repository root.
   • Expect .obsidian/ and Research vault/ to exist side by side.
   • Keep the internal directory name Research vault/ unchanged.
2. Verify prerequisites with non-mutating checks first.
   • Confirm Obsidian
   • Confirm Zotero
   • Confirm Better BibTeX for Zotero
   • Confirm Obsidian plugins Dataview and Zotero Integration
3. Run the readiness check first:

python .agents/skills/zotero-obsidian-codex-setup/scripts/check_windows_setup.py

4. If the user wants the template initialized, run:

python .agents/skills/zotero-obsidian-codex-setup/scripts/apply_windows_setup.py

5. If the user wants a different BibTeX filename, pass it explicitly:

python .agents/skills/zotero-obsidian-codex-setup/scripts/apply_windows_setup.py --bib-name my-library.bib

6. If the user only wants to preview changes, use:

python .agents/skills/zotero-obsidian-codex-setup/scripts/apply_windows_setup.py --dry-run

7. After setup completes:
   • Tell the user to reopen or reload Obsidian if needed.
   • Switch the working directory to Research vault/.
   • For daily literature work, rely on the nested AGENTS.md and $literature-processor.

Expected Check Output

The readiness check should clearly report:

• whether the repo shape is correct
• whether Obsidian and Zotero are discoverable on Windows
• whether Better BibTeX appears to be installed in Zotero
• whether the vault already lists Dataview and Zotero Integration
• whether the repo-standard Zotero Integration data.json already exists
• the exact next action when something is missing

What The Script Applies

• Ensures the public-template directories exist:
  • Research vault/literature/pdf/
  • Research vault/literature/notes/
  • Research vault/references.bib/
  • Research vault/inbox/
  • Research vault/projects/
• Creates the default BibTeX target if missing:
  • Research vault/references.bib/library.bib
• Writes the repo-standard Zotero Integration config to:
  • .obsidian/plugins/obsidian-zotero-desktop-connector/data.json
• Uses the bundled asset:
  • assets/zotero-integration-data.template.json

Guardrails

• Do not rename Research vault/.
• Do not use this skill for literature reading, writing, or note synthesis.
• Do not vendor Obsidian plugin binaries into the repository.
• Keep path instructions relative. Avoid machine-specific absolute paths in shared docs.
• If a prerequisite is missing, stop and tell the user exactly which desktop app or Obsidian plugin still needs manual installation.