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That error means your Python installation doesn’t have Tkinter’s C library (libtk8.6) available — it’s missing the system-level Tk and Tcl packages that provide the GUI backend.

On Arch Linux, Tkinter support isn’t bundled by default, so you need to install the correct system packages.

🧰 Fix: Install Tk and Tcl

Run this in your terminal:

This installs both tk and its dependency tcl, which includes the libtk8.6.so shared library that Tkinter needs.

✅ Then test again:

After installation, verify Tkinter works:

If a small empty GUI window appears, Tkinter is now working.

💡 Then re-run your script:

It should now start without the import error.

Would you like me to show you how to install it system-wide (so you can just run pdf_to_md from anywhere) instead of using python pdf_to_md.py each time?

Input: /home/zg/Downloads/ntsamplepaper-nat-IM.pdf Output: /home/zg/Downloads/test.md Options → CAPS→Headings=True, Defragment=True, HeadingRatio=1.15, OrphanLen=45, PageBreaks=False, RemoveHF=True, ExportImages=False, PreviewOnly=False ✖ Error: PyMuPDF (fitz) is not installed. Install with: pip install pymupdf getting this error in the app even though i installed it with pipx here is proof ○ pymupdf ⌂ 10:25 usage: pymupdf [-h] {show,clean,join,extract,embed-info,embed-add,embed-del,embed-upd,embed-extract,embed-copy,gettext,internal}... ------------------------- Basic PyMuPDF Functions ------------------------- options: -h, --help show this help message and exit Subcommands: {show,clean,join,extract,embed-info,embed-add,embed-del,embed-upd,embed-extract,embed-copy,gettext,internal} Enter 'command -h' for subcommand specific help ◎

Good — that tells us exactly what’s going on.
The issue isn’t with PyMuPDF itself, but where it’s installed.

Let’s unpack this:

🧩 What’s happening

• You installed pymupdf with pipx → that means it lives in an isolated environment, not in your main Python interpreter.
• When you run:
  it uses your system Python (3.13) — which does not have pymupdf installed.

So the script doesn’t see it.

✅ Fix Options

Option 1 — Install pymupdf into your system Python

This is the simplest fix:

If you’re on Arch and using Python 3.13, you can verify pip matches your version:

Then rerun:

Option 2 — Run it inside pipx (less ideal here)

Since pdf_to_md.py isn’t itself installed as a pip package, pipx isolation doesn’t help much — it’s meant for full tools, not local scripts.
So, Option 1 is better.

Option 3 — (Optional) Use a virtual environment

If you want to keep things clean:

💡 Quick sanity check

After installing, test PyMuPDF manually:

If it prints a short description, you’re good.

Would you like me to show how to add a simple pdf_to_md CLI wrapper so you can just run:

from anywhere, instead of python pdf_to_md.py?

i don't have pip

Got it 👍 — that’s easy to fix on Arch Linux.
Python comes preinstalled, but pip is often a separate package.

🧰 Step 1 — Install pip

Run this:

That gives you the correct version of pip for your Python (3.13).

🧩 Step 2 — Verify pip works

Check it with:

or safer:

You should see something like:

🧠 Step 3 — Install PyMuPDF for system Python

Now install the missing dependency:

You can confirm it’s installed:

✅ Step 4 — Run your tool again

It should now detect PyMuPDF (fitz) correctly and run.

Would you like me to make it so you can run the script just by typing pdf_to_md (without needing to cd into the folder)?

◄ 2s ⋈┈○ pip install pymupdf ⌂ 10:27 error: externally-managed-environment × This environment is externally managed ╰─> To install Python packages system-wide, try 'pacman -S python-xyz', where xyz is the package you are trying to install. If you wish to install a non-Arch-packaged Python package, create a virtual environment using 'python -m venv path/to/venv'. Then use path/to/venv/bin/python and path/to/venv/bin/pip. If you wish to install a non-Arch packaged Python application, it may be easiest to use 'pipx install xyz', which will manage a virtual environment for you. Make sure you have python-pipx installed via pacman. note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages. hint: See PEP 668 for the detailed specification. ◄ 6s ⋈┈○

Perfect — that’s Arch Linux doing its job 👏

Arch enforces PEP 668, which protects system Python from being modified by pip.
You have three clean options to fix this — here’s the breakdown:

🩵 Option 1 — Use a Virtual Environment (Recommended)

This keeps things clean and avoids touching system Python.

✅ Advantages

• No root needed
• Safe from Arch package conflicts
• Works exactly like a normal Python environment

Each time you want to use it:

You can exit the venv anytime with:

🩶 Option 2 — Use pip with --break-system-packages (Not ideal)

If you really want to install globally:

⚠️ Warning: This modifies the Arch-managed Python install.
Only do this if you understand the risks (it can interfere with pacman-managed Python packages).

🩷 Option 3 — Use pipx properly

You can install pdf_to_md itself via pipx and let it handle isolation automatically:

Then you’ll be able to just run:

from anywhere on your system.

💡 Recommended for you:
Since you already cloned the repo and are testing it manually, Option 1 (virtual environment) is the cleanest, most Arch-friendly approach.

Would you like me to make a one-liner script (run_pdf_to_md.sh) that automatically activates the venv and runs the converter with your input/output paths?