PlotTracks: PyPDF2 has depreciated the PdfFileMerger method #340
Description
Quick bug report - I believe that tobias currently installs the newest version of PyPDF2 which has since depreciated the PdfFileMerger method.
When running PlotTracks, the following error message is generated:
2025-12-12 15:29:45 (920418) [INFO] Plotting region: ['chr4', '119628321', '119629356']
Traceback (most recent call last):
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/bin/TOBIAS", line 8, in <module>
sys.exit(main())
^^^^^^
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/lib/python3.12/site-packages/tobias/TOBIAS.py", line 163, in main
args.func(args)
^^^^^^^^^^^^^^^
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/lib/python3.12/site-packages/tobias/tools/plot_tracks.py", line 391, in run_tracks
merger = PdfFileMerger(strict=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/lib/python3.12/site-packages/PyPDF2/_merger.py", line 817, in __init__
deprecation_with_replacement("PdfFileMerger", "PdfMerger", "3.0.0")
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/lib/python3.12/site-packages/PyPDF2/_utils.py", line 369, in deprecation_with_replacement
deprecation(DEPR_MSG_HAPPENED.format(old_name, removed_in, new_name))
File "/tomato/ModuleSoftware/tobias/tobias-0.17.2/lib/python3.12/site-packages/PyPDF2/_utils.py", line 351, in deprecation
raise DeprecationError(msg)
PyPDF2.errors.DeprecationError: PdfFileMerger is deprecated and was removed in PyPDF2 3.0.0. Use PdfMerger instead.
This solution was posted a couple years back (see below) and still fixed the issue by installing PyPDF2-2.12-1 to replace PyPDF2-3.0.1.
So - easy fix, but figured I would make note of it!
Insalling PyPDF2<3.0 fixed the issue.
pip install 'PyPDF2<3.0'
Originally posted in #200