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VS Code Jupyter extension
https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter
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PDF Export of Raw Cell - LaTeX Interprets Text #15968

Open Servinjesus1 opened 2 weeks ago

Servinjesus1 commented 2 weeks ago

The text within a raw cell is being interpreted when exporting to PDF leading to the following error:

! You can't use `macro parameter character #' in vertical mode.

during XeTeX processing.

Environment data

Context

I use raw cells to "turn off" code cells I don't want to run, but want to keep around for reference. As such these cells will contain plenty of special characters. In this case, I had a cell with a python comment (#). This is being interpreted by XeTeX as a "macro parameter character".

Possible Solution

Raw cells should be uninterpreted verbatim/code cells like other cells.

Steps to reproduce:

Put a # or other LaTeX-special character in a raw cell and try to export to PDF

Logs

Output for Jupyter in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Jupyter)

``` 16:19:12.632 [info] Process Execution: ~/miniconda3/envs/beest/bin/python -m jupyter nbconvert "/var/folders/rx/smbzb8cd0cq1hf5lg3m4fnp80000gn/T/6940fe85-1200-43af-aa22-d83a81bfb829/Compare and Calibrate.ipynb" --to pdf --output tmp-13539N6hlOH0XIROc.pdf --output-dir /var/folders/rx/smbzb8cd0cq1hf5lg3m4fnp80000gn/T --debug 16:19:16.265 [error] Export failed Error: [NbConvertApp] Searching ['/Users/~/miniconda3/envs/beest/etc/jupyter', '/Users/~/.jupyter', '/Users/~/.local/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files [NbConvertApp] Looking for jupyter_config in /etc/jupyter [NbConvertApp] Looking for jupyter_config in /usr/local/etc/jupyter [NbConvertApp] Looking for jupyter_config in /Users/~/.local/etc/jupyter [NbConvertApp] Looking for jupyter_config in /Users/~/.jupyter [NbConvertApp] Looking for jupyter_config in /Users/~/miniconda3/envs/beest/etc/jupyter [NbConvertApp] Looking for jupyter_nbconvert_config in /etc/jupyter [NbConvertApp] Looking for jupyter_nbconvert_config in /usr/local/etc/jupyter [NbConvertApp] Looking for jupyter_nbconvert_config in /Users/~/.local/etc/jupyter [NbConvertApp] Looking for jupyter_nbconvert_config in /Users/~/.jupyter [NbConvertApp] Looking for jupyter_nbconvert_config in /Users/~/miniconda3/envs/beest/etc/jupyter [NbConvertApp] Converting notebook /var/folders/rx/smbzb8cd0cq1hf5lg3m4fnp80000gn/T/6940fe85-1200-43af-aa22-d83a81bfb829/Compare and Calibrate.ipynb to pdf [NbConvertApp] Notebook name is 'tmp-13539N6hlOH0XIROc' [NbConvertApp] Template paths: /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/latex /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/base /Users/~/miniconda3/envs/beest/share/jupyter /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/compatibility /Users/~/Library/Jupyter /Users/~/Library/Jupyter/nbconvert/templates /Users/~/Library/Jupyter/nbconvert/templates/compatibility /Users/~/.local/share/jupyter /Users/~/.local/share/jupyter/nbconvert/templates /Users/~/.local/share/jupyter/nbconvert/templates/compatibility /usr/local/share/jupyter /usr/local/share/jupyter/nbconvert/templates /usr/local/share/jupyter/nbconvert/templates/compatibility /usr/share/jupyter /usr/share/jupyter/nbconvert/templates /usr/share/jupyter/nbconvert/templates/compatibility /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates [NbConvertApp] Applying preprocessor: TagRemovePreprocessor [NbConvertApp] Applying preprocessor: RegexRemovePreprocessor [NbConvertApp] Applying preprocessor: coalesce_streams [NbConvertApp] Applying preprocessor: SVG2PDFPreprocessor [NbConvertApp] Applying preprocessor: LatexPreprocessor [NbConvertApp] Applying preprocessor: HighlightMagicsPreprocessor [NbConvertApp] Applying preprocessor: ExtractOutputPreprocessor [NbConvertApp] Attempting to load template index.tex.j2 [NbConvertApp] template_paths: /Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/latex:/Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/base:/Users/~/miniconda3/envs/beest/share/jupyter:/Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates:/Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates/compatibility:/Users/~/Library/Jupyter:/Users/~/Library/Jupyter/nbconvert/templates:/Users/~/Library/Jupyter/nbconvert/templates/compatibility:/Users/~/.local/share/jupyter:/Users/~/.local/share/jupyter/nbconvert/templates:/Users/~/.local/share/jupyter/nbconvert/templates/compatibility:/usr/local/share/jupyter:/usr/local/share/jupyter/nbconvert/templates:/usr/local/share/jupyter/nbconvert/templates/compatibility:/usr/share/jupyter:/usr/share/jupyter/nbconvert/templates:/usr/share/jupyter/nbconvert/templates/compatibility:/Users/~/miniconda3/envs/beest/share/jupyter/nbconvert/templates /Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/utils/pandoc.py:51: RuntimeWarning: You are using an unsupported version of pandoc (3.3). Your version must be at least (1.12.1) but less than (3.0.0). Refer to https://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() [NbConvertApp] Support files will be in tmp-13539N6hlOH0XIROc_files/ [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 35095 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_1.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 21790 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_2.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 31702 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_3.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33357 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_4.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33173 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_5.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33541 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_6.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33018 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_7.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 35896 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_8.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 35461 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_9.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 28600 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_10.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 44345 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_11.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 43617 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_12.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 44528 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_13.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 41790 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_14.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 35637 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_15.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 50394 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_16.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 34011 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_17.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 27644 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_18.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 27498 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_8_19.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 26303 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_0.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33094 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_1.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 30050 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_2.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 28568 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_3.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 31762 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_4.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 31771 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_5.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 32041 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_6.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 32208 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_7.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 34001 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_8.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33770 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_9.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 34144 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_10.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 36120 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_11.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 34590 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_12.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 34497 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_13.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 33756 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_14.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 30239 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_15.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 35582 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_16.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 30294 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_17.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 30566 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_18.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 30954 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_10_19.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 16432 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_12_2.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 108201 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_16_1.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 41532 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_0.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 52378 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_1.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 51450 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_2.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 49987 bytes to support file 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[NbConvertApp] Writing 53109 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_9.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 56553 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_10.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 51441 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_11.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 49877 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_12.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 50968 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_13.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 52130 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_14.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 49740 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_15.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 47011 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_16.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 52194 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_17.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 48092 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_18.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 46862 bytes to support file ./tmp-13539N6hlOH0XIROc_files/tmp-13539N6hlOH0XIROc_25_19.png [NbConvertApp] Making directory ./tmp-13539N6hlOH0XIROc_files [NbConvertApp] Writing 113960 bytes to support file 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Building PDF [NbConvertApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet'] [NbConvertApp] CRITICAL | xelatex failed: ['xelatex', 'notebook.tex', '-quiet'] This is XeTeX, Version 3.141592653-2.6-0.999996 (TeX Live 2024) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (./notebook.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-05-08> (/Users/~/Library/TinyTeX/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/Users/~/Library/TinyTeX/texmf-dist/tex/latex/base/size11.clo)) (/Users/~/Library/TinyTeX/texmf-dist/tex/latex/tcolorbox/tcolorbox.sty (/Users/~/Library/TinyTeX/texmf-dist/tex/latex/pgf/basiclayer/pgf.sty (/Users/~/Library/TinyTeX/texmf-dist/tex/latex/pgf/utilities/pgfrcs.sty (/Users/~/Library/TinyTeX/texmf-dist/tex/generic/pgf/utilities/pgfutil-common.tex) (/Users/~/Library/TinyTeX/texmf-dist/tex/generic/pgf/utilities/pgfutil-latex.def) 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Traceback (most recent call last): File "/Users/~/miniconda3/envs/beest/bin/jupyter-nbconvert", line 11, in sys.exit(main()) ^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/jupyter_core/application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/traitlets/config/application.py", line 992, in launch_instance app.start() File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 423, in start self.convert_notebooks() File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 597, in convert_notebooks self.convert_single_notebook(notebook_filename) File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 560, in convert_single_notebook output, resources = self.export_single_notebook( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 488, in export_single_notebook output, resources = self.exporter.from_filename( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 189, in from_filename return self.from_file(f, resources=resources, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 206, in from_file return self.from_notebook_node( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/exporters/pdf.py", line 194, in from_notebook_node self.run_latex(tex_file) File "/Users/~/miniconda3/envs/beest/lib/python3.11/site-packages/nbconvert/exporters/pdf.py", line 164, in run_latex return self.run_command( ^^^^^^^^^^^^^^^^^ File 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Servinjesus1 commented 2 weeks ago

Workaround: Use

%%capture
%%markdown

magics at the top of cells to "turn them off" without using raw. The nice thing about this is it keeps syntax formatting albeit being a bit opaque what's actually happening (the cell contents are being interpreted as gobbledygook markdown and the output discarded). Not sure what alternatives exist for other languages.

amunger commented 2 weeks ago

another option for turning off a cell is to use the toggle comment command (ctrl+/ by default), which can be executed at the cell level.