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sisl / tufte_algorithms_book

A template for textbooks in the same style as Algorithms for Optimization
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Compile generates `ImportError` #30

Open danielchen26 opened 3 years ago

danielchen26 commented 3 years ago

Following the instruction, I have the following compiling error after make compile. I am not sure which issue is this. Is it related to some python packages? But this error does not seems to affect the output of the pdf. I

Output written on book.pdf (24 pages, 126772 bytes).
Transcript written on book.log.
This is PythonTeX 0.17
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 2394, in do_pygments
    lexer[codetype] = get_lexer_by_name(pygments_settings[codetype]['lexer'], **p)
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/lexers/__init__.py", line 116, in get_lexer_by_name
    for cls in find_plugin_lexers():
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/plugin.py", line 55, in find_plugin_lexers
    yield entrypoint.load()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2450, in load
    return self.resolve()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2456, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "<frozen zipimport>", line 259, in load_module
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments_julia-0.0.0-py3.8.egg/pygments_julia/__init__.py", line 19, in <module>
    from pygments.util import shebang_matches, unirange
ImportError: cannot import name 'unirange' from 'pygments.util' (/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/util.py)
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Library/TeX/texbin/pythontex", line 62, in <module>
    pythontex.main()
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 2811, in main
    do_multiprocessing(data, temp_data, old_data, engine_dict)
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 1383, in do_multiprocessing
    result = task.get()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
ImportError: cannot import name 'unirange' from 'pygments.util' (/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/util.py)
make: [compile] Error 1 (ignored)
tawheeler commented 3 years ago

These sorts of issues are usually related to the version of various python pip packages and the version of pygments itself. We are on PythonTeX 0.18dev. This error will not prevent PDF generation but it will affect the typesetting of any algorithms / code blocks.

danielchen26 commented 3 years ago

so, how should I install PythonTeX 0.18dev? after upgrading from 0.17 to 0.18v, will pygment.util ImportError go away?

mykelk commented 3 years ago

I don't think the issue is with pythontex. So long as it is v0.17 or later, you should be okay. I think the issue might be with the version of pygments. Can you confirm that version? You can run pygmentize -V.

danielchen26 commented 3 years ago

Pygments version 2.7.4, (c) 2006-2021 by Georg Brandl.

On February 3, 2021 at 15:36 GMT, Mykel Kochenderfer notifications@github.com wrote:

I don't think the issue is with pythontex. So long as it is v0.17 or later, you should be okay. I think the issue might be with the version of pygments. Can you confirm that version? You can run pygmentize -V.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

danielchen26 commented 3 years ago

I think this is the latest version for the Pygments.

On February 3, 2021 at 17:37 GMT, Tianchi Chen chentianchi@gmail.com wrote:

Pygments version 2.7.4, (c) 2006-2021 by Georg Brandl.

On February 3, 2021 at 15:36 GMT, Mykel Kochenderfer notifications@github.com wrote:

I don't think the issue is with pythontex. So long as it is v0.17 or later, you should be okay. I think the issue might be with the version of pygments. Can you confirm that version? You can run pygmentize -V.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

mykelk commented 3 years ago

I think the repo is pointing to an old version of the lexer. Would you mind trying updating the lexer by running:

pip install --upgrade git+https://github.com/sisl/pygments-julia#egg=pygments_julia
danielchen26 commented 3 years ago 
❯ pip install --upgrade git+https://github.com/sisl/pygments-julia#egg=pygments_julia
Collecting pygments_julia
  Cloning https://github.com/sisl/pygments-julia to /private/var/folders/dk/kg947qjx6hn_7cmgnjmdvxvr0000gn/T/pip-install-n3hj7qzi/pygments-julia_b7cd7fc93d9d4f21973ff76a28772429
Requirement already satisfied: pygments>=2.2 in ./opt/anaconda3/lib/python3.8/site-packages (from pygments_julia) (2.7.4)
mykelk commented 3 years ago

Hmm... I get something different:

$ pip install --upgrade git+https://github.com/sisl/pygments-julia#egg=pygments_julia
Collecting pygments_julia
  Cloning https://github.com/sisl/pygments-julia to c:\users\mykel\appdata\local\temp\pip-install-mdjzrxhv\pygments-julia_1d8b8967cf6346d28a55406308b3fb4f
Requirement already satisfied: pygments>=2.2 in c:\app\anaconda3\lib\site-packages (from pygments_julia) (2.7.4)
Building wheels for collected packages: pygments-julia
  Building wheel for pygments-julia (setup.py): started
  Building wheel for pygments-julia (setup.py): finished with status 'done'
  Created wheel for pygments-julia: filename=pygments_julia-0.0.0-py3-none-any.whl size=12386 sha256=b0d79a04b488c52da4977842ac7ab1dee6fc155085011bfdf0d7ee4a23b22b3d
  Stored in directory: C:\Users\mykel\AppData\Local\Temp\pip-ephem-wheel-cache-gmw6ixpu\wheels\48\7e\13\5a7b0457bdf67468ad978636f9f555dca053183632d11d9e6d
Successfully built pygments-julia
Installing collected packages: pygments-julia
  Attempting uninstall: pygments-julia
    Found existing installation: pygments-julia 0.0.0
    Uninstalling pygments-julia-0.0.0:
      Successfully uninstalled pygments-julia-0.0.0
Successfully installed pygments-julia-0.0.0
danielchen26 commented 3 years ago

I remember that when I first install it, I got the same thing as you posted. everything installed successfully. I got that because it is already installed.

danielchen26 commented 3 years ago

I uninstalled pygments and reinstall it. Here is what I got 

❯ pip list | grep Pygments
Pygments                           2.7.4
❯ pip uninstall Pygments
Found existing installation: Pygments 2.7.4
Uninstalling Pygments-2.7.4:
  Would remove:
    /Users/chentianchi/opt/anaconda3/bin/pygmentize
    /Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/Pygments-2.7.4.dist-info/*
    /Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/*
Proceed (y/n)? y
  Successfully uninstalled Pygments-2.7.4
❯ pip list | grep Pygments
❯ pip install --upgrade git+https://github.com/sisl/pygments-julia#egg=pygments_julia

Collecting pygments_julia
  Cloning https://github.com/sisl/pygments-julia to /private/var/folders/dk/kg947qjx6hn_7cmgnjmdvxvr0000gn/T/pip-install-gy2_7b4m/pygments-julia_5ac75135ea8f47bc938d3c5e3b0ce996
Collecting pygments>=2.2
  Using cached Pygments-2.7.4-py3-none-any.whl (950 kB)
Installing collected packages: pygments
Successfully installed pygments-2.7.4

But the make compile still give the same error. Should I do something additional after this?

danielchen26 commented 3 years ago

Also, my test run are successfull.

julia> include("runtests.jl")
reading preface.tex
reading acknowledgments.tex
reading introduction.tex
reading appendix.tex
reading preface.tex
reading acknowledgments.tex
reading introduction.tex
replacements = Dict("return x^2" => "return sin(x)")
reading appendix.tex
reading for test: preface.tex
reading for test: acknowledgments.tex
reading for test: introduction.tex
reading for test: appendix.tex
====================
Importing support code!
====================
Running tests!
ALL TESTS PASSED

I am also attaching all the message shown in my terminal

❯ make compile
julia --color=yes pull_julia_code.jl && \
        lualatex book && \
        pythontex book && \
        biber book && \
        lualatex book
reading preface.tex
reading acknowledgments.tex
reading introduction.tex
reading appendix.tex
reading preface.tex
reading acknowledgments.tex
reading introduction.tex
replacements = Dict("return x^2" => "return sin(x)")
reading appendix.tex
reading for test: preface.tex
reading for test: acknowledgments.tex
reading for test: introduction.tex
reading for test: appendix.tex
This is LuaHBTeX, Version 1.12.0 (TeX Live 2020) 
 restricted system commands enabled.
(./book.tex
LaTeX2e <2020-02-02> patch level 5
 L3 programming layer <2020-03-06> (./tufte_algorithms_book.cls
Document Class: tufte_algorithms_book 
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Package geometry Warning: Over-specification in `v'-direction.
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Overfull \hbox (2.88226pt too wide) in paragraph at lines 176--180
\TU/TeXGyrePagella(0)/m/n/10 script. The script searches for \TU/TeXGyrePagella
(0)/b/n/10 ?? \TU/TeXGyrePagella(0)/m/n/10 in the lines be-tween the be-gin-nin
g of the \TU/DejaVuSansMono(0)/m/n/10 algorithm
[5]

Package PythonTeX Warning: Non-existent Pygments content on input line 189.

Package PythonTeX Warning: Non-existent Pygments content on input line 195.

Package PythonTeX Warning: Non-existent Pygments content on input line 195.

(./fig/replacement_example.tex
Overfull \hbox (7.97636pt too wide) in paragraph at lines 116--117
 [] 
)

LaTeX Warning: Marginpar on page 6 moved.

) [6]

Package hyperref Warning: bookmark level for unknown appendixpart defaults to 0
.

[7] (./chapter/appendix.tex [8]
Appendix A.
) [9] [10]

LaTeX Warning: Empty bibliography on input line 44.

[11] [12]
No file book.ind.

Package imakeidx Warning: Remember to run lualatex again after calling
(imakeidx)                `texindy -M cms book.idx'.

(./book.aux (./copyrightpage.aux) (./dedication.aux) (./chapter/preface.aux)
(./chapter/acknowledgments.aux) (./chapter/introduction.aux)
(./chapter/appendix.aux))

LaTeX Warning: There were undefined references.

LaTeX Warning: There were multiply-defined labels.

Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                book
(biblatex)                and rerun LaTeX afterwards.

)
(see the transcript file for additional information)
 16627 words of node memory still in use:
   173 hlist, 14 vlist, 8 rule, 14 disc, 7 local_par, 39 math, 482 glue, 151 ke
rn, 31 penalty, 7 margin_kern, 216 glyph, 2003 attribute, 148 glue_spec, 1003 a
ttribute_list, 8 write, 562 pdf_literal, 1 pdf_start_link, 1 pdf_end_link, 1 pd
f_action, 24 pdf_colorstack nodes
   avail lists: 1:13,2:2726,3:1123,4:91,5:262,6:23,7:1904,8:44,9:313,10:11,11:1
17,12:1
{/usr/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/local/tex
live/2020/texmf-dist/fonts/opentype/public/tex-gyre/texgyrepagella-bold.otf></u
sr/local/texlive/2020/texmf-dist/fonts/truetype/public/dejavu/DejaVuSansMono.tt
f></usr/local/texlive/2020/texmf-dist/fonts/opentype/public/tex-gyre/texgyrepag
ella-regular.otf></usr/local/texlive/2020/texmf-dist/fonts/opentype/public/tex-
gyre/texgyrepagella-italic.otf></usr/local/texlive/2020/texmf-dist/fonts/openty
pe/public/tex-gyre/texgyrepagella-regular.otf></usr/local/texlive/2020/texmf-di
st/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/local/texlive/2020/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/local/texlive/2020/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2020/texmf-dist/f
onts/type1/public/mathpazo/fplmb.pfb></usr/local/texlive/2020/texmf-dist/fonts/
type1/public/mathpazo/fplmr.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1
/public/mathpazo/fplmri.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw
/palatino/uplb8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw/palati
no/uplr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw/palatino/uplr
i8a.pfb>
Output written on book.pdf (24 pages, 129173 bytes).
Transcript written on book.log.
This is PythonTeX 0.17
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 2394, in do_pygments
    lexer[codetype] = get_lexer_by_name(pygments_settings[codetype]['lexer'], **p)
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/lexers/__init__.py", line 116, in get_lexer_by_name
    for cls in find_plugin_lexers():
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/plugin.py", line 55, in find_plugin_lexers
    yield entrypoint.load()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2450, in load
    return self.resolve()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2456, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "<frozen zipimport>", line 259, in load_module
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments_julia-0.0.0-py3.8.egg/pygments_julia/__init__.py", line 19, in <module>
    from pygments.util import shebang_matches, unirange
ImportError: cannot import name 'unirange' from 'pygments.util' (/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/util.py)
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Library/TeX/texbin/pythontex", line 62, in <module>
    pythontex.main()
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 2811, in main
    do_multiprocessing(data, temp_data, old_data, engine_dict)
  File "/usr/local/texlive/2020/texmf-dist/scripts/pythontex/pythontex3.py", line 1383, in do_multiprocessing
    result = task.get()
  File "/Users/chentianchi/opt/anaconda3/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
ImportError: cannot import name 'unirange' from 'pygments.util' (/Users/chentianchi/opt/anaconda3/lib/python3.8/site-packages/pygments/util.py)
make: [compile] Error 1 (ignored)
mykelk commented 3 years ago

The issue is not with pygments. That is installed correctly. The issue is that your python installation isn't using the current version of pygments-julia: https://github.com/sisl/pygments-julia

The reason I know this is that the error message is complaining about the use of unirange, which hasn't been a part of this package since Sep 15, 2020.

danielchen26 commented 3 years ago

Ok, Thank you. I followed that link and install it again. The error seems gone right now. There is a new error like the following

This is PythonTeX 0.17

----  Messages for juliacon:default:default  ----
* PythonTeX error
    Running code for Julia console failed
ERROR: KeyError: key "tex" not found
Stacktrace:
 [1] getindex at ./dict.jl:467 [inlined]
 [2] get_format at /Users/chentianchi/.julia/packages/Weave/BarbQ/src/Weave.jl:48 [inlined]
 [3] run_doc(::Weave.WeaveDoc; doctype::String, out_path::Symbol, args::Dict{Any,Any}, mod::Nothing, fig_path::Nothing, fig_ext::Nothing, cache_path::String, cache::Symbol) at /Users/chentianchi/.julia/packages/Weave/BarbQ/src/run.jl:20
 [4] weave(::String; doctype::String, informat::Nothing, out_path::Symbol, args::Dict{Any,Any}, mod::Nothing, fig_path::Nothing, fig_ext::Nothing, cache_path::String, cache::Symbol, template::Nothing, css::Nothing, highlight_theme::Nothing, pandoc_options::Array{String,1}, latex_cmd::Array{String,1}, keep_unicode::Bool) at /Users/chentianchi/.julia/packages/Weave/BarbQ/src/Weave.jl:177
 [5] #weave#115 at /Users/chentianchi/.julia/packages/Weave/BarbQ/src/Weave.jl:233 [inlined]
 [6] weave(::String, ::String) at /Users/chentianchi/.julia/packages/Weave/BarbQ/src/Weave.jl:233
 [7] top-level scope at none:1

--------------------------------------------------
PythonTeX:  book - 1 error(s), 0 warning(s)

make: [compile] Error 1 (ignored)

What is this related to? is it about Weave.jl?

also when I tried

❯ make compile CHAPTER = 'introduction chapter2\/introduction'
make: *** empty variable name.  Stop.

it does not seems to work for excluding chapters. I have spacevim installed.

mykelk commented 3 years ago

@mossr ?

mossr commented 3 years ago

You can try to revert Weave.jl back to 0.10.2 (see this thread: https://github.com/JunoLab/Weave.jl/issues/391#issuecomment-688812973)

danielchen26 commented 3 years ago

ok, now it works. Thanks! what about 

❯ make compile CHAPTER = 'introduction chapter2\/introduction'
make: *** empty variable name.  Stop.

did I do something wrong for this partial compile?

mossr commented 3 years ago

Remove the spaces around the =

make compile CHAPTER='introduction chapter2\/introduction'

I'll update the README to reflect this.

danielchen26 commented 3 years ago

ok, it works now. Thanks for the clarification.

On Wed, Feb 3rd, 2021 at 9:13 PM, Robert Moss notifications@github.com wrote:

You can try to revert Weave.jl back to 0.10.2 (see this thread: JunoLab/Weave.jl#391 (comment) ( https://github.com/JunoLab/Weave.jl/issues/391#issuecomment-688812973 ) )

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub ( https://github.com/sisl/tufte_algorithms_book/issues/30#issuecomment-772971766 ) , or unsubscribe ( https://github.com/notifications/unsubscribe-auth/ABIHE7PMNGPWN2B5QE5K2ODS5H7FTANCNFSM4XAAORHQ ).