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View Code? Open in Web Editor NEWA template for textbooks in the same style as Algorithms for Optimization
A template for textbooks in the same style as Algorithms for Optimization
When running your example, this is the output I get. I added PythonTex v 0.18 dev as required
This is PythonTeX 0.18dev
---- Messages for juliacon:default:default ----
* PythonTeX error
Running code for Julia console failed
WARNING: Method definition latex(IO, Markdown.LaTeX) in module Markdown at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Markdown\src\IPython\IPython.jl:28 overwritten in module WeaveMarkdown at C:\Users\simon\.julia\packages\Weave\BarbQ\src\WeaveMarkdown\markdown.jl:10.
** incremental compilation may be fatally broken for this module **
ERROR: KeyError: key "tex" not found
Stacktrace:
[1] getindex at .\dict.jl:467 [inlined]
[2] get_format at C:\Users\simon\.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 C:\Users\simon\.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 C:\Users\simon\.julia\packages\Weave\BarbQ\src\Weave.jl:177
[5] #weave#115 at C:\Users\simon\.julia\packages\Weave\BarbQ\src\Weave.jl:233 [inlined]
[6] weave(::String, ::String) at C:\Users\simon\.julia\packages\Weave\BarbQ\src\Weave.jl:233
[7] top-level scope at none:1
--------------------------------------------------
PythonTeX: book - 1 error(s), 0 warning(s)
make: [makefile:14: compile] Error 1 (ignored)
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)
This:
\begin{juliaconsole}
rand(100);
\end{juliaconsole}
Prints 100 numbers in my latex document.
I noticed in the slides in your JuliaCon talk that a semicolon does suppress output. Any ideas what is going on here? I did find that this
\begin{juliaconsole}
rand(100); nothing
\end{juliaconsole}
Suppresses output. But, this is of course undesirable in a document.
you mentioned in the juliacon-talk that it is possible to compile chapters separately. How is this done?
not sure if this is expected, but on Julia 1.2
gink:tufte_algorithms_book abradley$ julia install_pkgs.jl REQUIRE
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Updating `~/.julia/environments/v1.2/Project.toml`
[92933f4c] + ProgressMeter v1.0.0
Updating `~/.julia/environments/v1.2/Manifest.toml`
[92933f4c] ↑ ProgressMeter v0.9.0 ⇒ v1.0.0
Resolving package versions...
Installed Suppressor ─ v0.1.1
Updating `~/.julia/environments/v1.2/Project.toml`
[fd094767] + Suppressor v0.1.1
Updating `~/.julia/environments/v1.2/Manifest.toml`
[fd094767] + Suppressor v0.1.1
[ Info: add and build julia 1.1
Progress: 9%|███▊ | ETA: 0:00:06
[ Info: add and build Colors
ERROR: LoadError: MethodError: no method matching iterate(::Nothing)
Closest candidates are:
iterate(!Matched::Core.SimpleVector) at essentials.jl:604
iterate(!Matched::Core.SimpleVector, !Matched::Any) at essentials.jl:604
iterate(!Matched::ExponentialBackOff) at error.jl:214
...
Stacktrace:
[1] first(::Nothing) at ./abstractarray.jl:342
[2] |>(::Nothing, ::typeof(first)) at ./operators.jl:854
[3] macro expansion at /Users/abradley/Dropbox/tufte_algorithms_book/install_pkgs.jl:41 [inlined]
[4] macro expansion at /Users/abradley/.julia/packages/ProgressMeter/NIpPa/src/ProgressMeter.jl:606 [inlined]
[5] top-level scope at /Users/abradley/Dropbox/tufte_algorithms_book/install_pkgs.jl:30
[6] include at ./boot.jl:328 [inlined]
[7] include_relative(::Module, ::String) at ./loading.jl:1094
[8] include(::Module, ::String) at ./Base.jl:31
[9] exec_options(::Base.JLOptions) at ./client.jl:295
[10] _start() at ./client.jl:464
in expression starting at /Users/abradley/Dropbox/tufte_algorithms_book/install_pkgs.jl:29
julia> versioninfo()
Julia Version 1.2.0
Commit c6da87ff4b (2019-08-20 00:03 UTC)
Platform Info:
OS: macOS (x86_64-apple-darwin18.6.0)
CPU: Intel(R) Core(TM) i5-8259U CPU @ 2.30GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-6.0.1 (ORCJIT, skylake)
Environment:
JULIA_NUM_THREADS = 4
Recently the CI fails with the following message:
Stage: deploy
Name: Deploy
Trace: exec /busybox/sh
else
echo shell not found
exit 1
fi
Any idea what could have gone wrong?
What is a good method for displaying code in a document and then using it in a juliaconsole
block?
The following seems to work, but I suspect there is a simpler way.
\begin{example}
\begin{juliablock}
some code
\end{juliablock}
\caption{example code}
\end{example}
Then I copy the code in the juliablock
by hand into a file called example_code.jl
.
Then I do this:
\begin{juliaconsole}
include("example_code.jl"); nothing
... use code...
\end{juliaconsole}
I found that you also need to add Colors
.
I had never used PythonTex before. make compile
results in
PythonTeX error
The version of the PythonTeX scripts does not match the last code
saved by the document--run LaTeX to create an updated version.
searching the web did not help. How would one fix this?
I have an algorithm defined as follows:
\begin{algorithm}
\begin{juliaverbatim}
function my_large_sum()
s = 0
for i=1:100000000000
s += i
end
return s
end
\end{juliaverbatim}
\end{algorithm}
This algorithm is rendered correctly and I can use it in tests, but not in the console environment:
\begin{juliaconsole}
import BenchmarkTools: @btime;
@btime my_large_sum()
\end{juliaconsole}
Doing this produces the following:
How can I access these functions in the console space?
is there any way to run the python scripts ( or get the things done they do ) without having to use sudo
?
I don't have admin rights on my work machine.
Is it possible to define eg. a function in a jlblock
and call that function in juliaconsole
? There is a workaround proposed in gpoore/pythontex#55 can this be applied to the julia version?
Looks like pythontex v0.17 (it was v0.17-dev) breaks the pipeline, I'll need some time to investigate it, just open an issue here in case others meet the same problem.
@tawheeler greatly improved the appearance of the TOC as part of the new Algorithms for Decision Making book. It would be good to get this merged in here.
Document the replacement feature for the algorithm environment.
After fully rebuilding the book with a new checkout from this repo, and manually adding ImageIO
which it requests, I still get an error that I can't get past:
---- Messages for jl:default:default ----
* PythonTeX notice
1 message(s) could not be classified
Interpreted as errors, based on the return code(s)
ERROR: LoadError: FileIO.File{FileIO.DataFormat{:UNKNOWN}}("/Users/abradley/Dropbox/Julia/linear_systems_book_v4/tmp_10000000000001.png") couldn't be recognized by FileIO.
Stacktrace:
[1] #save#30(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(FileIO.save), ::FileIO.Formatted, ::Any) at /Users/abradley/.julia/packages/FileIO/Glbhe/src/loadsave.jl:196
[2] save at /Users/abradley/.julia/packages/FileIO/Glbhe/src/loadsave.jl:196 [inlined]
It only happens for a particular figure in the book, which is a 2d image. Other figures that are just regular line plots work fine. So the offending command is
push!(g, Axis(Plots.Image(abs2.(f),(-1e-3,1e-3),(0.,3e-3),colormap=ColorMaps.Named("Blues"),colorbar=false),
width="5cm",height="10cm"))
I am using
julia> versioninfo()
Julia Version 1.3.1
Commit 2d5741174c (2019-12-30 21:36 UTC)
Platform Info:
OS: macOS (x86_64-apple-darwin18.6.0)
CPU: Intel(R) Core(TM) i5-8259U CPU @ 2.30GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-6.0.1 (ORCJIT, skylake)
Environment:
JULIA_NUM_THREADS = 4
Any help greatly appreciated!
When compiling the book, I am getting this error:
ImportError: cannot import name 'unirange' from 'pygments.util' (/usr/local/lib/python3.10/dist-packages/Pygments-2.15.1-py3.10.egg/pygments/util.py)
make: [makefile:14: compile] Error 1 (ignored)
On a fresh clone in MacOS Ventura, with julia 1.8.0:
make test
gives: ALL TESTS PASSED.
But make compile
gives
This is PythonTeX 0.18
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/Cellar/texlive/20220321_3/libexec/lib/python3.10/site-packages/pygments/styles/__init__.py", line 82, in get_style_by_name
mod = __import__('pygments.styles.' + mod, None, None, [cls])
ModuleNotFoundError: No module named 'pygments.styles.algforopt'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/Cellar/[email protected]/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/local/Cellar/texlive/20220321_3/share/texmf-dist/scripts/pythontex/pythontex3.py", line 2403, in do_pygments
formatter[codetype] = LatexFormatter(**p)
File "/usr/local/Cellar/texlive/20220321_3/libexec/lib/python3.10/site-packages/pygments/formatters/latex.py", line 257, in __init__
Formatter.__init__(self, **options)
File "/usr/local/Cellar/texlive/20220321_3/libexec/lib/python3.10/site-packages/pygments/formatter.py", line 66, in __init__
self.style = _lookup_style(options.get('style', 'default'))
File "/usr/local/Cellar/texlive/20220321_3/libexec/lib/python3.10/site-packages/pygments/formatter.py", line 21, in _lookup_style
return get_style_by_name(style)
File "/usr/local/Cellar/texlive/20220321_3/libexec/lib/python3.10/site-packages/pygments/styles/__init__.py", line 84, in get_style_by_name
raise ClassNotFound("Could not find style module %r" % mod +
pygments.util.ClassNotFound: Could not find style module 'algforopt'.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/Cellar/texlive/20220321_3/share/texmf-dist/scripts/pythontex/pythontex3.py", line 2882, in <module>
main(python=sys.version_info.major)
File "/usr/local/Cellar/texlive/20220321_3/share/texmf-dist/scripts/pythontex/pythontex3.py", line 2828, in main
do_multiprocessing(data, temp_data, old_data, engine_dict)
File "/usr/local/Cellar/texlive/20220321_3/share/texmf-dist/scripts/pythontex/pythontex3.py", line 1390, in do_multiprocessing
result = task.get()
File "/usr/local/Cellar/[email protected]/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
pygments.util.ClassNotFound: Could not find style module 'algforopt'.
make: [compile] Error 1 (ignored)
Hi,
Thank you very much for providing such a powerful toolchain, I like the style of your book, and I'm planning to use this to write some tutorial materials for undergraduate students.
According to the README, I've successfully set the dependencies up. When I look into the template details, I find four environments defined:
jlcode
jlblock
juliaconsole
juliatest
I'm not sure if this is correct, but here's my understanding:
* codes in jlcode
are used only once and don't affect the following codes, and jlblock
do.
* jlblock
and jlconsole
only diff in the pygments colors.
* juliatest
acts the same as juliaconsole
except they're separated and fed into two pipelines.
Also, I don't quite get the difference between jlblock
and juliaconsole
.
Could you please explain the usage of these four environments?
Best
Johnny Chen
my julia didn't come with jlpkg, so I could not issue the
jlpkg --project=@. add $(cat REQUIRE | grep -v julia)
command. Yes, I know, I can also install jlpkg...
For those not immediately famliar with with julia's internal (REPL) method, do:
using Pkg
Pkg.add("Colors")
(and all other packages listed in the REQUIRE file.
I'm not a julia expert yet, but I noticed this installs them in my private ~/,julia tree, not benefiting others that use the new system installed version of julia.
It would be nice to have toml files instead of the deprecated REQUIRE file such that people can just instantiate
the environment. I can prepare a PR if that would be helpful.
Weave creates a kind of gensym module or namespace that pollutes the rendered latex
\begin{juliaconsole}
struct A end
A()
\end{juliaconsole}
Renders as this:
julia> struct A end
julia> A()
Main.##WeaveSandBox#245.A()
Did you encounter this in your book? Is there a way around it?
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