Error building with showyourwork v0.4.2

[krosenfeld-IDM]

When I try to build (showyourwork, showyourwork build) using showyourwork v0.4.2 I get the following error:

(syw) [krosenfeld@internal.idm.ctr@ipapvwks25 pysr_paper]$  showyourwork build --conda-frontend=mamba
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Removing incomplete Conda environment /home/krosenfeld/mambaforge/envs/syw/lib/python3.9/site-packages/showyourwork/workflow/envs/environment.yml...
Creating conda environment /home/krosenfeld/mambaforge/envs/syw/lib/python3.9/site-packages/showyourwork/workflow/envs/environment.yml...
Downloading and installing remote packages.
Environment for /home/krosenfeld/mambaforge/envs/syw/lib/python3.9/site-packages/showyourwork/workflow/envs/environment.yml created (location: .snakemake/conda/7afa7ee2bbc22e456af866a145b290e5_)
Setting up the internal conda environment...
Setting up the workflow...
warning: accessing absolute path `/dev/null`; build may not be reproducible in other environments
warning: open of input /dev/null.tex failed
caused by: access to the path `/dev/null.tex` is forbidden
warning: open of input /dev/null.tex failed
caused by: access to the path `/dev/null.tex` is forbidden
warning: algorithm2e.sty:284:
Invalid UTF-8 byte or sequence at line 284 replaced by U+FFFD.
warning: algorithm2e.sty:299: Invalid UTF-8 byte or sequence at line 299 replaced by U+FFFD.
warning: algorithm2e.sty:550: Invalid UTF-8 byte or sequence at line 550 replaced by U+FFFD.
/usr/bin/which: no pygmentize in (/home/krosenfeld/.juliaup/bin:/home/krosenfeld/playpen/pysr_paper/.snakemake/conda/7afa7ee2bbc22e456af866a145b290e5_/bin:/home/krosenfeld/mambaforge/condabin:/home/krosenfeld/.local/bin:/home/krosenfeld/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
warning: command exited with error code 1
error: failed to execute the shell-escape command "which pygmentize && touch ms.aex": execution of the request failed
error: ms.tex:131: Package minted Error: You must have `pygmentize' installed to use this package.

See the minted package documentation for explanation.
Type  H <return>  for immediate help
error: halted on potentially-recoverable error as specified

! Package minted Error: You must have `pygmentize' installed to use this packag
e.

See the minted package documentation for explanation.
Type  H <return>  for immediate help.
 ...

l.131 \usepackage{cleveref} \begin{document}

No pages of output.

For more information, check out the log file:
/home/krosenfeld/playpen/pysr_paper/.showyourwork/logs/tectonic.log.

If I am running the development version (0.4.3rc3.dev16+g7fb81ba) then the workflow seems to run through.

[MilesCranmer]

Hi @krosenfeld-IDM,

The showyourwork version is given here:

https://github.com/MilesCranmer/pysr_paper/blob/b30687433fb32d3b9784fbedb1480d947dc46fc0/showyourwork.yml#L85

so it should only be ran with 0.4.1 for full reproducibility. Let me know if that gives you any issues!

[krosenfeld-IDM]

Thanks @MilesCranmer. After creating a new environment and installing showyourwork v0.4.1 I get the same error.

Below is the environment details:

# packages in environment at /home/krosenfeld/playpen/pysr_paper/env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
appdirs                   1.4.4                    pypi_0    pypi
arrow                     1.2.3                    pypi_0    pypi
attrs                     23.1.0                   pypi_0    pypi
binaryornot               0.4.4                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22                pypi_0    pypi
chardet                   5.1.0                    pypi_0    pypi
charset-normalizer        3.2.0                    pypi_0    pypi
click                     8.1.6                    pypi_0    pypi
configargparse            1.7                      pypi_0    pypi
connection-pool           0.0.3                    pypi_0    pypi
cookiecutter              2.2.3                    pypi_0    pypi
datrie                    0.8.2                    pypi_0    pypi
docutils                  0.20.1                   pypi_0    pypi
dpath                     2.1.6                    pypi_0    pypi
fastjsonschema            2.18.0                   pypi_0    pypi
gitdb                     4.0.10                   pypi_0    pypi
gitpython                 3.1.32                   pypi_0    pypi
idna                      3.4                      pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jsonschema                4.18.4                   pypi_0    pypi
jsonschema-specifications 2023.7.1                 pypi_0    pypi
jupyter-core              5.3.1                    pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.3                    pypi_0    pypi
nbformat                  5.9.2                    pypi_0    pypi
ncurses                   6.4                  hcb278e6_0    conda-forge
openssl                   3.1.1                hd590300_1    conda-forge
packaging                 23.1                     pypi_0    pypi
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
plac                      1.3.5                    pypi_0    pypi
platformdirs              3.10.0                   pypi_0    pypi
psutil                    5.9.5                    pypi_0    pypi
pulp                      2.7.0                    pypi_0    pypi
python                    3.9.16          h2782a2a_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python-graphviz           0.20.1                   pypi_0    pypi
python-slugify            8.0.1                    pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
ratelimiter               1.2.0.post0              pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.0                   pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
reretry                   0.11.8                   pypi_0    pypi
rpds-py                   0.9.2                    pypi_0    pypi
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
showyourwork              0.4.1                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
smart-open                6.3.0                    pypi_0    pypi
smmap                     5.0.0                    pypi_0    pypi
snakemake                 7.15.2                   pypi_0    pypi
stopit                    1.1.2                    pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
text-unidecode            1.3                      pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
toposort                  1.10                     pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.4                    pypi_0    pypi
wheel                     0.41.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.15.0                   pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
yte                       1.5.1                    pypi_0    pypi

[krosenfeld-IDM]

This is not-blocking. Just for your information!

[MilesCranmer]

Hm, that's weird. Everything should be installed automatically. That is how the GitHub actions is able to generate the paper each time it runs... I'll take a look.

[MilesCranmer]

pygments should be installed by this environment file: https://github.com/MilesCranmer/pysr_paper/blob/main/tectonic.yml

[MilesCranmer]

Could you try using the specific commit 8bfb4b7187bd6a0f7f781295e6208e92136bc581 in my branch, i.e.,

pip install git+https://github.com/MilesCranmer/showyourwork.git@8bfb4b7187bd6a0f7f781295e6208e92136bc581

?

[MilesCranmer]

I'm gonna try to fix this today and update it to the latest version.

Waiting on https://github.com/showyourwork/showyourwork/pull/364 to be merged first...

[krosenfeld-IDM]

Building from your commit worked.