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I think this is pretty much the same issue as #1086. The suggested fix got merged and it still doesn't seem to work, so here's a follow up issue.
to reproduce:
\documentclass[a4paper, 11pt]{article}
\usepackage[margin=2cm]{geometry}
\usepackage{pythontex}
\usepackage{graphicx}
\begin{document}
\begin{pycode}
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 2*np.pi, 100)
plt.plot(x, np.sin(x), label=r'$\sin(x)$')
plt.plot(x, np.cos(x), label=r'$\cos(x)$')
plt.xlabel(r'$x$')
plt.ylabel(r'$y$')
plt.title(r'Sine and Cosine Functions')
plt.legend()
plt.grid(True)
plt.savefig('sine_cosine.pdf')
plt.close()
name = 'sine_cosine.pdf'
\end{pycode}
\begin{figure}[h]
\centering
\includegraphics[width=0.8\textwidth]{sine_cosine.pdf}
\end{figure}
\end{document}
╰─[I] tectonic test.tex
Running TeX ...
error: test.tex:4: ! LaTeX Error: File `pythontex.sty' not found.
error: halted on potentially-recoverable error as specified
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