[Required]
make
iverilog

python3-numpy
python3-pip
flake8

Note that python2 is very much past its end-of-life; we support and
recommend using python3.

[optional]
Verilator
Yosys

python3-scipy
python3-matplotlib

=====
Summary, well tested on Debian Bookworm and Trixie:

apt-get install -y build-essential git iverilog gtkwave verilator python3-pip
apt-get install -y python3-numpy python3-flake8 python3-scipy python3-matplotlib
pip3 install cocotb cocotb-bus

=====
The setup instructions for bedrock on Fedora should be:

yum install iverilog gtkwave make g++ python3-numpy python3-scipy python3-pip
pip3 install cocotb cocotb-bus

but then we hit a iverilog-vpi configuration bug seemingly caused by RedHat.
The evasive action I suggest is to build iverilog from source:

sudo yum remove iverilog
sudo yum install bison flex
cd
wget ftp://icarus.com/pub/eda/verilog/v10/verilog-10.2.tar.gz
echo "96dedbddb12d375edb45a144a926a3ba1e3e138d6598b18e7d79f2ae6de9e500  verilog-10.2.tar.gz" | sha256sum -c
tar -xvzf verilog-10.2.tar.gz
cd verilog-10.2
./configure --prefix=$HOME
make
make install

=====
Windows Subsystem for Linux (WSL)
??? works?

=====
macOS
??? works?