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Fix installation issues and update dependencies and instructions#9

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michoug wants to merge 6 commits intobhagavadgitadu22:masterfrom
michoug:master
Open

Fix installation issues and update dependencies and instructions#9
michoug wants to merge 6 commits intobhagavadgitadu22:masterfrom
michoug:master

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@michoug
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@michoug michoug commented Mar 2, 2026

This pull request introduces several improvements to the installation process, updates dependencies, and makes minor fixes to documentation and resource handling. The most significant changes focus on making installation smoother (especially for conda users), clarifying troubleshooting steps, and ensuring compatibility with specific Python versions.

Installation and setup improvements:

  • Updated the installation instructions in README.md to recommend using conda and provided detailed troubleshooting steps for common compilation errors, including handling libclang issues and cleaning up Rust cache.
  • Added instructions for WSL users to install wslu to enable browser opening from the terminal.
  • Changed the recommended environment creation method in docs/INSTALL.md from mamba to conda for consistency.
  • Updated thebigbam_env.yaml to explicitly include rust, libclang, python=3.12, and blast as dependencies for smoother setup.

Dependency and compatibility updates:

  • Restricted the supported Python versions in pyproject.toml to >=3.9,<3.13 to avoid compatibility issues with some packages.
  • Changed the rust-htslib dependency in Cargo.toml to version 0.44 with the static feature for improved binary portability.

Minor fixes and housekeeping:

  • Moved the [project.urls] section in pyproject.toml below the dependencies to be able to install the package
  • Fixed a resource path in start_bokeh_server.py to use LOGO.png instead of logo.png.

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