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Add conda environment configuration#320

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rvosa merged 2 commits intomasterfrom
copilot/add-environment-yml-file
Dec 22, 2025
Merged

Add conda environment configuration#320
rvosa merged 2 commits intomasterfrom
copilot/add-environment-yml-file

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Copilot AI commented Dec 22, 2025

Adds environment.yml for reproducible conda-based build and deployment setup.

Configuration

  • Environment name: treebase
  • Channels: conda-forge, bioconda (excludes defaults)
  • Dependencies:
    • openjdk=17 (Java 17 LTS per BUILDING.md requirements)
    • tomcat
    • maven
    • postgresql

Users can create the environment with:

conda env create -f environment.yml
conda activate treebase
Original prompt

Create an environment.yml file in the root of the repo that sets up a conda environment for building and deploying treebase. Requirements:

  • don't use defaults channel, only conda-forge and bioconda
  • name the environment treebase
  • include the right (openjdk) Java version
  • include tomcat
  • include maven
  • include postgres

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
Copilot AI changed the title [WIP] Add environment.yml for treebase setup Add conda environment configuration Dec 22, 2025
Copilot AI requested a review from rvosa December 22, 2025 16:03
@rvosa rvosa marked this pull request as ready for review December 22, 2025 16:09
@rvosa rvosa merged commit 3acf5af into master Dec 22, 2025
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@rvosa rvosa deleted the copilot/add-environment-yml-file branch December 22, 2025 16:09
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2 participants