Add GitHub Copilot setup configuration file

[Copilot]

This PR adds a .github/copilot-setup-steps.yml file to configure the development environment when GitHub Copilot is launched in the repository.

Configuration Details

The setup file is structured as a proper GitHub Actions workflow that configures a Python 3.13 environment using Micromamba with the following components:

Workflow Structure

• Name: "Copilot Setup Steps"
• Triggers: workflow_dispatch, push, and pull_request for the copilot-setup-steps.yml file
• Job: copilot-setup-steps running on ubuntu-latest
• Permissions: contents: read for repository checkout
• Steps: Includes checkout action followed by Micromamba setup and dependency installation

Core Dependencies

• Python 3.13
• NumPy >= 2.0
• MKL, SciPy, pip, and mkl-service
• Build tools: graphviz, cython
• Testing framework: pytest, coverage, pytest-cov, pytest-benchmark, pytest-mock, pytest-sphinx

Optional Backend Support

• JAX: Includes jax, jaxlib, numpyro, equinox, and tfp-nightly
• Numba: numba >= 0.57

Excluded Dependencies

• PyTorch is intentionally excluded from this configuration

The configuration follows the GitHub Copilot documentation format for customizing the agent environment and is based on the existing .github/workflows/test.yml CI workflow, using the same Micromamba setup pattern (version 1.5.10-0) to ensure consistency between local development and CI environments.

This file will help contributors quickly set up a working development environment with the necessary dependencies for working on PyTensor and allows for easy validation through GitHub Actions.

Original prompt

Please create a new file named .github/copilot-setup-steps.yml in the pymc-devs/pytensor repository.

This file will be used by GitHub Copilot to set up a working environment when it's launched in the repository. The setup is based on the existing .github/workflows/test.yml file and is configured to:

• Use Python 3.13.
• Install the default dependencies.
• Install JAX and Numba dependencies.
• Exclude PyTorch.

Here is the content for the .github/copilot-setup-steps.yml file:

steps:
  - name: "Set up Micromamba"
    uses: mamba-org/setup-micromamba@v2
    with:
      environment-name: pytensor-test
      micromamba-version: "1.5.10-0"
      init-shell: bash
      post-cleanup: "all"
      create-args: python=3.13

  - name: "Install dependencies"
    shell: micromamba-shell {0}
    run: |
      micromamba install --yes -q -c conda-forge python=3.13 mkl "numpy>=2.0" scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock pytest-sphinx
      micromamba install --yes -q -c conda-forge "numba>=0.57"
      micromamba install --yes -q -c conda-forge jax jaxlib numpyro equinox
      pip install tfp-nightly
      pip install -e ./

*This pull request was created as a result of the following prompt from Copilot chat.* > Please create a new file named `.github/copilot-setup-steps.yml` in the `pymc-devs/pytensor` repository. > > This file will be used by GitHub Copilot to set up a working environment when it's launched in the repository. The setup is based on the existing `.github/workflows/test.yml` file and is configured to: > - Use Python 3.13. > - Install the default dependencies. > - Install JAX and Numba dependencies. > - Exclude PyTorch. > > Here is the content for the `.github/copilot-setup-steps.yml` file: > > ```yaml > steps: > - name: "Set up Micromamba" > uses: mamba-org/setup-micromamba@v2 > with: > environment-name: pytensor-test > micromamba-version: "1.5.10-0" > init-shell: bash > post-cleanup: "all" > create-args: python=3.13 > > - name: "Install dependencies" > shell: micromamba-shell {0} > run: | > micromamba install --yes -q -c conda-forge python=3.13 mkl "numpy>=2.0" scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock pytest-sphinx > micromamba install --yes -q -c conda-forge "numba>=0.57" > micromamba install --yes -q -c conda-forge jax jaxlib numpyro equinox > pip install tfp-nightly > pip install -e ./ > ``` >

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

[ricardoV94]

@copilot copilot According to the docs: https://docs.github.com/en/enterprise-cloud@latest/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment#preinstalling-tools-or-dependencies-in-copilots-environment

A copilot-setup-steps.yml file looks like a normal GitHub Actions workflow file, but must contain a single copilot-setup-steps job. This job will be executed in GitHub Actions before Copilot starts working.

Example:

name: "Copilot Setup Steps"

# Automatically run the setup steps when they are changed to allow for easy validation, and
# allow manual testing through the repository's "Actions" tab
on:
  workflow_dispatch:
  push:
    paths:
      - .github/workflows/copilot-setup-steps.yml
  pull_request:
    paths:
      - .github/workflows/copilot-setup-steps.yml

jobs:
  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
  copilot-setup-steps:
    runs-on: ubuntu-latest

    # Set the permissions to the lowest permissions possible needed for your steps.
    # Copilot will be given its own token for its operations.
    permissions:
      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
      contents: read

    # You can define any steps you want, and they will run before the agent starts.
    # If you do not check out your code, Copilot will do this for you.
    steps:
      - name: Checkout code
        uses: actions/checkout@v5

      - name: Set up Node.js
        uses: actions/setup-node@v4
        with:
          node-version: "20"
          cache: "npm"

      - name: Install JavaScript dependencies
        run: npm ci

Please update the file to follow the requirements as mentioned in the docs

[Copilot]

@copilot copilot According to the docs: https://docs.github.com/en/enterprise-cloud@latest/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment#preinstalling-tools-or-depend...

Updated the file to follow the proper GitHub Actions workflow format as specified in the documentation. The file now includes:

• Workflow name and triggers (workflow_dispatch, push, pull_request)
• A copilot-setup-steps job running on ubuntu-latest
• Proper permissions (contents: read)
• Checkout step before the setup steps

Changes committed in 6a6e2a4.

[ricardoV94]

should this be inside the workflows directory? The docs above state it should go directly in .github, but then reference regular workflows for the API. I guess we can just try or find another repo where it's working

[ricardoV94]

Talked with @maresb, he agreed to just merge and see