ci: upgrade Python 3.8 → 3.11 in tool_list_conversion workflow

[Copilot]

python-frontmatter now imports TypeGuard from typing, which requires Python 3.10+. This breaks both validation and registry-lookup jobs running on Python 3.8 with an ImportError.

Changes

• .github/workflows/tool_list_conversion.yml: bump python-version from 3.8 to 3.11 in both jobs

Original prompt

Fix the failing GitHub Actions job in repository elixir-europe/infectious-diseases-toolkit.

Context:

• Failing job URL: https://github.com/elixir-europe/infectious-diseases-toolkit/actions/runs/26404324139/job/77723909713
• Workflow file: .github/workflows/tool_list_conversion.yml
• The workflow currently uses Python 3.8 in both the validation and registry-lookup jobs.
• The install step installs ruamel.yaml requests python-frontmatter.
• The job log shows this import error:
  • ImportError: cannot import name 'TypeGuard' from 'typing' (/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/typing.py)
• This indicates an incompatibility between Python 3.8 and the currently resolved python-frontmatter dependency.

Requested fix:

• Update the workflow so the job no longer fails due to this dependency/runtime mismatch.
• Preferred approach: upgrade the workflow Python version from 3.8 to a compatible currently supported version such as 3.11 in both jobs.
• Keep the change minimal and focused on fixing the workflow failure.

Acceptance criteria:

• The workflow .github/workflows/tool_list_conversion.yml is updated so both jobs use a compatible Python version.
• No unrelated files are modified.
• Open a pull request with a concise title and summary explaining the compatibility fix.

The following is the prior conversation context from the user's chat exploration (may be truncated):

User: Please find a solution for this failing job. Use the logs, job definition, and any referenced files where the failure occurred. Keep your response focused on the solution and include code suggestions when appropriate.

Assistant: The failure is caused by an incompatible Python/package combination in the workflow, not by the validator script itself.

Root cause

The job runs on Python 3.8:

• .github/workflows/tool_list_conversion.yml lines 13–14
• .github/workflows/tool_list_conversion.yml lines 36–38

and installs python-frontmatter without pinning a compatible version:

• .github/workflows/tool_list_conversion.yml lines 22–25
• .github/workflows/tool_list_conversion.yml lines 49–52

The log shows:

• ImportError: cannot import name 'TypeGuard' from 'typing'

This happens because the installed python-frontmatter dependency now imports TypeGuard from typing, which requires a newer Python version than 3.8.

Solution

Use one of these fixes:

Preferred fix: upgrade the workflow to Python 3.10+

Update both job matrices from 3.8 to 3.10 or 3.11.

strategy:
  matrix:
    python-version: [3.11]

Apply that change in:

• validation job: https://github.com/elixir-europe/infectious-diseases-toolkit/blob/083b3a994b47c1eb4704b87485c14390a962d3dc/.github/workflows/tool_list_conversion.yml
• registry-lookup job: same file

A minimal patch would be:

jobs:
  validation:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.11]

and

  registry-lookup:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.11]

Alternative fix: pin python-frontmatter to a Python-3.8-compatible version

If you must stay on Python 3.8, pin the package in the install step instead of installing the latest release.

Example:

pip install ruamel.yaml requests "python-frontmatter<1.1"

This is less future-proof than upgrading Python, because Python 3.8 is already old and more dependencies may start breaking similarly.

Recommended final change

Update the workflow file at:

• https://github.com/elixir-europe/infectious-diseases-toolkit/blob/083b3a994b47c1eb4704b87485c14390a962d3dc/.github/workflows/tool_list_conversion.yml

Change:

python-version: [3.8]

to:

python-version: [3.11]

in both jobs.

If you want to make the install step more reproducible as well, use:

- name: Install dependencies
  run: |
    python -m pip install --upgrade pip
    pip install ruamel.yaml requests python-frontmatter

with Python 3.11, or pin all dependency versions explicitly.

User: you can make a PR fixing this

Assistant: I’ve prepared the PR fix and am currently waiting for your confirmation on the repo action before I can continue.

This pull request was created from Copilot chat.