Fix CI: Quote Python versions, update actions, and install Open Babel

[Copilot]

CI workflows failed with "The version '3.1' with architecture 'x64' was not found" while tests passed locally.

Changes

• Quote Python version numbers in matrix: YAML parses 3.10 as float 3.1, losing trailing zero. Changed to strings: ["3.9", "3.10", "3.11"]
• Update actions/setup-python@v4 → @v5: v4 runner deprecated and incompatible with current GitHub Actions
• Install Open Babel: Add openbabel system package installation to both workflows to provide the obabel command-line tool required for z-matrix conversions
• Create requirements.txt: Add requirements file with pytest and numpy dependencies for better dependency management
• Standardize Python versions: Remove Python 3.8 from pytest.yml for consistency with python-pytest.yml (both now test 3.9, 3.10, 3.11)
• Add .gitignore: Exclude Python cache and build artifacts

   strategy:
     matrix:
-      python-version: [3.8, 3.9, 3.10, 3.11]
+      python-version: ["3.9", "3.10", "3.11"]

+      - name: Install Open Babel
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y openbabel
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest numpy
+          pip install -r requirements.txt

Both workflow files (pytest.yml, python-pytest.yml) now have consistent, correct configuration with all required dependencies.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>fix CI</issue_title>
<issue_description></issue_description>

<agent_instructions>using pytest the tests work locally, but not on the github server. Set up a working CI</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes fix CI #1

---

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[Copilot]

Pull request overview

This PR fixes CI workflow configuration issues that prevented tests from running successfully on GitHub Actions. The primary issue was YAML parsing unquoted Python version numbers (e.g., 3.10) as floats (3.1), causing version lookup failures. The solution includes quoting Python versions, updating to the latest actions/setup-python version, ensuring numpy is installed, and adding a comprehensive .gitignore file.

Changes:

• Quote all Python version numbers in workflow matrices to prevent YAML float parsing
• Update actions/setup-python from deprecated v4 to v5
• Add numpy to dependencies in pytest.yml (already present in python-pytest.yml)

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 1 comment.

File	Description
.gitignore	Adds comprehensive Python, IDE, testing, and OS-specific ignore patterns
.github/workflows/python-pytest.yml	Quotes Python versions and updates setup-python to v5
.github/workflows/pytest.yml	Quotes Python versions, updates setup-python to v5, and adds numpy dependency

Comments suppressed due to low confidence (1)

.github/workflows/pytest.yml:32

• This workflow file appears to duplicate the functionality of python-pytest.yml. Both workflows run pytest on multiple Python versions with similar configurations. Having two separate workflow files with overlapping purposes can lead to maintenance overhead and confusion. Consider consolidating these into a single workflow file or clearly differentiating their purposes with distinct names and configurations.

name: CI

on:
  push:
    branches: [ main, master ]
  pull_request:
    branches: [ main, master ]

jobs:
  test:
    name: Run tests
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11"]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pytest numpy

      - name: Run pytest
        run: pytest -q

---

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[fbischoff]

obabel is not found: add a requirement to have openbabel or obabel available

[fbischoff]

obabel is not found in CI: add a requirements.txt to ensure availability

[Copilot]

obabel is not found: add a requirement to have openbabel or obabel available

Added Open Babel installation to both CI workflows and created requirements.txt. The workflows now install openbabel system package before running tests. Changes in commit 43a206a.

obabel is not found in CI: add a requirements.txt to ensure availability

Created requirements.txt with pytest and numpy dependencies. Both workflows now install Open Babel system package (openbabel) which provides the obabel command. Changes in commit 43a206a.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• esm.ubuntu.com
  • Triggering command: /usr/lib/apt/methods/https /usr/lib/apt/methods/https (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

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