chore/ci and community files

[jasmin-guven]

1. Moved the broken "tests"

• Moved the existing tests/test_*.py scripts (no assertions, print-debugging against local filesystem) into tests/legacy_scripts/
• Added a placeholder test tests/test_placeholder.py (def test_import(): import meze)
• A late PR will delete legacy_scripts/ as it replaces each file with a real test

2. pyproject.toml and dev-environment.yml additions

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "slow: requires real MD/BSS runs",
    "gpu: requires a GPU / AMBERHOME",
]

Add pytest, pytest-cov, and ambertools (conda-forge — free, unlocks tleap/antechamber/MCPB.py for CI without needing the licensed GPU pmemd build):

  - pytest
  - pytest-cov
  - ambertools

4. .github/workflows/tests.yml

• Triggers: push to main, and all pull_requests
• mamba-org/setup-micromamba@v2 with environment-file: dev-environment.yml, caching enabled (a full BioSimSpace/openbiosim solve is slow — cache is the difference between ~1 min and ~8 min per run).
• Single job, ubuntu-latest, one Python version to start (3.12, matching the pin) — no matrix yet, nothing here is OS-sensitive and GPU/SLURM paths can't run in CI anyway.
• Step: pytest tests/ -m "not slow and not gpu" --cov=meze --cov-report=term-missing.
• Added linting with flake8, in two steps: 1st run covers syntax errors, 2nd covers style

5. CONTRIBUTING.md

• Dev setup: mamba env create -f dev-environment.yml && mamba activate meze-dev.
• How to run tests locally (same command as CI).
• Branch naming convention (type/short-description, matching what's already in use).
• PR expectations: one logical change per PR, tests for new functionality, CI must pass.

6. CITATION.cff 🚫 -> move to a separate issue later

• Authors: Güven (ORCID 0000-0003-1555-0075, pulled from paper.md) ...
• license: MIT, repository-code URL.

7. .github/PULL_REQUEST_TEMPLATE.md (doesn't exist yet — only ISSUE_TEMPLATE/ does) 🚫 -> maybe add later

• Short: description, related issue link, checklist (tests added, docs updated, CI passing).

8. README badges 🚫 -> move to a separate issue later

• CI status badge (![tests](.../workflows/tests.yml/badge.svg)) and license badge, added under the title. Skip a docs badge for now — nothing's hosted until PR bug/uncomment-run-lines #11.

Edited from @claude output