fix: make fitting test self-contained

[john-halloran]

@sbillinge This PR was made with your comments here in mind. All test data is now self-contained. If we want to run on the real data, that can be something we do as part of the release process, but we no longer need to distribute large data files with the sdist.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.28%. Comparing base (d7586bc) to head (92c0ddb).
⚠️ Report is 10 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #201      +/-   ##
==========================================
- Coverage   77.50%   74.28%   -3.22%     
==========================================
  Files           3        3              
  Lines          40       35       -5     
==========================================
- Hits           31       26       -5     
  Misses          9        9              

Files with missing lines	Coverage Δ
tests/test_snmf_optimizer.py	100.00% <100.00%> (ø)

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[sbillinge]

@john-halloran please see my comment below.

[sbillinge]

If we make this change we need to make an issue to change it back. The fix I think though is to include the change from docformatter to ruff. Please look at the scikit-package code to see the changes that are needed. There is an update to this yaml file and then also to the pyproject.toml. Then the pre-commit will work on 3.14.

[sbillinge]

please see my comment

[sbillinge]

please remove this. We don't want this, but update all the pre-commit versions, e.g. the below is copied from diffpy.utils:

default_language_version:
  python: python3
ci:
  autofix_commit_msg: |
    [pre-commit.ci] auto fixes from pre-commit hooks
  autofix_prs: true
  autoupdate_branch: "pre-commit-autoupdate"
  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
  autoupdate_schedule: monthly
  skip: [no-commit-to-branch]
  submodules: false
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: check-yaml
      - id: end-of-file-fixer
      - id: trailing-whitespace
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-toml
      - id: check-added-large-files
  - repo: https://github.com/psf/black
    rev: 26.5.1
    hooks:
      - id: black
  - repo: https://github.com/pycqa/flake8
    rev: 7.3.0
    hooks:
      - id: flake8
  - repo: https://github.com/pycqa/isort
    rev: 9.0.0a3
    hooks:
      - id: isort
        args: ["--profile", "black"]
  - repo: https://github.com/kynan/nbstripout
    rev: 0.9.1
    hooks:
      - id: nbstripout
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: no-commit-to-branch
        name: Prevent Commit to Main Branch
        args: ["--branch", "main"]
        stages: [pre-commit]
  - repo: https://github.com/codespell-project/codespell
    rev: v2.4.2
    hooks:
      - id: codespell
        additional_dependencies:
          - tomli
  # prettier - multi formatter for .json, .yml, and .md files
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v4.0.0-alpha.8
    hooks:
      - id: prettier
        additional_dependencies:
          - "prettier@^3.2.4"
  # docformatter - PEP 257 compliant docstring formatter
  - repo: https://github.com/PyCQA/docformatter
    rev: v1.7.8
    hooks:
      - id: docformatter
        additional_dependencies: [tomli]
        args: [--in-place, --config, ./pyproject.toml]

and the relevant block in pyproject.toml is

[tool.docformatter]
recursive = true
wrap-summaries = 72
wrap-descriptions = 72

please adapt as needed here.