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lint/deps #29

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b2250fa
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Adafede Feb 3, 2026
43c89a4
Update ci.yml
Adafede Feb 3, 2026
8a880ca
Update .pre-commit-config.yaml
Adafede Feb 3, 2026
137c604
Fix typo in funding organization name
Adafede Feb 3, 2026
b6b7028
Update .pre-commit-config.yaml
Adafede Feb 3, 2026
11c3de7
Update .pre-commit-config.yaml
Adafede Feb 3, 2026
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23 changes: 11 additions & 12 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,11 @@
name: CI Pipeline (PRs and pushes main)
run-name: Merged to main by ${{ github.actor }}

on:
push:
branches:
- main
branches: [main]
pull_request:
branches:
- main
branches: [main]

permissions:
contents: read
Expand All @@ -23,16 +22,16 @@ jobs:
- name: Checkout repository
uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: pip

- name: Install package with pip
run: |
python -m pip install --upgrade pip
pip install .[dev]
- name: Install uv
uses: astral-sh/setup-uv@v3

- name: Install dependencies
run: uv sync --group dev

- name: Run tests
run: pytest
run: uv run pytest
55 changes: 47 additions & 8 deletions .pre-commit-config.yaml
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@@ -1,19 +1,58 @@
fail_fast: true
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
rev: v6.0.0
hooks:
- id: check-ast
- id: check-builtin-literals
- id: check-case-conflict
- id: check-docstring-first
- id: check-illegal-windows-names
- id: check-merge-conflict
- id: check-shebang-scripts-are-executable
- id: check-symlinks
- id: check-toml
- id: check-yaml
- repo: https://github.com/astral-sh/uv-pre-commit
rev: 0.9.5
- id: debug-statements
# - id: end-of-file-fixer
# - id: mixed-line-ending
# - id: trailing-whitespace
- repo: https://github.com/fpgmaas/deptry
rev: 0.24.0
hooks:
- id: uv-lock
- id: deptry
language: python
additional_dependencies: [deptry]
exclude: '^(?!.*\.py$).*$'
- repo: https://github.com/asottile/pyupgrade
rev: v3.21.2
hooks:
- id: pyupgrade
- repo: https://github.com/asottile/add-trailing-comma
rev: v4.0.0
hooks:
- id: add-trailing-comma
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.5.0
rev: v0.14.14
hooks:
- id: ruff
args: [ --fix ]
- id: ruff-check
args:
- --fix
- id: ruff-format
- repo: https://github.com/astral-sh/uv-pre-commit
rev: 0.9.28
hooks:
- id: uv-lock
- repo: https://github.com/tombi-toml/tombi-pre-commit
rev: v0.7.25
hooks:
- id: tombi-format
- id: tombi-lint
- repo: https://github.com/crate-ci/typos
rev: v1
hooks:
- id: typos
exclude: "CITATION.cff|README.md"
- repo: local
hooks:
- id: uv-upgrade
Expand All @@ -25,4 +64,4 @@ repos:
name: pytest
entry: uv run pytest
language: system
types: [ file, python ]
types: [ file, python ]
2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -71,7 +71,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Changelog: flattened structure, changed identifiers to ORCID, changed versioning to major alone (before 'major.minor')
- Evidence: flattened structure to a single object (before: a list of objects)
- Reaction database IDs: flattened structure, changed formatting of EC to the code (e.g. 1.2.3.4) alone (before: string had to start with 'EC'), drop MITE crosslinks
- References: removed non-peristing reference types, only DOI allowed (before: url, pubmed, patent)
- References: removed non-persisting reference types, only DOI allowed (before: url, pubmed, patent)
- Tailoring reaction terms: removed 'FADH2 supply for chlorination' since it is not tailoring per se
- Status: removed 'embargoed' specification

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6 changes: 3 additions & 3 deletions mite_schema/main.py
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Expand Up @@ -45,8 +45,8 @@ def config_logger(verboseness: str) -> logging.Logger:
console_handler = logging.StreamHandler(sys.stdout)
console_handler.setFormatter(
coloredlogs.ColoredFormatter(
"%(asctime)s - %(name)s - %(levelname)s - %(message)s"
)
"%(asctime)s - %(name)s - %(levelname)s - %(message)s",
),
)
logger.addHandler(console_handler)
return logger
Expand Down Expand Up @@ -98,7 +98,7 @@ def main() -> None:
logger = config_logger(args.v)

logger.info(
f"Validate file '{args.i}' with MITE schema v{metadata.version('mite_schema')}."
f"Validate file '{args.i}' with MITE schema v{metadata.version('mite_schema')}.",
)

for file in args.i:
Expand Down
124 changes: 50 additions & 74 deletions pyproject.toml
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@@ -1,57 +1,45 @@
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "mite_schema"
version = "1.8.4"
description = "Containing the Minimum Information about a Tailoring Enzymes data standard schema and auxiliary methods"
readme = "README.md"
requires-python = ">=3.11"
license-files = { paths = ["LICENSE"] }
authors = [
{ name = "Mitja M. Zdouc", email = "zdoucmm@gmail.com" }
]
keywords = [
"cheminformatics",
"genomics"
]
license-files = ["LICENSE"]
authors = [{ name = "Mitja M. Zdouc", email = "zdoucmm@gmail.com" }]
keywords = ["cheminformatics", "genomics"]
classifiers = [
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: MIT License",
"Operating System :: POSIX :: Linux",
"Development Status :: 4 - Beta",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry"
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry"
]
dependencies = [
"argparse~=1.4",
"coloredlogs~=15.0",
"jsonschema~=4.25",
"pydantic~=2.11",
"coloredlogs~=15.0",
"jsonschema~=4.25",
"pydantic~=2.11",
]

[project.urls]
Website = "https://mite.bioinformatics.nl/"
Discussions = "https://github.com/orgs/mite-standard/discussions/3"
Homepage = "https://github.com/mite-standard/mite_schema"
Issues = "https://github.com/mite-standard/mite_schema/issues"
Discussions = "https://github.com/orgs/mite-standard/discussions/3"
Website = "https://mite.bioinformatics.nl/"

[project.scripts]
mite_schema = "mite_schema.main:main"

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Copilot AI Feb 3, 2026

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The change from [project.optional-dependencies] to [dependency-groups] is a significant breaking change for users. The [project.optional-dependencies] section is a PEP 621 standard that allows installing dev dependencies with pip install .[dev]. The [dependency-groups] section is a uv-specific feature (PEP 735) that requires users to use uv for installation. This change will break existing workflows for users who install the package with pip using pip install -e .[dev]. Consider maintaining backward compatibility or documenting this breaking change clearly.

Suggested change
[project.optional-dependencies]
dev = ["pre-commit~=4.3", "pytest~=8.4", "ruff~=0.13"]

Copilot uses AI. Check for mistakes.
[project.optional-dependencies]
dev = [
"pre-commit~=4.3",
"pytest~=8.4",
"ruff~=0.13"
]
[dependency-groups]
dev = ["pre-commit~=4.3", "pytest~=8.4", "ruff~=0.13"]
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Copilot AI Feb 3, 2026

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The pyproject.toml specifies ruff~=0.13 in the dev dependency group, but uv.lock has resolved to version 0.14.14. The ~= operator allows minor version updates (0.13.x) but should not allow 0.14.x. This indicates the lockfile is inconsistent with the dependency specification. Either update pyproject.toml to ruff~=0.14 to match the locked version, or regenerate the lockfile with the correct version constraint.

Suggested change
dev = ["pre-commit~=4.3", "pytest~=8.4", "ruff~=0.13"]
dev = ["pre-commit~=4.3", "pytest~=8.4", "ruff~=0.14"]

Copilot uses AI. Check for mistakes.

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.envs.dev]
features = [
"dev"
]
features = ["dev"]

[tool.hatch.build.targets.sdist]
exclude = [
Expand All @@ -71,48 +59,36 @@ exclude = [
[tool.hatch.build.targets.wheel]
packages = ["mite_schema"]

[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra -q"
testpaths = [
"tests",
]
pythonpath = [
"mite_schema"
]

[tool.ruff.lint]
select = [
# flake8-bugbear
"B",
# flake8-comprehensions
"C4",
# flake8-eradicate/eradicate
"ERA",
# isort
"I",
# pep8-naming
"N",
# flake8-pie
"PIE",
# pygrep
"PGH",
# ruff checks
"RUF",
# flake8-simplify
"SIM",
# flake8-type-checking
"TCH",
# flake8-tidy-imports
"TID",
# pyupgrade
"UP",
# flake8-bugbear
"B",
# flake8-comprehensions
"C4",
# flake8-eradicate/eradicate
"ERA",
# isort
"I",
# pep8-naming
"N",
# flake8-pie
"PIE",
# pygrep
"PGH",
# ruff checks
"RUF",
# flake8-simplify
"SIM",
# flake8-tidy-imports
"TID",
# pyupgrade
"UP",
]
ignore = [
# whitespace-before-punctuation
"E203",
# percent-format-invalid-format
"E501",
# mixed-case-variable-in-class-scope
"N815"
# whitespace-before-punctuation
"E203",
# percent-format-invalid-format
"E501",
# mixed-case-variable-in-class-scope
"N815"
]
9 changes: 6 additions & 3 deletions tests/test_main_cli.py
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Expand Up @@ -12,7 +12,8 @@ def test_no_attrs(monkeypatch):

def test_cli_single_valid(monkeypatch):
monkeypatch.setattr(
"sys.argv", ["mite-schema", "-i", "tests/example_files/example_valid.json"]
"sys.argv",
["mite-schema", "-i", "tests/example_files/example_valid.json"],
)
with pytest.raises(SystemExit) as e:
main()
Expand All @@ -36,7 +37,8 @@ def test_cli_multi_valid(monkeypatch):

def test_cli_single_invalid(monkeypatch):
monkeypatch.setattr(
"sys.argv", ["mite-schema", "-i", "tests/example_files/example_invalid.json"]
"sys.argv",
["mite-schema", "-i", "tests/example_files/example_invalid.json"],
)
with pytest.raises(SystemExit) as e:
main()
Expand All @@ -45,7 +47,8 @@ def test_cli_single_invalid(monkeypatch):

def test_cli_multi_invalid(monkeypatch):
monkeypatch.setattr(
"sys.argv", ["mite-schema", "-i", "tests/example_files/example_invalid.json"]
"sys.argv",
["mite-schema", "-i", "tests/example_files/example_invalid.json"],
)
with pytest.raises(SystemExit) as e:
main()
Expand Down
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