pip to uv CI migration (#321)

* bump ruff + auto-fixes

* use uv to install deps in CI

* revert to editable install

* split 'dev' optional deps into dev + lint

.github/workflows/test.yml

@@ -34,6 +34,9 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
 
+      - name: Install uv
+        run: pip install uv
+
       - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
@@ -43,7 +46,7 @@ jobs:
         run: conda install -c conda-forge openbabel
 
       - name: Install dependencies
-        run: pip install '.[dev]'
+        run: uv pip install -e '.[dev]' --system
 
       - name: pytest
         env:

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.3.2
     hooks:
       - id: ruff
         args: [--fix, --ignore, D]

custodian/__init__.py

@@ -3,7 +3,6 @@
 framework written in Python.
 """
 
-
 import os
 
 from .custodian import Custodian

custodian/feff/handlers.py

@@ -1,6 +1,5 @@
 """This module implements specific error handler for FEFF runs."""
 
-
 import logging
 import re
 

custodian/qchem/__init__.py

@@ -1,5 +1,4 @@
 """This package implements various QChem Jobs and Error Handlers."""
 
-
 __author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath"
 __credits__ = "Xiaohui Qu"

pyproject.toml

@@ -41,7 +41,8 @@ dependencies = ["monty>=2.0.6", "psutil", "ruamel.yaml>=0.15.6"]
 vasp = ["pymatgen"]
 nwchem = ["pymatgen"]
 qchem = ["pymatgen"]
-dev = ["mypy", "pre-commit", "pymatgen", "pytest", "pytest-cov", "ruff"]
+dev = ["pymatgen", "pytest", "pytest-cov"]
+lint = ["mypy", "pre-commit", "ruff"]
 error-statistics = ["sentry-sdk>=0.8.0"]
 
 [project.scripts]
@@ -63,7 +64,9 @@ exclude = ["*.tests", "*.tests.*"]
 [tool.ruff]
 target-version = "py39"
 line-length = 120
-lint.select = [
+
+[tool.ruff.lint]
+select = [
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
   "D",    # pydocstyle
@@ -94,14 +97,15 @@ lint.select = [
   "W",    # pycodestyle warning
   "YTT",  # flake8-2020
 ]
-lint.ignore = [
+ignore = [
   "B023",    # Function definition does not bind loop variable
   "B028",    # No explicit stacklevel keyword argument found
   "B904",    # Within an except clause, raise exceptions with ...
   "C408",    # unnecessary-collection-call
   "D105",    # Missing docstring in magic method
   "D205",    # 1 blank line required between summary line and description
   "D212",    # Multi-line docstring summary should start at the first line
+  "ISC001",
   "PD011",   # pandas-use-of-dot-values
   "PD901",   # pandas-df-variable-name
   "PERF203", # try-except-in-loop
@@ -111,8 +115,8 @@ lint.ignore = [
   "RUF012",  # Disable checks for mutable class args. This is a non-problem.
   "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
 ]
-lint.pydocstyle.convention = "google"
-lint.isort.split-on-trailing-comma = false
+pydocstyle.convention = "google"
+isort.split-on-trailing-comma = false
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]