linting with ruff 3

.github/workflows/testing.yml

@@ -29,8 +29,7 @@ jobs:
       - name: ruff
         run: |
           ruff --version
-          ruff .
-          ruff format --check .
+          ruff check
 
       - name: mypy
         run: |

src/rxn_network/__init__.py

@@ -1,4 +1,5 @@
 """The reaction-network package."""
+
 from __future__ import annotations
 
 from importlib.metadata import version

src/rxn_network/core.py

@@ -1,4 +1,5 @@
 """Composition class used to represent a chemical composition."""
+
 from __future__ import annotations
 
 from functools import cached_property

src/rxn_network/costs/base.py

@@ -1,4 +1,5 @@
 """Basic interface and implementation for a Calculator and CostFunction."""
+
 from __future__ import annotations
 
 from abc import ABCMeta, abstractmethod

src/rxn_network/costs/calculators.py

@@ -1,4 +1,5 @@
 """A calculator class for determining chemical potential distance of reactions."""
+
 from __future__ import annotations
 
 from itertools import chain, combinations, product

src/rxn_network/costs/functions.py

@@ -1,4 +1,5 @@
 """Implementation of cost functions used in the package (e.g., Softplus, WeightedSum)."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/costs/pareto.py

@@ -1,4 +1,5 @@
 """Functions for performing Pareto front analysis."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/entries/corrections.py

@@ -1,4 +1,5 @@
 """Energy correction classes for entry objects."""
+
 from __future__ import annotations
 
 import math

src/rxn_network/entries/entry_set.py

@@ -1,6 +1,7 @@
 """An entry set class for automatically building GibbsComputedEntry objects. Some of this
 code has been adapted from the EntrySet class in pymatgen.
 """
+
 from __future__ import annotations
 
 import collections

src/rxn_network/entries/experimental.py

@@ -1,4 +1,5 @@
 """Implements an Entry that looks up NIST pre-tabulated Gibbs free energies."""
+
 from __future__ import annotations
 
 import hashlib

src/rxn_network/entries/freed.py

@@ -1,6 +1,7 @@
 """Implements an Entry that looks up pre-tabulated Gibbs free energies from the NIST-JANAF
 tables.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/entries/gibbs.py

@@ -2,6 +2,7 @@
 this is similar to the implementation within pymatgen, but has been refactored here to
 add extra functionality.
 """
+
 from __future__ import annotations
 
 from copy import deepcopy

src/rxn_network/entries/interpolated.py

@@ -1,4 +1,5 @@
 """Class for intepolated entries."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/entries/nist.py

@@ -1,6 +1,7 @@
 """Implements an Entry that looks up pre-tabulated Gibbs free energies from the NIST-JANAF
 tables.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/entries/utils.py

@@ -1,4 +1,5 @@
 """Utility functions for acquiring, processing, or modifiying entries."""
+
 from __future__ import annotations
 
 import itertools

src/rxn_network/enumerators/base.py

@@ -1,4 +1,5 @@
 """Basic interface for a reaction Enumerator."""
+
 from __future__ import annotations
 
 import logging

src/rxn_network/enumerators/basic.py

@@ -1,4 +1,5 @@
 """This module implements two types of basic (combinatorial) reaction enumerators."""
+
 from __future__ import annotations
 
 from copy import deepcopy

src/rxn_network/enumerators/minimize.py

@@ -1,6 +1,7 @@
 """This module implements two types of reaction enumerators using a free energy
 minimization technique, with or without the option of an open entry.
 """
+
 from __future__ import annotations
 
 from itertools import product

src/rxn_network/enumerators/utils.py

@@ -1,4 +1,5 @@
 """Utility functions used by the reaction enumerator classes."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/flows/core.py

@@ -1,4 +1,5 @@
 """Core flows for the reaction-network package."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass, field

src/rxn_network/jobs/schema.py

@@ -1,4 +1,5 @@
 """Core definition for various task and synthesis recipe documents."""
+
 from typing import Any, Optional
 
 from pydantic import BaseModel, Field

src/rxn_network/jobs/utils.py

@@ -1,4 +1,5 @@
 """Definitions of common job functions."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/network/base.py

@@ -1,4 +1,5 @@
 """Basic interface for a reaction network and its graph."""
+
 from __future__ import annotations
 
 from abc import ABCMeta, abstractmethod

src/rxn_network/network/entry.py

@@ -1,6 +1,7 @@
 """Entry objects used in a Network. These network entry objects hold multiple entries and
 can be used as data for a node in the graph.
 """
+
 from __future__ import annotations
 
 from enum import Enum, auto

src/rxn_network/network/network.py

@@ -1,4 +1,5 @@
 """Implementation of reaction network and graph classes."""
+
 from __future__ import annotations
 
 from queue import Empty, PriorityQueue

src/rxn_network/network/visualize.py

@@ -1,4 +1,5 @@
 """Functions for visualizing/plotting reaction networks."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/pathways/balanced.py

@@ -1,4 +1,5 @@
 """Implements a class for storing a balanced reaction pathway."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/pathways/base.py

@@ -1,4 +1,5 @@
 """Basic interface for a reaction pathway."""
+
 from __future__ import annotations
 
 from abc import ABCMeta

src/rxn_network/pathways/basic.py

@@ -1,6 +1,7 @@
 """Implements a class for storing (unbalanced/unconstrained) collection of reactions
 forming a reaction pathway.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/pathways/pathway_set.py

@@ -1,6 +1,7 @@
 """Implements a class for conveniently and efficiently storing sets of Pathway-based
 objects which share entries/reactions.
 """
+
 from __future__ import annotations
 
 from functools import cached_property

src/rxn_network/pathways/plotting.py

@@ -1,4 +1,5 @@
 """This module contains functions for plotting experimental reaction pathway data."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/pathways/solver.py

@@ -1,6 +1,7 @@
 """Implements a reaction pathway solver class which efficiently solves mass balance
 equations using matrix operations.
 """
+
 from __future__ import annotations
 
 from abc import ABCMeta

src/rxn_network/reactions/base.py

@@ -1,4 +1,5 @@
 """Basic interface for a (chemical) Reaction."""
+
 from __future__ import annotations
 
 from abc import ABCMeta, abstractmethod

src/rxn_network/reactions/basic.py

@@ -1,6 +1,7 @@
 """This module for defining chemical reaction objects was originally sourced from
 pymatgen and streamlined for the reaction-network code.
 """
+
 from __future__ import annotations
 
 import re

src/rxn_network/reactions/computed.py

@@ -1,6 +1,7 @@
 """A reaction class that builds reactions based on ComputedEntry objects and provides
 information about reaction thermodynamics.
 """
+
 from __future__ import annotations
 
 from functools import cached_property

src/rxn_network/reactions/hull.py

@@ -1,4 +1,5 @@
 """Code for analyzing sets of reactions between two phases."""
+
 from __future__ import annotations
 
 from functools import cached_property, lru_cache

src/rxn_network/reactions/open.py

@@ -2,6 +2,7 @@
 of an open entry (e.g. O2), and provides information about reaction thermodynamics
 computed as changes in grand potential.
 """
+
 from __future__ import annotations
 
 from functools import cached_property

src/rxn_network/reactions/plotting.py

@@ -1,4 +1,5 @@
 """Utility functions for plotting reaction data & performing analysis."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/reactions/reaction_set.py

@@ -1,6 +1,7 @@
 """Implements a class for conveniently and efficiently storing sets of ComputedReaction
 objects which share entries.
 """
+
 from __future__ import annotations
 
 from collections import OrderedDict

src/rxn_network/thermo/chempot_diagram.py

@@ -1,6 +1,7 @@
 """This module implements added features to the ChemicalPotentialDiagram class from
 pymatgen.
 """
+
 from __future__ import annotations
 
 from functools import cached_property

src/rxn_network/thermo/utils.py

@@ -1,4 +1,5 @@
 """Utility functions used in the thermodynamic analysis classes."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/rxn_network/utils/database.py

@@ -1,4 +1,5 @@
 """Utility functions for interfacing with a reaction database."""
+
 from __future__ import annotations
 
 from jobflow import SETTINGS

src/rxn_network/utils/funcs.py

@@ -1,4 +1,5 @@
 """Utility functions used throughout the reaction-network package."""
+
 from __future__ import annotations
 
 import logging

src/rxn_network/utils/ray.py

@@ -1,4 +1,5 @@
 """Functions for working with Ray (parallelization library)."""
+
 from __future__ import annotations
 
 import os

tests/costs/test_calculators.py

@@ -1,4 +1,5 @@
-""" Tests for ChempotDistanceCalculator """
+"""Tests for ChempotDistanceCalculator"""
+
 from pathlib import Path
 
 import pytest

tests/costs/test_softplus.py

@@ -1,4 +1,5 @@
 """Tests for Softplus"""
+
 import pytest
 from rxn_network.costs.functions import Softplus
 

tests/entries/test_corrections.py

@@ -1,4 +1,5 @@
-""" Tests for entry corrections. """
+"""Tests for entry corrections."""
+
 import pytest
 from rxn_network.entries.corrections import CARBONATE_CORRECTION, CarbonateCorrection
 

tests/entries/test_entry_set.py

@@ -1,4 +1,5 @@
-""" Tests for GibbsEntrySet. """
+"""Tests for GibbsEntrySet."""
+
 from copy import deepcopy
 
 import pytest

tests/entries/test_gibbs.py

@@ -1,4 +1,5 @@
-""" Tests for GibbsComputedEntry. Some tests adapted from pymatgen."""
+"""Tests for GibbsComputedEntry. Some tests adapted from pymatgen."""
+
 from pathlib import Path
 
 import pytest

tests/entries/test_nist.py

@@ -1,4 +1,5 @@
-""" Tests for NISTReferenceEntry. """
+"""Tests for NISTReferenceEntry."""
+
 import pytest
 from pymatgen.core.periodic_table import Element
 from pymatgen.entries.computed_entries import ManualEnergyAdjustment

tests/enumerators/test_basic.py

@@ -1,4 +1,5 @@
-""" Tests for BasicEnumerator and BasicOpenEnumerator """
+"""Tests for BasicEnumerator and BasicOpenEnumerator"""
+
 from pathlib import Path
 
 import pytest

tests/enumerators/test_minimize.py

@@ -1,4 +1,5 @@
-""" Tests for MinimizeGibbsEnumerator and MinimizeGrandPotentialEnumerator """
+"""Tests for MinimizeGibbsEnumerator and MinimizeGrandPotentialEnumerator"""
+
 import pytest
 from pymatgen.core.composition import Element
 from rxn_network.enumerators.minimize import MinimizeGibbsEnumerator, MinimizeGrandPotentialEnumerator

tests/network/test_entry.py

@@ -1 +1 @@
-""" Tests for NetworkEntry """
+"""Tests for NetworkEntry"""

tests/network/test_network.py

@@ -1,4 +1,4 @@
-""" Tests for ReactionNetwork """
+"""Tests for ReactionNetwork"""
 
 
 def test_from_dict(ymno_rn):

tests/pathways/test_basic.py

@@ -1 +1 @@
-""" Tests for BasicPathway """
+"""Tests for BasicPathway"""

tests/pathways/test_plotting.py

@@ -1,4 +1,5 @@
 """Tests for pathway plotter"""
+
 import pytest
 from rxn_network.pathways.plotting import PathwayPlotter
 

tests/pathways/test_solver.py

@@ -1,4 +1,5 @@
-""" Tests for PathwaySolver"""
+"""Tests for PathwaySolver"""
+
 from pathlib import Path
 
 import numpy as np

tests/reactions/test_basic.py

@@ -2,6 +2,7 @@
 Test for BasicReaction. Several tests adapted from
 test module for pymatgen.analysis.reaction_calculator
 """
+
 import pytest
 from pymatgen.core.composition import Element
 from rxn_network.core import Composition

tests/reactions/test_computed.py

@@ -1,4 +1,5 @@
-""" Tests for ComputedReaction. Some tests adapted from pymatgen. """
+"""Tests for ComputedReaction. Some tests adapted from pymatgen."""
+
 from pathlib import Path
 
 import pytest

tests/reactions/test_hull.py

@@ -1,4 +1,5 @@
-""" Tests for InterfaceReactionHull. """
+"""Tests for InterfaceReactionHull."""
+
 import pytest
 from rxn_network.reactions.hull import InterfaceReactionHull