Add Ruff to pre-commit hooks (#1207)

* update CI and precommit files

* add ruff changes

* remove gmso lines

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* change error type in test

* raise the error that is created

* remove duplicate windows 3.12 test

* fix precommit errors

* fix import error

* fix CI error

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/CI.yaml

@@ -13,16 +13,13 @@ on:
 jobs:
   test:
     if: github.event.pull_request.draft == false
-    name: mBuild Tests
+    name: mBuild Tests (python)
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, macOS-13, ubuntu-latest]
+        os: [ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
-        include:
-          - os: windows-latest
-            python-version: "3.12"
 
     defaults:
       run:
@@ -60,6 +57,45 @@ jobs:
           name: mBuild-Coverage
           verbose: true
           files: ./coverage.xml
+  arch-test:
+    if: github.event.pull_request.draft == false
+    name: mBuild Tests (arch)
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest]
+        python-version: ["3.12"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba (Linux)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
+        if: runner.os != 'Windows'
+
+      - name: Install Mamba (Windows)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev-win.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
+        if: runner.os == 'Windows'
+
+      - name: Install Package
+        run: python -m pip install -e .
+
+      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+        run: python -m pytest -v --cov=mbuild --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs mbuild
 
   bleeding-edge-test:
     if: github.event.pull_request.draft == false
@@ -77,7 +113,7 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
-          create-args: python=3.11
+          create-args: python=3.12
 
       - name: Clone Foyer and GMSO
         run: |

.pre-commit-config.yaml

@@ -1,35 +1,32 @@
 ci:
     autofix_commit_msg: |
         [pre-commit.ci] auto fixes from pre-commit.com hooks
-
         for more information, see https://pre-commit.ci
     autofix_prs: true
     autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
     autoupdate_schedule: weekly
     skip: []
     submodules: false
 repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.7.0
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--line-length=80, --fix]
+    # Run the formatter.
+    - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v5.0.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
-      exclude: setup.cfg
-- repo: https://github.com/psf/black
-  rev: 24.10.0
-  hooks:
-    - id: black
-      args: [--line-length=80]
+
 - repo: https://github.com/pycqa/isort
   rev: 5.13.2
   hooks:
     - id: isort
       name: isort (python)
       args: [--profile=black, --line-length=80]
-- repo: https://github.com/pycqa/pydocstyle
-  rev: '6.3.0'
-  hooks:
-    - id: pydocstyle
-      exclude: ^(mbuild/tests/|docs/|devtools/|setup.py|setup.cfg|mbuild/formats/charmm_writer.py|mbuild/formats/gomc_conf_writer.py|mbuild/utils/specific_ff_to_residue.py)
-      args: [--convention=numpy]

docs/conf.py

@@ -16,6 +16,7 @@
 import sys
 
 import mock
+import sphinx_rtd_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -205,7 +206,6 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 # html_theme = 'default'
-import sphinx_rtd_theme
 
 html_theme = "sphinx_rtd_theme"
 hhtml_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

docs/sphinxext/notebook_sphinxext.py

@@ -130,8 +130,6 @@ def setup(app):
     setup.config = app.config
     setup.confdir = app.confdir
 
-    app.add_node(
-        notebook_node, html=(visit_notebook_node, depart_notebook_node)
-    )
+    app.add_node(notebook_node, html=(visit_notebook_node, depart_notebook_node))
 
     app.add_directive("notebook", NotebookDirective)

mbuild/__init__.py

@@ -1,3 +1,5 @@
+# ruff: noqa: F401
+# ruff: noqa: F403
 """mBuild: a hierarchical, component based molecule builder."""
 
 from mbuild.box import Box

mbuild/bond_graph.py

@@ -39,8 +39,6 @@
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
 
-from collections import defaultdict
-
 import networkx as nx
 
 

mbuild/box.py

@@ -98,9 +98,7 @@ def from_uvec_lengths(cls, uvec, lengths, precision=None):
         scaled_vec = (uvec.T * lengths).T
         (alpha, beta, gamma) = _calc_angles(scaled_vec)
 
-        return cls(
-            lengths=lengths, angles=(alpha, beta, gamma), precision=precision
-        )
+        return cls(lengths=lengths, angles=(alpha, beta, gamma), precision=precision)
 
     @classmethod
     def from_mins_maxs_angles(cls, mins, maxs, angles, precision=None):
@@ -123,28 +121,20 @@ def from_vectors(cls, vectors, precision=None):
         Ly = np.linalg.norm(v2)
         Lz = np.linalg.norm(v3)
         lengths = (Lx, Ly, Lz)
-        return cls(
-            lengths=lengths, angles=(alpha, beta, gamma), precision=precision
-        )
+        return cls(lengths=lengths, angles=(alpha, beta, gamma), precision=precision)
 
     @classmethod
-    def from_lengths_tilt_factors(
-        cls, lengths, tilt_factors=None, precision=None
-    ):
+    def from_lengths_tilt_factors(cls, lengths, tilt_factors=None, precision=None):
         """Generate a box from box lengths and tilt factors."""
         (Lx, Ly, Lz) = lengths
         if tilt_factors is None:
             (xy, xz, yz) = (0.0, 0.0, 0.0)
         else:
             (xy, xz, yz) = tilt_factors
 
-        vecs = np.asarray(
-            [[Lx, 0.0, 0.0], [Ly * xy, Ly, 0.0], [Lz * xz, Lz * yz, Lz]]
-        )
+        vecs = np.asarray([[Lx, 0.0, 0.0], [Ly * xy, Ly, 0.0], [Lz * xz, Lz * yz, Lz]])
         (alpha, beta, gamma) = _calc_angles(vecs)
-        return cls(
-            lengths=lengths, angles=[alpha, beta, gamma], precision=precision
-        )
+        return cls(lengths=lengths, angles=[alpha, beta, gamma], precision=precision)
 
     @classmethod
     def from_lo_hi_tilt_factors(cls, lo, hi, tilt_factors, precision=None):
@@ -159,9 +149,7 @@ def from_lo_hi_tilt_factors(cls, lo, hi, tilt_factors, precision=None):
         yhi_bound = yhi + max([0.0, yz])
 
         lengths = [xhi_bound - xlo_bound, yhi_bound - ylo_bound, zhi - zlo]
-        return cls.from_lengths_tilt_factors(
-            lengths=lengths, tilt_factors=tilt_factors
-        )
+        return cls.from_lengths_tilt_factors(lengths=lengths, tilt_factors=tilt_factors)
 
     @property
     def vectors(self):
@@ -327,8 +315,6 @@ def _lengths_angles_to_vectors(lengths, angles, precision):
     cos_b = np.clip(np.cos(beta), -1.0, 1.0)
     cos_g = np.clip(np.cos(gamma), -1.0, 1.0)
 
-    sin_a = np.clip(np.sin(alpha), -1.0, 1.0)
-    sin_b = np.clip(np.sin(beta), -1.0, 1.0)
     sin_g = np.clip(np.sin(gamma), -1.0, 1.0)
     a_vec = np.asarray([a, 0.0, 0.0])
 
@@ -376,9 +362,7 @@ def _normalize_box(vectors):
     sign = np.linalg.det(Q)
     R = R * sign
 
-    signs = np.diag(
-        np.diag(np.where(R < 0, -np.ones(R.shape), np.ones(R.shape)))
-    )
+    signs = np.diag(np.diag(np.where(R < 0, -np.ones(R.shape), np.ones(R.shape))))
     transformed_vecs = R.dot(signs)
     return _reduced_form_vectors(transformed_vecs.T)
 

mbuild/coarse_graining.py

@@ -113,9 +113,7 @@ def _clone(self, clone_of=None, root_container=None):
         if self.labels:
             for label, compound in self.labels.items():
                 if not isinstance(compound, list):
-                    newone.labels[label] = compound._clone(
-                        clone_of, root_container
-                    )
+                    newone.labels[label] = compound._clone(clone_of, root_container)
                     compound.referrers.add(clone_of[compound])
                 else:
                     # compound is a list of compounds, so we create an empty
@@ -150,13 +148,11 @@ def _create_proxy_compounds(real_thing, memo, particle_classes):
     proxy = Proxy(real_thing)
     memo[real_thing] = proxy
 
-    if not type(real_thing) in particle_classes:
+    if type(real_thing) not in particle_classes:
         if not is_leaf(real_thing):  # Recurse only if it has parts.
             # Recursively create proxies for parts.
             for part in real_thing.children:
-                part_proxy = _create_proxy_compounds(
-                    part, memo, particle_classes
-                )
+                part_proxy = _create_proxy_compounds(part, memo, particle_classes)
                 proxy.add(part_proxy)
 
     return proxy