Add ruff linting and formatting configuration

.github/workflows/ruff.yml

@@ -0,0 +1,31 @@
+name: Lint and Format
+
+on:
+  push:
+    branches:
+      - master
+      - 'release/*'
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+env:
+  CLICOLOR: 1
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Ruff format check
+        uses: astral-sh/ruff-action@v3
+        with:
+          args: "format --check"
+
+      - name: Ruff lint
+        uses: astral-sh/ruff-action@v3
+        with:
+          args: "check"

.ruff.toml

@@ -0,0 +1,14 @@
+target-version = "py312"
+line-length = 79
+exclude = ["deps"]
+extend-include = ["*.drs"]
+
+[lint]
+ignore = ["E741"]
+
+[format]
+docstring-code-format = true
+
+[lint.per-file-ignores]
+"*.ipynb" = ["F403", "F405"]
+"*.drs" = ["F403", "F405", "F821"]

docs/conf.py

@@ -31,38 +31,40 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.imgconverter',
-    'sphinx.ext.githubpages'
-    ]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.imgconverter",
+    "sphinx.ext.githubpages",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'drudge'
-copyright = '2017, Jinmo Zhao and Gustavo E Scuseria'
-author = 'Jinmo Zhao and Gustavo E Scuseria'
+project = "drudge"
+copyright = "2017, Jinmo Zhao and Gustavo E Scuseria"
+author = "Jinmo Zhao and Gustavo E Scuseria"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-from drudge import __version__
+from drudge import __version__  # noqa: E402
+
 version = __version__
 # The full version, including alpha/beta/rc tags.
 release = __version__
@@ -77,10 +79,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -91,7 +93,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -102,13 +104,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'drudgedoc'
+htmlhelp_basename = "drudgedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -117,15 +119,15 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
+    #
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
+    #
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
+    #
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -135,19 +137,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'drudge.tex', 'drudge Documentation',
-     'Jinmo Zhao and Gustavo E Scuseria', 'manual'),
+    (
+        master_doc,
+        "drudge.tex",
+        "drudge Documentation",
+        "Jinmo Zhao and Gustavo E Scuseria",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'drudge', 'drudge Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "drudge", "drudge Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -156,19 +160,25 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'drudge', 'drudge Documentation',
-     author, 'drudge', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "drudge",
+        "drudge Documentation",
+        author,
+        "drudge",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 
-doctest_global_setup = '''
+doctest_global_setup = """
 import os
 
 from dummy_spark import SparkContext
 
 from sympy import *
 from drudge import *
-'''
+"""

docs/examples/ccd.drs

@@ -10,9 +10,7 @@
 set_dbbar_base(t, 2)
 
 # Einstein summation convention can be used for easy tensor creation.
-t2 = einst(
-    t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4
-)
+t2 = einst(t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4)
 
 # Get the similarity-transformed Hamiltonian.  Note that ``|`` operator
 # computes the commutator between operators.
@@ -21,22 +19,17 @@ c1 = simplify(c0 | t2)
 c2 = simplify(c1 | t2)
 c3 = simplify(c2 | t2)
 c4 = simplify(c3 | t2)
-h_bar = simplify(
-    c0 + c1 + (1/2) * c2 + (1/6) * c3 + (1/24) * c4
-)
+h_bar = simplify(c0 + c1 + (1 / 2) * c2 + (1 / 6) * c3 + (1 / 24) * c4)
 
-print('Similarity-transformed Hamiltonian has {} terms'.format(
-    n_terms(h_bar)
-))
+print("Similarity-transformed Hamiltonian has {} terms".format(n_terms(h_bar)))
 
 # Derive the working equations by projection.
 en_eqn = simplify(eval_fermi_vev(h_bar))
 proj = c_dag[i] * c_dag[j] * c_[b] * c_[a]
 t2_eqn = simplify(eval_fermi_vev(proj * h_bar))
 
-print('Working equation derived!')
-
-with report('ccd.html', 'CCD theory') as rep:
-    rep.add('Energy equation', en_eqn)
-    rep.add('Doubles amplitude equation', t2_eqn)
+print("Working equation derived!")
 
+with report("ccd.html", "CCD theory") as rep:
+    rep.add("Energy equation", en_eqn)
+    rep.add("Doubles amplitude equation", t2_eqn)

docs/examples/ccd_adv.drs

@@ -7,9 +7,8 @@
 #
 
 set_dbbar_base(t, 2)
-t2 = einst(
-    t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4
-)
+t2 = einst(t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4)
+
 
 def compute_h_bar():
     """Compute the similarity transformed Hamiltonian."""
@@ -21,11 +20,12 @@ def compute_h_bar():
         h_bar += curr
     return simplify(h_bar)
 
+
 # By using the `memoise` function, the result can be automatically dumped into
 # the given pickle file, and read from it if it is already available.  This can
 # be convenient for large multi-step jobs.
-h_bar = memoize(compute_h_bar, 'h_bar.pickle')
-print('H-bar has {} terms'.format(n_terms(h_bar)))
+h_bar = memoize(compute_h_bar, "h_bar.pickle")
+print("H-bar has {} terms".format(n_terms(h_bar)))
 
 # Derive the working equations by projection.  Here we make them into tensor
 # definition with explicit left-hand side, so that they can be used for
@@ -34,13 +34,11 @@ e <<= simplify(eval_fermi_vev(h_bar))
 proj = c_dag[i] * c_dag[j] * c_[b] * c_[a]
 r2[a, b, i, j] <<= simplify(eval_fermi_vev(proj * h_bar))
 
-print('Working equation derived!')
+print("Working equation derived!")
 
 # When the gristmill package is also installed, the evaluation of the working
 # equations can also be optimized with it.
-eval_seq = optimize(
-    [e, r2], substs={no: 1000, nv: 10000}
-)
+eval_seq = optimize([e, r2], substs={no: 1000, nv: 10000})
 
 # In addition to HTML report, we can also have LaTeX report.  Note that the
 # report can be structured into sections with descriptions.  For LaTeX output,
@@ -53,11 +51,10 @@ The optimization is based on 1000 occupied orbitals and 10000 virtual orbitals,
 which should be representative of common problems for CCD theory.
 """
 
-with report('ccd.tex', 'CCD theory') as rep:
-    rep.add(title='Working equations')
-    rep.add(content=e, description='The energy equation')
-    rep.add(content=r2, description='Doubles amplitude equation', env='dmath')
-    rep.add(title='Optimized evaluation', description=opt_description)
+with report("ccd.tex", "CCD theory") as rep:
+    rep.add(title="Working equations")
+    rep.add(content=e, description="The energy equation")
+    rep.add(content=r2, description="Doubles amplitude equation", env="dmath")
+    rep.add(title="Optimized evaluation", description=opt_description)
     for step in eval_seq:
-        rep.add(content=step, env='dmath')
-
+        rep.add(content=step, env="dmath")

docs/examples/ccsd.ipynb

@@ -29,7 +29,8 @@
    "outputs": [],
    "source": [
     "from pyspark import SparkContext\n",
-    "ctx = SparkContext('local[*]', 'ccsd')"
+    "\n",
+    "ctx = SparkContext(\"local[*]\", \"ccsd\")"
    ]
   },
   {
@@ -49,6 +50,7 @@
    "outputs": [],
    "source": [
     "from dummy_spark import SparkContext\n",
+    "\n",
     "ctx = SparkContext()"
    ]
   },
@@ -99,11 +101,11 @@
    },
    "outputs": [],
    "source": [
-    "t = IndexedBase('t')\n",
+    "t = IndexedBase(\"t\")\n",
     "\n",
     "clusters = dr.einst(\n",
-    "    t[a, i] * c_dag[a] * c_[i] +\n",
-    "    t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4\n",
+    "    t[a, i] * c_dag[a] * c_[i]\n",
+    "    + t[a, b, i, j] * c_dag[a] * c_dag[b] * c_[j] * c_[i] / 4\n",
     ")"
    ]
   },
@@ -165,12 +167,7 @@
     }
    ],
    "source": [
-    "dr.set_symm(\n",
-    "    t,\n",
-    "    Perm([1, 0, 2, 3], NEG),\n",
-    "    Perm([0, 1, 3, 2], NEG),\n",
-    "    valence=4\n",
-    ")"
+    "dr.set_symm(t, Perm([1, 0, 2, 3], NEG), Perm([0, 1, 3, 2], NEG), valence=4)"
    ]
   },
   {
@@ -444,9 +441,9 @@
     ")\n",
     "\n",
     "working_eqn = [\n",
-    "    dr.define(Symbol('e'), en_eqn), \n",
-    "    dr.define(r1[a, i], t1_eqn), \n",
-    "    dr.define(r2[a, b, i, j], t2_eqn)\n",
+    "    dr.define(Symbol(\"e\"), en_eqn),\n",
+    "    dr.define(r1[a, i], t1_eqn),\n",
+    "    dr.define(r2[a, b, i, j], t2_eqn),\n",
     "]"
    ]
   },
@@ -511,8 +508,9 @@
     "%%time\n",
     "\n",
     "eval_seq = optimize(\n",
-    "    working_eqn, substs={p.nv: 5000, p.no: 1000}, \n",
-    "    contr_strat=ContrStrat.EXHAUST\n",
+    "    working_eqn,\n",
+    "    substs={p.nv: 5000, p.no: 1000},\n",
+    "    contr_strat=ContrStrat.EXHAUST,\n",
     ")"
    ]
   },

docs/examples/conf_ph_spin.py

@@ -1,5 +1,4 @@
-"""Configuration for particle-hole problem with explicit spin.
-"""
+"""Configuration for particle-hole problem with explicit spin."""
 
 from pyspark import SparkContext
 from drudge import RestrictedPartHoleDrudge