Merge branch 'main' into production-pilot-update

.github/workflows/ci.yml

@@ -20,6 +20,13 @@ jobs:
                 pip install ruff
                 ruff check
 
+    typos:
+        name: Typos
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: crate-ci/typos@master
+
     pylint:
         name: Pylint
         runs-on: ubuntu-latest

doc/conf.py

@@ -1,5 +1,6 @@
 from urllib.request import urlopen
 
+
 _conf_url = \
         "https://raw.githubusercontent.com/inducer/sphinxconfig/main/sphinxconfig.py"
 with urlopen(_conf_url) as _inf:
@@ -42,6 +43,8 @@
 # this needs a setting of the same name across all packages involved, that's
 # why this name is as global-sounding as it is.
 import sys
+
+
 sys._BUILDING_SPHINX_DOCS = True
 
 nitpick_ignore_regex = [

examples/advection.py

@@ -1,13 +1,15 @@
 #!/usr/bin/env python
+import functools
+
 import numpy as np
 import pytest
-import functools
-from dg_tools import DGDiscr1D, integrate, DGOps1D, DGOps1DRef
+from dg_tools import DGDiscr1D, DGOps1D, DGOps1DRef, integrate
+
 
 memoized = functools.lru_cache(maxsize=None)
 
 
-class AdvectionOperator(object):
+class AdvectionOperator:
     """A class representing a DG advection operator."""
 
     def __init__(self, discr, c, flux_type, dg_ops):
@@ -138,8 +140,9 @@ def test_advection_convergence(order, flux_type):
     errors = []
     hs = []
 
-    import pytato as pt
     import pyopencl as cl
+
+    import pytato as pt
     cl_ctx = cl.create_some_context()
     queue = cl.CommandQueue(cl_ctx)
 
@@ -169,8 +172,9 @@ def test_advection_convergence(order, flux_type):
 
 
 def main():
-    import pytato as pt
     import pyopencl as cl
+
+    import pytato as pt
     cl_ctx = cl.create_some_context()
     queue = cl.CommandQueue(cl_ctx)
 

examples/demo.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env python
 
 import numpy as np
+
 import pytato as pt
 
+
 n = pt.make_size_param("n")
 a = pt.make_placeholder(name="a", shape=(n, n), dtype=np.float64)
 
@@ -15,6 +17,8 @@
 
 import pyopencl as cl
 import pyopencl.array as cla
+
+
 ctx = cl.create_some_context()
 queue = cl.CommandQueue(ctx)
 
@@ -27,6 +31,8 @@
 
 # interface for efficient execution
 import loopy as lp
+
+
 prg = pt.generate_loopy(
         result, options=lp.Options(no_numpy=True, return_dict=True)
         ).bind_to_context(ctx)
@@ -47,6 +53,8 @@
 print("============= End Loopy code ===============")
 
 import loopy as lp
+
+
 print("============== OpenCL code =================")
 print(lp.generate_code_v2(prg.program).device_code())
 print("============ End OpenCL code ===============")

examples/demo_distributed_node_duplication.py

@@ -4,10 +4,12 @@
 partitioning routine is to recompute expressions that appear in multiple
 partitions but are not materialized.
 """
-import pytato as pt
 import numpy as np
 from mpi4py import MPI
 
+import pytato as pt
+
+
 comm = MPI.COMM_WORLD
 
 size = 2

examples/dg_tools.py

@@ -1,7 +1,9 @@
+import contextlib
+
 import numpy as np
-import numpy.polynomial.legendre as leg
 import numpy.linalg as la
-import contextlib
+import numpy.polynomial.legendre as leg
+
 
 __doc__ = """
 Notation convention for operator shapes
@@ -36,7 +38,7 @@ def ortholegval(x, c):
     return leg.legval(x, c * factors)
 
 
-class DGDiscr1D(object):
+class DGDiscr1D:
     """A one-dimensional Discontinuous Galerkin discretization."""
 
     def __init__(self, left, right, nelements, nnodes):
@@ -260,7 +262,7 @@ def elementwise(mat, vec):
     return np.einsum("ij,kj->ki", mat, vec)
 
 
-class AbstractDGOps1D(object):
+class AbstractDGOps1D:
     def __init__(self, discr):
         self.discr = discr
 

examples/einsum.py

@@ -1,7 +1,9 @@
 import numpy as np
-import pytato as pt
+
 import pyopencl as cl
 
+import pytato as pt
+
 
 ctx = cl.create_some_context()
 queue = cl.CommandQueue(ctx)

examples/mpi-distributed.py

@@ -1,17 +1,24 @@
 #!/usr/bin/env python
 
 from mpi4py import MPI  # pylint: disable=import-error
+
+
 comm = MPI.COMM_WORLD
 
-import pytato as pt
+import numpy as np
+
 import pyopencl as cl
 import pyopencl.array as cl_array
-import numpy as np
 
-from pytato import (find_distributed_partition, generate_code_for_partition,
-        number_distributed_tags,
-        execute_distributed_partition,
-        staple_distributed_send, make_distributed_recv)
+import pytato as pt
+from pytato import (
+    execute_distributed_partition,
+    find_distributed_partition,
+    generate_code_for_partition,
+    make_distributed_recv,
+    number_distributed_tags,
+    staple_distributed_send,
+)
 
 
 def main():

examples/reduction.py

@@ -1,7 +1,10 @@
 import numpy as np
-import pytato as pt
+
 import pyopencl as cl
 
+import pytato as pt
+
+
 ctx = cl.create_some_context()
 queue = cl.CommandQueue(ctx)
 

examples/visualization.py

@@ -2,10 +2,11 @@
 """Demonstrates graph visualization with Graphviz."""
 
 import logging
-import numpy as np
 import shutil
 import subprocess
 
+import numpy as np
+
 import pytato as pt
 
 

pyproject.toml

@@ -5,12 +5,13 @@ extend-select = [
     "C",    # flake8-comprehensions
     "E",    # pycodestyle
     "F",    # pyflakes
-    # not yet
-    # "I",    # flake8-isort
+    "I",    # flake8-isort
     "N",    # pep8-naming
     "Q",    # flake8-quotes
     "W",    # pycodestyle
-    "NPY"   # numpy
+    "NPY",   # numpy
+    "RUF",
+    "UP",
 ]
 extend-ignore = [
   "E226",
@@ -26,15 +27,24 @@ extend-ignore = [
   # numpy random generators---disable for now
   "NPY002",
 ]
+
+allowed-confusables = [
+  "∪", # union
+  " ", # nbsp
+  ]
+
 [tool.ruff.lint.per-file-ignores]
 "examples/advection.py" = ["B023"]
 "test/test_linalg.py" = ["N806"]
+"doc/*.py" = ["I002"]
+"examples/*.py" = ["I002"]
 
 [tool.ruff.lint.isort]
-known-first-party = ["pytools", "pymbolic", "loopy"]
+known-first-party = ["pytools", "pymbolic", "loopy", "pyopencl"]
 known-local-folder = ["pytato"]
 lines-after-imports = 2
 combine-as-imports = true
+required-imports = ["from __future__ import annotations"]
 
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = "double"
@@ -59,3 +69,17 @@ module = [
   "pytato.scalar_expr",
 ]
 allow_subclassing_any = true
+
+
+[tool.typos.default]
+extend-ignore-re = [
+  "(?Rm)^.*(#|//)\\s*spellchecker:\\s*disable-line$"
+]
+
+[tool.typos.default.extend-words]
+# like the numpy function, array range
+arange = "arange"
+
+[tool.typos.files]
+extend-exclude = [
+]