Enable linting with ruff #6

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Merged

Wrzlprmft merged 9 commits into neurophysik:master from alexfikl:ruff

Mar 9, 2025

.editorconfig

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,6 +7,7 @@ root = true @@
     [*]
     end_of_line = lf
     insert_final_newline = true
+    trim_trailing_whitespace = false
     # Matches multiple files with brace expansion notation
     # Set default charset
@@ Expand Down @@

.github/workflows/ci.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -14,6 +14,20 @@ concurrency: @@
       cancel-in-progress: true
     jobs:
+      typos:
+        name: Spelling (typos)
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v4
+        - uses: crate-ci/typos@master
+      ruff:
+        name: Linting (ruff)
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
       test:
         name: Unittest (${{ matrix.os }}-${{ matrix.compiler }}-py${{ matrix.python-version }})
         runs-on: ${{ matrix.os }}
@@ Expand Down @@

docs/conf.py

            
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    @@ -1,57 +1,61 @@
  
    import sys

    import os

    import sys

    from unittest.mock import MagicMock as Mock

    from setuptools_scm import get_version

    MOCK_MODULES = [

    	'numpy', 'numpy.testing', 'numpy.random',

    	'symengine', 'symengine.printing', 'symengine.lib.symengine_wrapper',

    	'jitcxde_common.helpers','jitcxde_common.numerical','jitcxde_common.symbolic'

    	"numpy", "numpy.testing", "numpy.random",

    	"symengine", "symengine.printing", "symengine.lib.symengine_wrapper",

    	"jitcxde_common.helpers","jitcxde_common.numerical","jitcxde_common.symbolic"

    	]

    sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

    class GroupHandler_mock(object): pass

    sys.modules['jitcxde_common.transversal'] = Mock(GroupHandler=GroupHandler_mock)

    class GroupHandler_mock:

    	pass

    sys.modules["jitcxde_common.transversal"] = Mock(GroupHandler=GroupHandler_mock)

    sys.path.insert(0,os.path.abspath("../examples"))

    sys.path.insert(0,os.path.abspath("../jitcsde"))

    needs_sphinx = '1.3'

    needs_sphinx = "1.3"

    extensions = [

        'sphinx.ext.autodoc',

        'sphinx.ext.autosummary',

        'sphinx.ext.mathjax',

        'numpydoc',

        "sphinx.ext.autodoc",

        "sphinx.ext.autosummary",

        "sphinx.ext.mathjax",

        "numpydoc",

    ]

    source_suffix = '.rst'

    source_suffix = ".rst"

    master_doc = 'index'

    master_doc = "index"

    project = u'JiTCSDE'

    copyright = u'2017, Gerrit Ansmann'

    project = "JiTCSDE"

    copyright = "2017, Gerrit Ansmann"

    release = version = get_version(root='..', relative_to=__file__)

    release = version = get_version(root="..", relative_to=__file__)

    default_role = "any"

    add_function_parentheses = True

    add_module_names = False

    html_theme = 'nature'

    pygments_style = 'colorful'

    htmlhelp_basename = 'JiTCSDEdoc'

    html_theme = "nature"

    pygments_style = "colorful"

    htmlhelp_basename = "JiTCSDEdoc"

    numpydoc_show_class_members = False

    autodoc_member_order = 'bysource'

    autodoc_member_order = "bysource"

    def on_missing_reference(app, env, node, contnode):

    	if node['reftype'] == 'any':

    	if node["reftype"] == "any":

    		return contnode

    	else:

    		return None

    def setup(app):

    	app.connect('missing-reference', on_missing_reference)

    	app.connect("missing-reference", on_missing_reference)

docs/index.rst

-Original file line number
+Diff line change
@@ Expand Up / @@ -104,7 +104,7 @@ References @@
     .. [RN17] C. Rackauckas, Q. Nie: Adaptive methods for stochastic differential equations via natural embeddings and rejection sampling with memory, Discrete Cont. Dyn.-B 22, pp. 2731–2761 (2017), `10.3934/dcdsb.2017133 <http://dx.doi.org/10.3934/dcdsb.2017133>`_.
-    .. [R10] A. Rößler, Runge–Kutta methods for the strong approximation of solutions of stochastic differential equations, SIAM J. Numer. Anal. 48, pp. 922–952 (2010) `10.1137/09076636X <http://dx.doi.org/10.1137/09076636X>`_.
+    .. [R10] A. Rößler, Runge–Kutta methods for the strong approximation of solutions of stochastic differential equations, SIAM J. Numerical Anal. 48, pp. 922–952 (2010) `10.1137/09076636X <http://dx.doi.org/10.1137/09076636X>`_.
     .. _JiTCODE: http://github.com/neurophysik/jitcode
@@ Expand Down @@

examples/noisy_and_jumpy_lorenz.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,6 +1,3 @@
  
    #!/usr/bin/python3

    # -*- coding: utf-8 -*-

    """

    As an example, suppose that we want to add jumps to the noisy Lorenz oscillator from `example`.

    These shall have exponentially distributed waiting times (i.e. they are a Poisson process) with a scale parameter :math:`β=1.0`.

    @@ -29,10 +26,12 @@
  
    """

    if __name__ == "__main__":

    	from jitcsde import y, jitcsde_jump

    	import numpy

    	import numpy as np

    	import symengine

    	from jitcsde import jitcsde_jump, y

    	rng = np.random.default_rng(seed=42)

    	ρ = 28

    	σ = 10

    	β = symengine.Rational(8,3)

    @@ -47,22 +46,22 @@
  
    	g = [ p*y(i) for i in range(3) ]

    	def IJI(time,state):

    		return numpy.random.exponential(1.0)

    		return rng.exponential(1.0)

    	def jump(time,state):

    		return numpy.array([

    		return np.array([

    				0.0,

    				0.0,

    				numpy.random.normal(0.0,abs(state[2]))

    				rng.normal(0.0,abs(state[2]))

    			])

    	SDE = jitcsde_jump(IJI,jump,f,g)

    	initial_state = numpy.random.random(3)

    	initial_state = rng.random(3)

    	SDE.set_initial_value(initial_state,0.0)

    	data = []

    	for time in numpy.arange(0.0, 100.0, 0.01):

    	for time in np.arange(0.0, 100.0, 0.01):

    		data.append( SDE.integrate(time) )

    	numpy.savetxt("timeseries.dat", data)

    	np.savetxt("timeseries.dat", data)

examples/noisy_lorenz.py

            
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    @@ -1,7 +1,4 @@
  
    #!/usr/bin/python3

    # -*- coding: utf-8 -*-

    """

    r"""

    Suppose we want to integrate Lorenz oscillator each of whose components is subject to a diffusion that amounts to :math:`p` of the respective component, i.e.:

    .. math::

    @@ -72,10 +69,12 @@
  
    """

    if __name__ == "__main__":

    	from jitcsde import y, jitcsde

    	import numpy

    	import numpy as np

    	import symengine

    	from jitcsde import jitcsde, y

    	rng = np.random.default_rng(seed=42)

    	ρ = 28

    	σ = 10

    	β = symengine.Rational(8,3)

    @@ -91,11 +90,11 @@
  
    	SDE = jitcsde(f,g)

    	initial_state = numpy.random.random(3)

    	initial_state = rng.random(3)

    	SDE.set_initial_value(initial_state,0.0)

    	data = []

    	for time in numpy.arange(0.0, 100.0, 0.01):

    	for time in np.arange(0.0, 100.0, 0.01):

    		data.append( SDE.integrate(time) )

    	numpy.savetxt("timeseries.dat", data)

    	np.savetxt("timeseries.dat", data)

jitcsde/__init__.py

            
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    @@ -1,12 +1,8 @@
  
    from ._jitcsde import (

    		jitcsde, jitcsde_jump,

    		t, y,

    		UnsuccessfulIntegration,

    		test

    	)

    from ._jitcsde import UnsuccessfulIntegration, jitcsde, jitcsde_jump, t, test, y  # noqa: F401

    try:

    	from .version import version as __version__

    	from .version import version as __version__  # noqa: F401

    except ImportError:

    	from warnings import warn

    	warn('Failed to find (autogenerated) version.py. Do not worry about this unless you really need to know the version.')

    	warn("Failed to find (autogenerated) version.py. Do not worry about this unless you really need to know the version.", stacklevel=2)

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