Move to ruff for linting

.github/pull_request_template.md

@@ -22,4 +22,4 @@ The optional `-- format` and `-- write` arguments (see above) attempt to correct
 ## Further checks:
 - [ ] The documentation builds: `$ nox -s docs`.
 - [ ] Code is commented, particularly in hard-to-understand areas.
-- [ ] Tests are added that prove fix is effective or that feature works.
+- [ ] Tests are added that prove fix is effective or that feature works.

CHANGELOG.md

@@ -14,6 +14,7 @@
 ### Breaking Changes
 
 ### Chores
+- Move to using `ruff` for linting and start tracking `Cython` addition issue ([#45](https://github.com/NatLabRockies/scikit-sundae/pull/45))
 - Make GitHub hyperlinks reference new org name `NREL` -> `NatLabRockies` ([#42](https://github.com/NatLabRockies/scikit-sundae/pull/42))
 - Allow single backticks for sphinx inline code (`default_role = 'literal'`) ([#40](https://github.com/NatLabRockies/scikit-sundae/pull/40))
 - Rebrand NREL to NLR, and include name change for Alliance as well ([#39](https://github.com/NatLabRockies/scikit-sundae/pull/39))

noxfile.py

@@ -2,7 +2,6 @@
 
 import os
 import shutil
-import importlib
 
 import nox
 
@@ -12,7 +11,6 @@
 @nox.session(name='cleanup', python=False)
 def run_cleanup(_) -> None:
     """Use os/shutil to remove some files/directories"""
-
     if os.path.exists('.coverage'):
         os.remove('.coverage')
 
@@ -23,22 +21,27 @@ def run_cleanup(_) -> None:
 
 
 @nox.session(name='linter', python=False)
-def run_flake8(session: nox.Session) -> None:
+def run_ruff(session: nox.Session) -> None:
     """
-    Run flake8 with the github config file
+    Run ruff to check for linting errors.
 
-    Use the optional 'format' argument to run autopep8 prior to the linter.
+    Use the optional 'format' or 'format-unsafe' arguments to run ruff with the
+    --fix or --unsafe-fixes option prior to the linter. You can also use 'stats'
+    to show a summary of the found errors rather than a full report.
 
     """
+    session.run('pip', 'install', '--upgrade', '--quiet', 'ruff')
 
-    session.run('pip', 'install', '--upgrade', '--quiet', 'flake8')
-    session.run('pip', 'install', '--upgrade', '--quiet', 'autopep8')
+    command = ['ruff', 'check']
+    if 'stats' in session.posargs:
+        command.append('--statistics')
 
     if 'format' in session.posargs:
-        session.run('autopep8', '.', '--in-place', '--recursive',
-                    '--global-config=.github/linters/.flake8')
+        command.append('--fix')
+    elif 'format-unsafe' in session.posargs:
+        command.extend(['--fix', '--unsafe-fixes'])
 
-    session.run('flake8', '--config=.github/linters/.flake8')
+    session.run(*command)
 
 
 @nox.session(name='codespell', python=False)
@@ -50,7 +53,6 @@ def run_codespell(session: nox.Session) -> None:
     the files. Otherwise, you will only see a summary of the found errors.
 
     """
-
     session.run('pip', 'install', '--upgrade', '--quiet', 'codespell')
 
     command = ['codespell', '--config=.github/linters/.codespellrc']
@@ -69,7 +71,6 @@ def run_spellcheck(session: nox.Session) -> None:
     the files. Otherwise, you will only see a summary of the found errors.
 
     """
-
     run_codespell(session)
 
     command = ['codespell', '--config=.github/linters/.codespellrc']
@@ -89,20 +90,25 @@ def run_pytest(session: nox.Session) -> None:
     you can specify the number of workers using an int, e.g., parallel=4.
 
     """
-
-    package = importlib.util.find_spec('sksundae')
-    coverage_folder = os.path.dirname(package.origin)
-
     if 'no-reports' in session.posargs:
         command = [
             'pytest',
-            f'--cov={coverage_folder}',  # for editable or site-packages
+            '--cov=sksundae',
+            'tests/',
+        ]
+    elif 'codecov' in session.posargs:
+        command = [
+            'pytest',
+            '--cov=sksundae',
+            '--cov-report=xml',
             'tests/',
         ]
     else:
+        os.makedirs('reports', exist_ok=True)
+
         command = [
             'pytest',
-            '--cov=src/sksundae',
+            '--cov=sksundae',
             '--cov-report=html:reports/htmlcov',
             '--cov-report=xml:reports/coverage.xml',
             '--junitxml=reports/junit.xml',
@@ -117,15 +123,13 @@ def run_pytest(session: nox.Session) -> None:
         elif arg.startswith('parallel'):
             command[1:1] = ['-n', 'auto']
 
+    os.environ['MPLBACKEND'] = 'Agg'
     session.run(*command)
 
-    run_cleanup(session)
-
 
 @nox.session(name='badges', python=False)
 def run_genbadge(session: nox.Session) -> None:
     """Run genbadge to make test/coverage badges"""
-
     session.run(
         'genbadge', 'coverage', '-l',
         '-i', 'reports/coverage.xml',
@@ -150,7 +154,6 @@ def run_sphinx(session: nox.Session) -> None:
     are not showing new pages. In general, try without 'clean' first.
 
     """
-
     if 'clean' in session.posargs:
         os.chdir('docs')
         session.run('make', 'clean')
@@ -173,12 +176,11 @@ def run_pre_commit(session: nox.Session) -> None:
     """
     Run all linters/tests and make new badges
 
-    Order of sessions: flake8, spellcheck, pytest, genbadge. Using 'format' for
+    Order of sessions: ruff, spellcheck, pytest, genbadge. Using 'format' for
     linter, 'write' for spellcheck, and/or 'parallel' for pytest is permitted.
 
     """
-
-    run_flake8(session)
+    run_ruff(session)
     run_spellcheck(session)
 
     run_pytest(session)
@@ -197,6 +199,5 @@ def run_build_ext(session: nox.Session) -> None:
     extension files (.pyx, .pxd) are updated.
 
     """
-
     session.run('pip', 'install', '--upgrade', '--quiet', 'cython')
     session.run('python', 'setup.py', 'build_ext', '--inplace')

pyproject.toml

@@ -43,6 +43,31 @@ version = {attr = "sksundae.__version__"}
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.ruff]
+line-length = 80
+exclude = ["build", "docs", "images", "reports", "C_programs"]
+
+[tool.ruff.lint]
+preview = true
+select = [
+    "E",  # All pycodestyle errors
+    "W",  # All pycodestyle warnings
+    "F",  # All pyflakes errors
+    "B",  # All flake8-bugbear checks
+    "D",  # All pydocstyle checks
+]
+extend-select = [
+    "E302", "E305",  # Expected blank lines (requires preview=true, above)
+]
+ignore = [
+    "B007", "B009", "B010", "B028", "B905",
+    "D1", "D203", "D205", "D212", "D400", "D401", "D415",
+    "E201", "E202", "E226", "E241", "E731",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**/*" = ["D"]
+
 [project.optional-dependencies]
 docs = [
     "sphinx",
@@ -62,8 +87,7 @@ tests = [
 ]
 dev = [
     "nox",
-    "flake8",
-    "autopep8",
+    "ruff",
     "codespell",
     "genbadge[all]",
     "scikit-sundae[docs,tests]",

scripts/version_checker.py

@@ -28,7 +28,6 @@ def get_latest_version(package: str, prefix: str = None) -> str:
         Failed to fetch PyPI data for requested package.
 
     """
-
     url = f"https://pypi.org/pypi/{package}/json"
 
     response = requests.get(url)
@@ -73,7 +72,6 @@ def check_against_pypi(pypi: str, local: str) -> None:
         Local package is older than PyPI.
 
     """
-
     pypi = Version(pypi)
     local = Version(local)
 
@@ -104,7 +102,6 @@ def check_against_tag(tag: str, local: str) -> None:
         Version mismatch: tag differs from local.
 
     """
-
     tag = Version(tag)
     local = Version(local)
 

src/sksundae/cvode/_jactimes.py

@@ -50,7 +50,6 @@ def __init__(self, setupfn: Callable | None, solvefn: Callable) -> None:
         'rhsfn' -> 'setupfn' -> 'solvefn' for each integration step.
 
         """
-
         if setupfn is None:
             pass
         elif not isinstance(setupfn, Callable):

src/sksundae/cvode/_precond.py

@@ -92,7 +92,6 @@ def psolvefn(t, y, yp, rvec, zvec, gamma, delta, lr, userdata):
             cvode/Usage/index.html#preconditioner-solve-iterative-linear-solvers
 
         """
-
         if setupfn is None:
             pass
         elif not isinstance(setupfn, Callable):

src/sksundae/cvode/_solver.py

@@ -15,7 +15,7 @@ class CVODE:
 
     def __init__(self, rhsfn: Callable, **options) -> None:
         """
-        This class wraps the C-based variable-coefficient ordinary differential
+        A class to wrap the C-based variable-coefficient ordinary differential
         equations (CVODE) solver from SUNDIALS [1]_ [2]_.
 
         Parameters
@@ -138,7 +138,7 @@ def __init__(self, rhsfn: Callable, **options) -> None:
 
         Notes
         -----
-        Return values from all user-defined function (e.g., 'rhsfn', 'eventsfn',
+        Return values from user-defined functions (e.g., 'rhsfn', 'eventsfn',
         and 'jacfn') are ignored by the solver. Instead the solver directly
         reads from pre-allocated memory. Output arrays (e.g., 'yp', 'events',
         and 'JJ') from each user-defined callable should be filled within each
@@ -338,10 +338,14 @@ class CVODEResult(_CVODEResult):
     def __init__(self, **kwargs) -> None:
         """
         Inherits from :class:`~sksundae.common.RichResult`. The solution class
-        groups output from :class:`CVODE` into an object with the fields:
+        groups output from :class:`CVODE` into an object. Descriptions of the
+        fields are given below.
 
         Parameters
         ----------
+        **kwargs : dict
+            Keyword arguments for the result fields. The full list of fields is
+            given below.
         message : str
             Human-readable description of the status value.
         success : bool
@@ -382,7 +386,7 @@ def __init__(self, **kwargs) -> None:
         Notes
         -----
         Terminal events are appended to the end of 't' and 'y'. However, if an
-        event was not terminal then it will only appear in '\\*_events' outputs
+        event was not terminal then it will only appear in `*_events` outputs
         and not within the main output arrays.
 
         'nfev' and 'njev' are cumulative for stepwise solution approaches. The

src/sksundae/ida/_jactimes.py

@@ -50,7 +50,6 @@ def __init__(self, setupfn: Callable | None, solvefn: Callable) -> None:
         'resfn' -> 'setupfn' -> 'solvefn' for each integration step.
 
         """
-
         if setupfn is None:
             pass
         elif not isinstance(setupfn, Callable):

src/sksundae/ida/_precond.py

@@ -63,7 +63,6 @@ def __init__(self, setupfn: Callable | None, solvefn: Callable) -> None:
             ida/Usage/index.html#preconditioner-setup-iterative-linear-solvers
 
         """
-
         if setupfn is None:
             pass
         elif not isinstance(setupfn, Callable):

src/sksundae/ida/_solver.py

@@ -15,7 +15,7 @@ class IDA:
 
     def __init__(self, resfn: Callable, **options) -> None:
         """
-        This class wraps the implicit differential algebraic (IDA) solver from
+        A class to wrap the implicit differential algebraic (IDA) solver from
         SUNDIALS [1]_ [2]_. IDA solves both ordinary differential equations
         (ODEs) and differiential agebraic equations (DAEs).
 
@@ -144,7 +144,7 @@ def __init__(self, resfn: Callable, **options) -> None:
 
         Notes
         -----
-        Return values from all user-defined function (e.g., 'resfn', 'eventsfn',
+        Return values from user-defined functions (e.g., 'resfn', 'eventsfn',
         and 'jacfn') are ignored by the solver. Instead the solver directly
         reads from pre-allocated memory. Output arrays (e.g., 'res', 'events',
         and 'JJ') from each user-defined callable should be filled within each
@@ -363,10 +363,14 @@ class IDAResult(_IDAResult):
     def __init__(self, **kwargs) -> None:
         """
         Inherits from :class:`~sksundae.common.RichResult`. The solution class
-        groups output from :class:`IDA` into an object with the fields:
+        groups output from :class:`IDA` into an object. Descriptions of the
+        fields are given below.
 
         Parameters
         ----------
+        **kwargs : dict
+            Keyword arguments for the result fields. The full list of fields is
+            given below.
         message : str
             Human-readable description of the status value.
         success : bool
@@ -413,7 +417,7 @@ def __init__(self, **kwargs) -> None:
         Notes
         -----
         Terminal events are appended to the end of 't', 'y', and 'yp'. However,
-        if an event was not terminal then it will only appear in '\\*_events'
+        if an event was not terminal then it will only appear in `*_events`
         outputs and not within the main output arrays.
 
         'nfev' and 'njev' are cumulative for stepwise solution approaches. The

src/sksundae/jacband.py

@@ -21,7 +21,6 @@
 def _cvode_pattern(rhsfn: Callable, t0: float, y0: ndarray,
                    userdata: Any = None) -> ndarray:
     """Jacobian pattern for CVODE functions. Access via j_pattern()."""
-
     # wrap rhsfn for cases w/ and w/o userdata
     signature = inspect.signature(rhsfn)
 
@@ -76,7 +75,6 @@ def j_pattern(j):
 def _ida_pattern(resfn: Callable, t0: float, y0: ndarray, yp0: ndarray = None,
                  userdata: Any = None) -> ndarray:
     """Jacobian pattern for IDA functions. Access via j_pattern()."""
-
     # wrap resfn for cases w/ and w/o userdata
     signature = inspect.signature(resfn)
 
@@ -175,7 +173,6 @@ def j_pattern(rhsfn: Callable, t0: float, y0: ndarray, yp0: ndarray = None,
         either is or is not dependedent on variable `y_j`, respectively.
 
     """
-
     if yp0 is None:
         y0 = np.asarray(y0, dtype=float)
         return _cvode_pattern(rhsfn, t0, y0, userdata)