Format code in docstrings

This requires ruff 0.1.9 or newer.

noxfile.py

@@ -88,6 +88,6 @@ def docs(session):
 def ruff(session):
     """Check code for linter warnings and formatting issues."""
     check_files = ['src', 'tests', 'doc', 'noxfile.py']
-    session.install('ruff ~= 0.1.2')
+    session.install('ruff ~= 0.1.9')
     session.run('ruff', 'check', *check_files)
     session.run('ruff', 'format', '--diff', *check_files)

pyproject.toml

@@ -59,14 +59,17 @@ addopts = """\
     """
 
 [tool.ruff]
-# Enable pyflakes (F), pycodestyle (E, W), and flake8-bugbear (B).
-select = ["F", "E", "W", "B"]
 line-length = 78
 target-version = "py38"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint]
+# Enable pyflakes (F), pycodestyle (E, W), and flake8-bugbear (B).
+select = ["F", "E", "W", "B"]
+
+[tool.ruff.lint.per-file-ignores]
 # Ignore "Ambiguous variable name" for SIR state variable `I`.
 "sir.py" = ["E741"]
 
 [tool.ruff.format]
 quote-style = "single"
+docstring-code-format = true

src/pypfilt/io.py

@@ -53,18 +53,19 @@ def read_table(path, columns, comment='#', encoding='utf-8'):
     >>> from pypfilt.io import date_column, read_table
     >>> import numpy as np
     >>> import datetime
-    >>> path = "input_data.ssv"
+    >>> path = 'input_data.ssv'
     >>> with open(path, 'w') as f:
-    ...    _ = f.write('time value\\n')
-    ...    _ = f.write('2020-01-01 1\\n')
-    ...    _ = f.write('2020-01-02 3\\n')
-    ...    _ = f.write('2020-01-03 5\\n')
+    ...     _ = f.write('time value\\n')
+    ...     _ = f.write('2020-01-01 1\\n')
+    ...     _ = f.write('2020-01-02 3\\n')
+    ...     _ = f.write('2020-01-03 5\\n')
     >>> columns = [date_column('time'), ('value', np.int64)]
     >>> data = read_table(path, columns)
     >>> isinstance(data['time'][0], datetime.datetime)
     True
-    >>> observations = [{'time': row['time'], 'value': row['value']}
-    ...                 for row in data]
+    >>> observations = [
+    ...     {'time': row['time'], 'value': row['value']} for row in data
+    ... ]
     >>> # Remove the input file when it is no longer needed.
     >>> import os
     >>> os.remove(path)
@@ -162,6 +163,7 @@ def read_fields(time_scale, path, fields, comment='#', encoding='utf-8'):
        import numpy as np
        import pypfilt.io
 
+
        def load_time_series(self, filename, time_scale):
            fields = [pypfilt.io.time_field('time'), ('value', np.float64)]
            return pypfilt.io.read_fields(time_scale, filename, fields)
@@ -240,10 +242,10 @@ def read_lookup_table(path, time, dtype='f8', comment='#', encoding='utf-8'):
     >>> from pypfilt.io import read_lookup_table, lookup
     >>> from pypfilt.time import Datetime
     >>> import datetime
-    >>> path = "input_data.ssv"
+    >>> path = 'input_data.ssv'
     >>> with open(path, 'w') as f:
-    ...    _ = f.write('time value1 value2 value3\\n')
-    ...    _ = f.write('2020-01-01 1.0 1.5 2.0\\n')
+    ...     _ = f.write('time value1 value2 value3\\n')
+    ...     _ = f.write('2020-01-01 1.0 1.5 2.0\\n')
     >>> time = Datetime()
     >>> table = read_lookup_table(path, time)
     >>> isinstance(table['time'][0], datetime.datetime)

src/pypfilt/obs.py

@@ -182,6 +182,7 @@ class Obs(abc.ABC):
            import numpy as np
            import pypfilt.io
 
+
            def from_file(self, filename, time_scale):
                fields = [pypfilt.io.time_field('time'), ('value', np.float64)]
                return pypfilt.io.read_fields(time_scale, filename, fields)
@@ -305,7 +306,6 @@ class Univariate(Obs):
     ...         expect = snapshot.state_vec['x']
     ...         sdev = self.settings['parameters']['sdev']
     ...         return scipy.stats.norm(loc=expect, scale=self.sdev)
-    ...
     >>> observation_unit = 'x'
     >>> settings = {'parameters': {'sdev': 0.1}}
     >>> obs_model = MyObsModel(observation_unit, settings)

src/pypfilt/scenario.py

@@ -158,8 +158,9 @@ def load_instances(sources):
     >>> data_file = 'output.hdf5'
     >>> for instance in pypfilt.load_instances(config_file):
     ...     context = instance.build_context()
-    ...     state = pypfilt.forecast(context, forecast_times,
-    ...                              filename=data_file)
+    ...     state = pypfilt.forecast(
+    ...         context, forecast_times, filename=data_file
+    ...     )
     >>> # Remove the output file when it is no longer needed.
     >>> import os
     >>> os.remove(data_file)

src/pypfilt/state.py

@@ -226,11 +226,14 @@ def repack(svec, astype=float):
 
     >>> import numpy as np
     >>> from pypfilt.state import repack
-    >>> xs = np.array([(1.2, (2.2, 3.2)), (4.2, (5.2, 6.2))],
-    ...               dtype=[('x', float), ('y', float, 2)])
+    >>> xs = np.array(
+    ...     [(1.2, (2.2, 3.2)), (4.2, (5.2, 6.2))],
+    ...     dtype=[('x', float), ('y', float, 2)],
+    ... )
     >>> ys = repack(xs)
-    >>> assert np.array_equal(ys, np.array([[1.2, 2.2, 3.2],
-    ...                                     [4.2, 5.2, 6.2]]))
+    >>> assert np.array_equal(
+    ...     ys, np.array([[1.2, 2.2, 3.2], [4.2, 5.2, 6.2]])
+    ... )
     """
 
     def is_compat(dt):