From fb694fedd536a7a93a6bcf1ab55993a55b382820 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 10:35:59 +0100
Subject: [PATCH 01/10] Minor formatting changes

---
 pybv/__init__.py        | 2 +-
 specification/README.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pybv/__init__.py b/pybv/__init__.py
index 92eb443..22ee46a 100644
--- a/pybv/__init__.py
+++ b/pybv/__init__.py
@@ -1,7 +1,7 @@
 """A lightweight I/O utility for the BrainVision data format."""
 
-
 __version__ = "0.8.0.dev5"
+
 from .io import write_brainvision
 
 __all__ = ["write_brainvision"]
diff --git a/specification/README.md b/specification/README.md
index ee895ce..049fa41 100644
--- a/specification/README.md
+++ b/specification/README.md
@@ -1,4 +1,4 @@
-The `BrainVisionCoreDataFormat_1-0.pdf` file can be contains the specification
+The file [`BrainVisionCoreDataFormat_1-0.pdf`](BrainVisionCoreDataFormat_1-0.pdf) contains the specification
 for the BrainVision Core Data Format (BVCDF).
 
 The document stored in this repository exists for backup reasons.

From 9e0d0c3f28a68cea1ca2c51ad41e9c3d6205e46d Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 12:39:41 +0100
Subject: [PATCH 02/10] Replace flake8/isort/black with ruff

---
 .pre-commit-config.yaml      |  41 ++--
 pybv/_export.py              |  44 ++--
 pybv/io.py                   | 376 +++++++++++++++++------------------
 pybv/tests/test_bv_writer.py |  42 ++--
 pyproject.toml               |   3 +
 5 files changed, 244 insertions(+), 262 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1d06339..75fde44 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,27 +1,20 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-json
-    -   id: check-ast
-    -   id: check-added-large-files
-    -   id: check-case-conflict
-    -   id: check-docstring-first
--   repo: https://github.com/pycqa/isort
-    rev: "5.12.0"
-    hooks:
-    -   id: isort
--   repo: https://github.com/psf/black
-    rev: "23.9.1"
-    hooks:
-    -   id: black
--   repo: https://github.com/pycqa/flake8
-    rev: "6.1.0"
-    hooks:
-    -   id: flake8
-        additional_dependencies: [flake8-docstrings]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-json
+    - id: check-ast
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-docstring-first
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.1
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
diff --git a/pybv/_export.py b/pybv/_export.py
index d0cabfe..c843d8e 100644
--- a/pybv/_export.py
+++ b/pybv/_export.py
@@ -19,31 +19,31 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
         The raw data to export.
     fname : str | pathlib.Path
         The name of the file where raw data will be exported to. Must end with
-        ``".vhdr"``, and accompanying *.vmrk* and *.eeg* files will be written
-        inside the same directory.
+        ``".vhdr"``, and accompanying *.vmrk* and *.eeg* files will be written inside
+        the same directory.
     events : np.ndarray | None
-        Events to be written to the marker file (*.vmrk*). When array, must be in
-        `MNE-Python format <https://mne.tools/stable/glossary.html#term-events>`_.
-        When ``None`` (default), events will be written based on ``raw.annotations``.
+        Events to be written to the marker file (*.vmrk*). If array, must be in
+        `MNE-Python format <https://mne.tools/stable/glossary.html#term-events>`_. If
+        ``None`` (default), events will be written based on ``raw.annotations``.
     overwrite : bool
         Whether or not to overwrite existing data. Defaults to ``False``.
+
     """
-    # Prepare file location
+    # prepare file location
     if not str(fname).endswith(".vhdr"):
         raise ValueError("`fname` must have the '.vhdr' extension for BrainVision.")
     fname = Path(fname)
     folder_out = fname.parents[0]
     fname_base = fname.stem
 
-    # Prepare data from raw
+    # prepare data from raw
     data = raw.get_data()  # gets data starting from raw.first_samp
     sfreq = raw.info["sfreq"]  # in Hz
     meas_date = raw.info["meas_date"]  # datetime.datetime
     ch_names = raw.ch_names
 
-    # write voltage units as micro-volts and all other units without
-    # scaling
-    # We write units that we don't know as n/a
+    # write voltage units as micro-volts and all other units without scaling
+    # write units that we don't know as n/a
     unit = []
     for ch in raw.info["chs"]:
         if ch["unit"] == FIFF.FIFF_UNIT_V:
@@ -54,9 +54,9 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
             unit.append(_unit2human.get(ch["unit"], "n/a"))
     unit = [u if u != "NA" else "n/a" for u in unit]
 
-    # We enforce conversion to float32 format
-    # XXX: Could add a feature that checks data and optimizes `unit`, `resolution`,
-    #      and `format` so that raw.orig_format could be retained if reasonable.
+    # enforce conversion to float32 format
+    # XXX: Could add a feature that checks data and optimizes `unit`, `resolution`, and
+    #      `format` so that raw.orig_format could be retained if reasonable.
     if raw.orig_format != "single":
         warn(
             f"Encountered data in '{raw.orig_format}' format. "
@@ -67,12 +67,12 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
     fmt = "binary_float32"
     resolution = 0.1
 
-    # Handle events
+    # handle events
     # if we got an ndarray, this is in MNE-Python format
     msg = "`events` must be None or array in MNE-Python format."
     if events is not None:
-        # Subtract raw.first_samp because brainvision marks events starting from
-        # the first available data point and ignores the raw.first_samp
+        # Subtract raw.first_samp because brainvision marks events starting from the
+        # first available data point and ignores the raw.first_samp
         assert isinstance(events, np.ndarray), msg
         assert events.ndim == 2, msg
         assert events.shape[-1] == 3, msg
@@ -107,14 +107,14 @@ def _mne_annots2pybv_events(raw):
     """Convert mne Annotations to pybv events."""
     events = []
     for annot in raw.annotations:
-        # Handle onset and duration: seconds to sample,
-        # relative to raw.first_samp / raw.first_time
+        # handle onset and duration: seconds to sample, relative to
+        # raw.first_samp / raw.first_time
         onset = annot["onset"] - raw.first_time
         onset = raw.time_as_index(onset).astype(int)[0]
         duration = int(annot["duration"] * raw.info["sfreq"])
 
-        # Triage type and description
-        # Defaults to type="Comment", and the full description
+        # triage type and description
+        # defaults to type="Comment" and the full description
         etype = "Comment"
         description = annot["description"]
         for start in ["Stimulus/S", "Response/R", "Comment/"]:
@@ -137,11 +137,11 @@ def _mne_annots2pybv_events(raw):
         )
 
         if "ch_names" in annot:
-            # Handle channels
+            # handle channels
             channels = list(annot["ch_names"])
             event_dict["channels"] = channels
 
-        # Add a "pybv" event
+        # add a "pybv" event
         events += [event_dict]
 
     return events
diff --git a/pybv/io.py b/pybv/io.py
index 6fa6245..b745c4e 100644
--- a/pybv/io.py
+++ b/pybv/io.py
@@ -43,123 +43,118 @@ def write_brainvision(
     Parameters
     ----------
     data : np.ndarray, shape (n_channels, n_times)
-        The raw data to export. Voltage data is assumed to be in **volts** and
-        will be scaled as specified by `unit`. Non-voltage channels (as
-        specified by `unit`) are never scaled (e.g., `"°C"`).
+        The raw data to export. Voltage data is assumed to be in **volts** and will be
+        scaled as specified by `unit`. Non-voltage channels (as specified by `unit`) are
+        never scaled (e.g., `"°C"`).
     sfreq : int | float
         The sampling frequency of the data in Hz.
     ch_names : list of {str | int}, len (n_channels)
         The names of the channels. Integer channel names are converted to string.
     ref_ch_names : str | list of str, len (n_channels) | None
-        The name of the channel used as a reference during the recording. If
-        references differed between channels, you may supply a list of
-        reference channel names corresponding to each channel in `ch_names`.
-        If ``None`` (default), assume that all channels are referenced to a
-        common channel that is not further specified (BrainVision default).
-
-        .. note:: The reference channel name specified here does not need to
-                  appear in `ch_names`. It is permissible to specify a
-                  reference channel that is not present in `data`.
+        The name of the channel used as a reference during the recording. If references
+        differ between channels, you may supply a list of reference channel names
+        corresponding to each channel in `ch_names`. If ``None`` (default), assume that
+        all channels are referenced to a common channel that is not further specified
+        (BrainVision default).
+
+        .. note:: The reference channel name specified here does not need to appear in
+                  `ch_names`. It is permissible to specify a reference channel that is
+                  not present in `data`.
     fname_base : str
-        The base name for the output files. Three files will be created
-        (*.vhdr*, *.vmrk*, *.eeg*) and all will share this base name.
+        The base name for the output files. Three files will be created (*.vhdr*,
+        *.vmrk*, *.eeg*), and all will share this base name.
     folder_out : str
-        The folder where output files will be saved. Will be created if it does
-        not exist yet.
+        The folder where output files will be saved. Will be created if it does not
+        exist.
     overwrite : bool
         Whether or not to overwrite existing files. Defaults to ``False``.
     events : np.ndarray, shape (n_events, {2, 3}) | list of dict, len (n_events) | None
-        Events to write in the marker file (*.vmrk*). Defaults to ``None``
-        (not writing any events).
-
-        If an array is passed, it must have either two or three columns and
-        consist of non-negative integers. The first column is always the
-        zero-based *onset* index of each event (corresponding to the
-        time dimension of the `data` array). The second column is a number
-        associated with the *description* of the event. The (optional) third
-        column specifies the *duration* of each event in samples (defaults to
-        ``1``). All events are written as *type* "Stimulus" and interpreted
-        as relevant to all *channels*. For more fine-grained control over how to
-        write events, pass a list of dict as described next.
-
-        If list of dict is passed, each dict in the list corresponds to an
-        event and may have the following entries:
+        Events to write in the marker file (*.vmrk*). Defaults to ``None`` (not writing
+        any events).
+
+        If an array is passed, it must have either two or three columns and consist of
+        non-negative integers. The first column is always the zero-based *onset* index
+        of each event (corresponding to the time dimension of the `data` array). The
+        second column is a number associated with the *description* of the event. The
+        (optional) third column specifies the *duration* of each event in samples
+        (defaults to ``1``). All events are written as *type* "Stimulus" and interpreted
+        as relevant to all *channels*. For more fine-grained control over how to write
+        events, pass a list of dict as described next.
+
+        If a list of dict is passed, each dict in the list corresponds to an event and
+        may have the following entries:
 
             - ``"onset"`` : int
-                The zero-based index of the event onset, corresponding to the
-                time dimension of the `data` array.
+                The zero-based index of the event onset, corresponding to the time
+                dimension of the `data` array.
             - ``"duration"`` : int
                 The duration of the event in samples (defaults to ``1``).
             - ``"description"`` : str | int
-                The description of the event. Must be a non-negative int when
-                `type` (see below) is either ``"Stimulus"`` or ``"Response"``, and may
-                be a str when `type` is ``"Comment"``.
+                The description of the event. Must be a non-negative int when `type`
+                (see below) is either ``"Stimulus"`` or ``"Response"``, and may be a str
+                when `type` is ``"Comment"``.
             - ``"type"`` : str
                 The type of the event, must be one of ``{"Stimulus", "Response",
-                "Comment"}`` (defaults to ``"Stimulus"``). Additional types like
-                the known BrainVision types ``"New Segment"``, ``"SyncStatus"``, etc.
-                are currently not supported.
+                "Comment"}`` (defaults to ``"Stimulus"``). Additional types like the
+                known BrainVision types ``"New Segment"``, ``"SyncStatus"``, etc. are
+                currently not supported.
             - ``"channels"`` : str | list of {str | int}
                 The channels that are impacted by the event. Can be ``"all"``
-                (reflecting all channels), or a channel name, or a list of
-                channel names. An empty list means the same as ``"all"``.
-                Integer channel names are converted to strings, as in the
-                `ch_names` parameter. Defaults to ``"all"``.
-
-        Note that ``onset`` and ``description`` MUST be specified in each
-        dict.
-
-        .. note:: When specifying more than one but less than "all" channels
-                  that are impacted by an event, ``pybv`` will write the same
-                  event for as many times as channels are specified (see
-                  :gh:`77` for a discussion). This is valid according to the
-                  BrainVision specification, however for maximum compatibility
-                  with other BrainVision readers, we do not (yet) recommend
-                  using this feature.
+                (reflecting all channels), or a channel name, or a list of channel
+                names. An empty list means the same as ``"all"``. Integer channel names
+                are converted to strings, as in the `ch_names` parameter. Defaults to
+                ``"all"``.
+
+        Note that ``"onset"`` and ``"description"`` MUST be specified in each dict.
+
+        .. note:: When specifying more than one but less than "all" channels that are
+                  impacted by an event, ``pybv`` will write the same event for as many
+                  times as channels are specified (see :gh:`77` for a discussion). This
+                  is valid according to the BrainVision specification, but for maximum
+                  compatibility with other BrainVision readers, we do not recommend
+                  using this feature yet.
 
     resolution : float | np.ndarray, shape (n_channels,)
-        The resolution in `unit` in which you'd like the data to be stored. If
-        float, the same resolution is applied to all channels. If array with
-        n_channels elements, each channel is scaled with its own corresponding
-        resolution from the array. Note that `resolution` is applied on top
-        of the default resolution that a data format (see `fmt`) has. For
-        example, the ``"binary_int16"`` format by design has no floating point
-        support, but when scaling the data in µV for ``0.1`` resolution (default),
-        accurate writing for all values >= 0.1 µV is guaranteed. In contrast,
-        the ``"binary_float32"`` format by design already supports floating points
-        up to 1e-6 resolution, and writing data in µV with 0.1 resolution
-        will thus guarantee accurate writing for all values >= 1e-7 µV
+        The resolution in `unit` in which you'd like the data to be stored. If float,
+        the same resolution is applied to all channels. If array with `n_channels`
+        elements, each channel is scaled with its own corresponding resolution from the
+        array. Note that `resolution` is applied on top of the default resolution that a
+        data format (see `fmt`) has. For example, the ``"binary_int16"`` format by
+        design has no floating point support, but when scaling the data in µV for
+        ``0.1`` resolution (default), accurate writing for all values ≥ 0.1 µV is
+        guaranteed. In contrast, the ``"binary_float32"`` format by design alread
+        supports floating points up to 1e-6 resolution, and writing data in µV with 0.1
+        resolution will thus guarantee accurate writing for all values ≥ 1e-7 µV
         (``1e-6 * 0.1``).
     unit : str | list of str
         The unit of the exported data. This can be one of ``"V"``, ``"mV"``, ``"µV"``
-        (or equivalently ``"uV"``) , or ``"nV"``, which will scale the data
-        accordingly. Defaults to ``"µV"``. Can also be a list of units with one unit
-        per channel. Non-voltage channels are stored "as is", for example
-        temperature might be available in ``"°C"``, which ``pybv`` will not scale.
+        (or equivalently ``"uV"``), or ``"nV"``, which will scale the data accordingly.
+        Defaults to ``"µV"``. Can also be a list of units with one unit per channel.
+        Non-voltage channels are stored "as is", for example temperature might be
+        available in ``"°C"``, which ``pybv`` will not scale.
     fmt : str
         Binary format the data should be written as. Valid choices are
         ``"binary_float32"`` (default) and ``"binary_int16"``.
     meas_date : datetime.datetime | str | None
         The measurement date specified as a :class:`datetime.datetime` object.
-        Alternatively, can be a str in the format "YYYYMMDDhhmmssuuuuuu"
-        ("u" stands for microseconds). Note that setting a measurement date
-        implies that one additional event is created in the *.vmrk* file. To
-        prevent this, set this parameter to ``None`` (default).
+        Alternatively, can be a string in the format "YYYYMMDDhhmmssuuuuuu" ("u" stands
+        for microseconds). Note that setting a measurement date implies that one
+        additional event is created in the *.vmrk* file. To prevent this, set this
+        parameter to ``None`` (default).
 
     Notes
     -----
-    iEEG/EEG/MEG data is assumed to be in V, and ``pybv`` will scale these data
-    to µV by default. Any unit besides µV is officially unsupported in the
-    BrainVision specification. However, if one specifies other voltage units
-    such as mV or nV, we will still scale the signals accordingly in the
-    exported file. We will also write channels with non-voltage units such as
-    °C as is (without scaling). For maximum compatibility, all signals
-    should be written as µV.
-
-    When passing a list of dict to `events`, the event ``type`` that can be passed
-    is currently limited to one of ``{"Stimulus", "Response", "Comment"}``. The
-    BrainVision specification itself does not limit event types, and future
-    extensions of ``pybv`` may permit additional or even arbitrary event types.
+    iEEG/EEG/MEG data is assumed to be in V, and ``pybv`` will scale these data to µV by
+    default. Any unit besides µV is officially unsupported in the BrainVision
+    specification. However, if one specifies other voltage units such as mV or nV, we
+    will still scale the signals accordingly in the exported file. We will also write
+    channels with non-voltage units such as °C as is (without scaling). For maximum
+    compatibility, all signals should be written as µV.
+
+    When passing a list of dict to `events`, the event ``type`` that can be passed is
+    currently limited to one of ``{"Stimulus", "Response", "Comment"}``. The BrainVision
+    specification itself does not limit event types, and future extensions of ``pybv``
+    may permit additional or even arbitrary event types.
 
     References
     ----------
@@ -169,19 +164,24 @@ def write_brainvision(
     --------
     >>> data = np.random.random((3, 5))
     >>> # write data with varying units
-    ... # Note channels A1 and A2 are expected to be in volt and will get
-    ... # rescaled to µV and mV respectively.
-    ... # TEMP is expected to be in some other unit (i.e., NOT volt), and
-    ... # will not get scaled (it is written "as is")
-    ... write_brainvision(data=data, sfreq=1, ch_names=["A1", "A2", "TEMP"],
-    ...                   folder_out="./",
-    ...                   fname_base="pybv_test_file",
-    ...                   unit=["µV", "mV", "°C"])
+    ... # channels A1 and A2 are expected to be in volt and will get rescaled to µV and
+    ... # mV, respectively.
+    ... # TEMP is expected to be in some other unit (i.e., NOT volt), and will not get
+    ... # scaled (it is written "as is")
+    ... write_brainvision(
+    ...     data=data,
+    ...     sfreq=1,
+    ...     ch_names=["A1", "A2", "TEMP"],
+    ...     folder_out="./",
+    ...     fname_base="pybv_test_file",
+    ...     unit=["µV", "mV", "°C"]
+    ... )
     >>> # remove the files
     >>> for ext in [".vhdr", ".vmrk", ".eeg"]:
     ...     os.remove("pybv_test_file" + ext)
-    """  # noqa: E501
-    # Input checks
+
+    """
+    # input checks
     if not isinstance(data, np.ndarray):
         raise ValueError(f"data must be np.ndarray, but found: {type(data)}")
 
@@ -201,8 +201,8 @@ def write_brainvision(
 
     if len(data) != nchan:
         raise ValueError(
-            f"Number of channels in data ({len(data)}) does not "
-            f"match number of channel names ({len(ch_names)})"
+            f"Number of channels in data ({len(data)}) does not match number of "
+            f"channel names ({len(ch_names)})."
         )
 
     if len(set(ch_names)) != nchan:
@@ -210,7 +210,7 @@ def write_brainvision(
 
     events = _chk_events(events, ch_names, data.shape[1])
 
-    # Ensure we have a list of strings as reference channel names
+    # ensure we have a list of strings as reference channel names
     if ref_ch_names is None:
         ref_ch_names = [""] * nchan  # common but unspecified reference
     elif isinstance(ref_ch_names, str):
@@ -218,30 +218,27 @@ def write_brainvision(
     else:
         if "" in ref_ch_names:
             msg = (
-                f"ref_ch_names contains an empty string: {ref_ch_names}\n"
-                f"Empty strings are reserved values and not permitted "
-                f"as reference channel names."
+                f"ref_ch_names contains an empty string: {ref_ch_names}\nEmpty strings "
+                "are reserved values and not permitted as reference channel names."
             )
             raise ValueError(msg)
         ref_ch_names = [str(ref_ch_name) for ref_ch_name in ref_ch_names]
 
     if len(ref_ch_names) != nchan:
         raise ValueError(
-            f"The number of reference channel names ({len(ref_ch_names)})"
-            f"must match the number of channels in your data ({nchan})"
+            f"The number of reference channel names ({len(ref_ch_names)}) must match "
+            f"the number of channels in your data ({nchan})."
         )
 
     # ensure ref chs that are in data are zero
     for ref_ch_name in list(set(ref_ch_names) & set(ch_names)):
         if not np.allclose(data[ch_names.index(ref_ch_name), :], 0):
             raise ValueError(
-                f"The provided data for the reference channel "
-                f"{ref_ch_name} does not appear to be zero across "
-                f"all time points. This indicates that this channel "
-                f"either did not serve as a reference during the recording, "
-                f"or the data has been altered since. Please either pick a "
-                f"different reference channel, or omit the "
-                f"ref_ch_name parameter."
+                f"The provided data for the reference channel {ref_ch_name} does not "
+                "appear to be zero across all time points. This indicates that this "
+                "channel either did not serve as a reference during the recording, or "
+                "the data has been altered since. Please either pick a different "
+                "reference channel, or omit the ref_ch_name parameter."
             )
 
     if not isinstance(sfreq, (int, float)):
@@ -264,8 +261,8 @@ def write_brainvision(
         unit = [unit] * nchan
     if len(unit) != nchan:
         raise ValueError(
-            f"Number of channels in unit ({len(unit)}) does not "
-            f"match number of channel names ({nchan})"
+            f"Number of channels in unit ({len(unit)}) does not match number of channel"
+            f" names ({nchan})"
         )
     units = unit
 
@@ -281,15 +278,15 @@ def write_brainvision(
     # only show the warning once if a greek letter was encountered
     if show_warning:
         warn(
-            f"Encountered small Greek letter mu 'μ' or 'u' in unit: {unit}. "
-            f"Converting to micro sign 'µ'."
+            f"Encountered small Greek letter mu 'μ' or 'u' in unit: {unit}. Converting "
+            "to micro sign 'µ'."
         )
 
     # measurement date
     if not isinstance(meas_date, (str, datetime.datetime, type(None))):
         raise ValueError(
-            f"`meas_date` must be of type str, datetime.datetime,"
-            f' or None but is of type "{type(meas_date)}"'
+            f"`meas_date` must be of type str, datetime.datetime, or None but is of "
+            f'type "{type(meas_date)}"'
         )
     elif isinstance(meas_date, datetime.datetime):
         meas_date = meas_date.strftime("%Y%m%d%H%M%S%f")
@@ -297,12 +294,11 @@ def write_brainvision(
         pass
     elif not (meas_date.isdigit() and len(meas_date) == 20):
         raise ValueError(
-            "Got a str for `meas_date`, but it was not formatted "
-            "as expected. Please supply a str in the format: "
-            '"YYYYMMDDhhmmssuuuuuu".'
+            "Got a str for `meas_date`, but it was not formatted as expected. Please "
+            'supply a str in the format: "YYYYMMDDhhmmssuuuuuu".'
         )
 
-    # Create output file names/paths, checking if they already exist
+    # create output file names/paths, checking if they already exist
     folder_out_created = not op.exists(folder_out)
     os.makedirs(folder_out, exist_ok=True)
     eeg_fname = op.join(folder_out, fname_base + ".eeg")
@@ -310,11 +306,11 @@ def write_brainvision(
     vhdr_fname = op.join(folder_out, fname_base + ".vhdr")
     for fname in (eeg_fname, vmrk_fname, vhdr_fname):
         if op.exists(fname) and not overwrite:
-            raise IOError(
+            raise OSError(
                 f"File already exists: {fname}.\n" f"Consider setting overwrite=True."
             )
 
-    # Write output files, but delete everything if we come across an error
+    # write output files, but delete everything if we come across an error
     try:
         _write_bveeg_file(
             eeg_fname,
@@ -354,16 +350,16 @@ def write_brainvision(
 def _chk_events(events, ch_names, n_times):
     """Check that the events parameter is as expected.
 
-    This function will always return `events` as a list of dicts.
-    If `events` is ``None``, it will be an empty list.
-    If `events` is a list of dict, it will add missing keys to each dict with
-    default values, and it will -- for each ith event -- turn ``events[i]["channels"]``
-    into a list of 1-based channel name indices, where ``0`` equals ``"all"``.
-    Event descriptions for ``"Stimulus"`` and ``"Response"`` will be reformatted to
-    a str of the format ``"S{:>n}"`` (or with a leading ``"R"`` for ``"Response"``),
-    where ``n`` is determined by the description with the most digits (minimum 3).
-    For each ith event, the onset (``events[i]["onset"]``) will be incremented by 1
-    to comply with the 1-based indexing used in BrainVision marker files (*.vmrk*).
+    This function will always return `events` as a list of dicts. If `events` is
+    ``None``, it will be an empty list. If `events` is a list of dict, it will add
+    missing keys to each dict with default values, and it will, for each ith event, turn
+    ``events[i]["channels"]`` into a list of 1-based channel name indices, where ``0``
+    equals ``"all"``. Event descriptions for ``"Stimulus"`` and ``"Response"`` will be
+    reformatted to a str of the format ``"S{:>n}"`` (or with a leading ``"R"`` for
+    ``"Response"``), where ``n`` is determined by the description with the most digits
+    (minimum 3). For each ith event, the onset (``events[i]["onset"]``) will be
+    incremented by 1 to comply with the 1-based indexing used in BrainVision marker
+    files (*.vmrk*).
 
     Parameters
     ----------
@@ -378,6 +374,7 @@ def _chk_events(events, ch_names, n_times):
     -------
     events_out : list of dict, len (n_events)
         The preprocessed events, always provided as list of dict.
+
     """
     if not isinstance(events, (type(None), np.ndarray, list)):
         raise ValueError("events must be an array, a list of dict, or None")
@@ -387,8 +384,8 @@ def _chk_events(events, ch_names, n_times):
         events_out = []
 
     # default events
-    # NOTE: using "ch_names" as default for channels translates directly
-    #       into "all" but is robust with respect to channels named "all"
+    # NOTE: using "ch_names" as default for channels translates directly into "all" but
+    # is robust with respect to channels named "all"
     event_defaults = dict(duration=1, type="Stimulus", channels=ch_names)
 
     # validate input: ndarray
@@ -397,13 +394,11 @@ def _chk_events(events, ch_names, n_times):
             raise ValueError(f"When array, events must be 2D, but got {events.ndim}")
         if events.shape[1] not in (2, 3):
             raise ValueError(
-                "When array, events must have 2 or 3 columns, "
-                f"but got: {events.shape[1]}"
+                "When array, events must have 2 or 3 columns, but got {events.shape[1]}"
             )
         if not all([np.issubdtype(i, np.integer) for i in events.flat]):
             raise ValueError(
-                "When array, all entries in events must be int, but "
-                "found other types"
+                "When array, all entries in events must be int, but found other types"
             )
 
         # convert array to list of dict
@@ -432,8 +427,8 @@ def _chk_events(events, ch_names, n_times):
         # each item must be dict
         if not isinstance(event, dict):
             raise ValueError(
-                "When list, events must be a list of dict, but found "
-                "non-dict element in list"
+                "When list, events must be a list of dict, but found non-dict element "
+                "in list"
             )
 
     # NOTE: We format 1 -> "S  1", 10 -> "S 10", 100 -> "S100", etc.,
@@ -449,13 +444,13 @@ def _chk_events(events, ch_names, n_times):
     twidth = max(3, int(np.ceil(np.log10(max_event_descr))))
 
     # do full validation
-    for iev, event in enumerate(events_out):
+    for event in events_out:
         # required keys
         for required_key in ["onset", "description"]:
             if required_key not in event:
                 raise ValueError(
-                    "When list of dict, each dict in events must have "
-                    "the keys 'onset' and 'description'"
+                    "When list of dict, each dict in events must have the keys 'onset' "
+                    "and 'description'"
                 )
 
         # populate keys with default if missing (in-place)
@@ -470,20 +465,20 @@ def _chk_events(events, ch_names, n_times):
 
         if not (0 <= event["onset"] < n_times):
             raise ValueError(
-                "events: at least one onset sample is not in range of "
-                f"data (0-{n_times-1})"
+                "events: at least one onset sample is not in range of data (0-"
+                f"{n_times - 1})"
             )
 
         if event["duration"] < 0:
             raise ValueError(
-                "events: at least one duration is negative. Durations "
-                "must be >= 0 samples."
+                "events: at least one duration is negative. Durations must be >= 0 "
+                "samples."
             )
 
         if not (0 <= event["onset"] + event["duration"] <= n_times):
             raise ValueError(
-                "events: at least one event has a duration that exceeds "
-                f"the range of data (0-{n_times-1})"
+                "events: at least one event has a duration that exceeds the range of "
+                f"data (0-{n_times - 1})"
             )
 
         event["onset"] = event["onset"] + 1  # VMRK uses 1-based indexing
@@ -497,14 +492,14 @@ def _chk_events(events, ch_names, n_times):
         if event["type"] in ["Stimulus", "Response"]:
             if not isinstance(event["description"], int):
                 raise ValueError(
-                    f"events: when `type` is {event['type']}, "
-                    "`description` must be non-negative int"
+                    f"events: when `type` is {event['type']}, `description` must be "
+                    "non-negative int"
                 )
 
             if event["description"] < 0:
                 raise ValueError(
-                    f"events: when `type` is {event['type']}, "
-                    "descriptions must be non-negative ints."
+                    f"events: when `type` is {event['type']}, descriptions must be "
+                    "non-negative ints."
                 )
 
             tformat = event["type"][0] + "{:>" + str(twidth) + "}"
@@ -514,14 +509,14 @@ def _chk_events(events, ch_names, n_times):
             assert event["type"] == "Comment"
             if not isinstance(event["description"], (int, str)):
                 raise ValueError(
-                    f"events: when `type` is {event['type']}, "
-                    "`description` must be str or int"
+                    f"events: when `type` is {event['type']}, `description` must be str"
+                    "or int"
                 )
             event["description"] = str(event["description"])
 
         # `channels`
-        # "all" becomes ch_names (list of all channel names)
-        # single str 'ch_name' becomes [ch_name]
+        # "all" becomes ch_names (list of all channel names), single str 'ch_name'
+        # becomes [ch_name]
         if not isinstance(event["channels"], (list, str)):
             raise ValueError("events: `channels` must be str or list of str")
 
@@ -531,8 +526,8 @@ def _chk_events(events, ch_names, n_times):
                     raise ValueError(
                         "Found channel named 'all'. Your `channels` specification in "
                         "events is also 'all'. This is ambiguous, because 'all' is a "
-                        "reserved keyword. Either rename the channel called 'all', "
-                        "or explicitly list all ch_names in `channels` in each event "
+                        "reserved keyword. Either rename the channel called 'all', or "
+                        "explicitly list all ch_names in `channels` in each event "
                         "instead of using 'all'."
                     )
                 event["channels"] = ch_names
@@ -543,8 +538,8 @@ def _chk_events(events, ch_names, n_times):
         for ch in event["channels"]:
             if not isinstance(ch, (str, int)):
                 raise ValueError(
-                    "events: `channels` must be list of str or list of "
-                    "int corresponding to ch_names"
+                    "events: `channels` must be list of str or list of int "
+                    "corresponding to ch_names"
                 )
 
             if str(ch) not in ch_names:
@@ -557,15 +552,13 @@ def _chk_events(events, ch_names, n_times):
         if len(set(event["channels"])) != len(event["channels"]):
             raise ValueError("events: found duplicate channel names")
 
-        # warn if more than one but less than all channels are specified
-        # (experimental feature)
+        # warn if more than one but less than all channels are specified (experimental)
         if len(event["channels"]) > 1 and len(event["channels"]) < len(ch_names):
             warn(
-                "events: you specified at least one event that impacts more "
-                "than one but less than all channels in the data. "
-                "Such events will be written to .vmrk for as many times as "
-                "channels are specified.\n\n"
-                "This feature may not be supported by all BrainVision readers."
+                "events: you specified at least one event that impacts more than one "
+                "but less than all channels in the data. Such events will be written to"
+                " .vmrk for as many times as channels are specified.\n\nThis feature "
+                "may not be supported by all BrainVision readers."
             )
 
         # convert channels to indices (1-based, 0="all")
@@ -584,8 +577,8 @@ def _chk_fmt(fmt):
     """Check that the format string is valid, return (BV, numpy) datatypes."""
     if fmt not in SUPPORTED_FORMATS:
         errmsg = (
-            f"Data format {fmt} not supported. Currently supported "
-            f'formats are: {", ".join(SUPPORTED_FORMATS)}'
+            f"Data format {fmt} not supported. Currently supported formats are: "
+            f'{", ".join(SUPPORTED_FORMATS)}'
         )
         raise ValueError(errmsg)
     return SUPPORTED_FORMATS[fmt]
@@ -595,8 +588,8 @@ def _chk_multiplexed(orientation):
     """Validate an orientation, return if it is multiplexed or not."""
     if orientation not in SUPPORTED_ORIENTS:
         errmsg = (
-            f"Orientation {orientation} not supported. Currently "
-            f'supported orientations are: {", ".join(SUPPORTED_ORIENTS)}'
+            f"Orientation {orientation} not supported. Currently supported orientations"
+            f'are: {", ".join(SUPPORTED_ORIENTS)}'
         )
         raise ValueError(errmsg)
     return orientation == "multiplexed"
@@ -647,14 +640,12 @@ def _write_vmrk_file(vmrk_fname, eeg_fname, events, meas_date):
 
 def _scale_data_to_unit(data, units):
     """Scale `data` in Volts to `data` in `units`."""
-    # only µV is supported by the BrainVision specs, but we support additional
-    # voltage prefixes (e.g., V, mV, nV); if such voltage units are used, we
-    # issue a warning
+    # only µV is supported by the BrainVision specs, but we support additional voltage
+    # prefixes (e.g., V, mV, nV); if such voltage units are used, we issue a warning
     voltage_units = set()
 
-    # similar to voltages other than µV, we also support arbitrary units, but
-    # since these are not supported by the BrainVision specs we issue a warning
-    # related signals
+    # similar to voltages other than µV, we also support arbitrary units, but since
+    # these are not supported by the BrainVision specs, we issue a warning
     non_voltage_units = set()
 
     # create a vector to multiply with to play nice with numpy
@@ -671,19 +662,16 @@ def _scale_data_to_unit(data, units):
 
     if len(voltage_units) > 0:
         msg = (
-            f"Encountered unsupported voltage units: "
-            f'{", ".join(voltage_units)}\n'
-            f"We will scale the data appropriately, but for maximum "
-            f"compatibility you should use µV for all channels."
+            f'Encountered unsupported voltage units: {", ".join(voltage_units)}\n'
+            "We will scale the data appropriately, but for maximum compatibility you "
+            "should use µV for all channels."
         )
         warn(msg)
 
     if len(non_voltage_units) > 0:
         msg = (
-            f"Encountered unsupported non-voltage units: "
-            f'{", ".join(non_voltage_units)}\n'
-            f"Note that the BrainVision format specification supports only "
-            f"µV."
+            f'Encountered unsupported non-voltage units: {", ".join(non_voltage_units)}'
+            "\nNote that the BrainVision format specification supports only µV."
         )
         warn(msg)
     return data * scales
@@ -785,33 +773,33 @@ def _write_bveeg_file(eeg_fname, data, orientation, format, resolution, units):
     # convert the data to the desired unit
     data = _scale_data_to_unit(data, units)
 
-    # Invert the resolution so that we know how much to scale our data
+    # invert the resolution so that we know how much to scale our data
     scaling_factor = 1 / resolution
     data = data * np.atleast_2d(scaling_factor).T
 
-    # Convert the data to required format
+    # convert the data to required format
     if not _check_data_in_range(data, dtype):
         mod = " ('{resolution}')"
         if isinstance(resolution, np.ndarray):
             # if we have individual resolutions, do not print them all
             mod = "s"
         msg = (
-            f"`data` can not be represented in '{format}' given "
-            f"the desired resolution{mod} and units ('{units}')."
+            f"`data` can not be represented in '{format}' given the desired "
+            f"resolution{mod} and units ('{units}')."
         )
         if format == "binary_int16":
             msg += "\nPlease consider writing using 'binary_float32' format."
         raise ValueError(msg)
     data = data.astype(dtype=dtype)
 
-    # We always write data as little-endian without BOM
-    # `data` is already in native byte order due to numpy operations that
-    # result in copies of the `data` array (see above)
+    # we always write data as little-endian without BOM
+    # `data` is already in native byte order due to NumPy operations that result in
+    # copies of the `data` array (see above)
     assert data.dtype.byteorder == "="
 
     # swap bytes if system architecture is big-endian
     if sys.byteorder == "big":  # pragma: no cover
         data = data.byteswap()
 
-    # Save to binary
+    # save to binary
     data.ravel(order="F").tofile(eeg_fname)
diff --git a/pybv/tests/test_bv_writer.py b/pybv/tests/test_bv_writer.py
index 2e8e9a6..055b6cd 100644
--- a/pybv/tests/test_bv_writer.py
+++ b/pybv/tests/test_bv_writer.py
@@ -294,8 +294,7 @@ def test_bv_writer_inputs(tmpdir):
             fname_base=fname,
             folder_out=tmpdir,
         )
-    # Passing data that's not all-zero for a reference channel should raise
-    # an exception
+    # passing data that's not all-zero for a reference channel should raise an exception
     data_ = data.copy()
     data_[ch_names.index(ref_ch_name), :] = 5
     with pytest.raises(ValueError, match="reference channel.*not.*zero"):
@@ -307,7 +306,7 @@ def test_bv_writer_inputs(tmpdir):
             fname_base=fname,
             folder_out=tmpdir,
         )
-    # Empty str is a reserved value for ref_ch_names
+    # empty str is a reserved value for ref_ch_names
     with pytest.raises(ValueError, match="Empty strings are reserved values"):
         _ref_ch_names = [""] + ch_names[1:]
         write_brainvision(
@@ -318,7 +317,7 @@ def test_bv_writer_inputs(tmpdir):
             fname_base=fname,
             folder_out=tmpdir,
         )
-    # Try ambiguous list of dict events with "all" ch
+    # try ambiguous list of dict events with "all" ch
     with pytest.raises(ValueError, match="Found channel named 'all'.*ambiguous"):
         write_brainvision(
             data=data[:1, :],
@@ -505,18 +504,17 @@ def test_write_read_cycle(tmpdir, meas_date, ref_ch_names):
 def test_format_resolution_unit(tmpdir, format, resolution, unit):
     """Test different combinations of formats, resolutions, and units.
 
-    This test would raise warnings for several cases of "unit"
-    (Encountered unsupported voltage units), and a specific warning
-    if "unit" is "uV" (Encountered small Greek letter mu).
-    We ignore those warnings throughout the test.
+    This test would raise warnings for several cases of "unit" ("Encountered unsupported
+    voltage units"), and a specific warning if "unit" is "uV" ("Encountered small Greek
+    letter mu"). We ignore those warnings throughout the test.
 
-    Each run of the test is furthermore expected to exit early
-    with a ValueError for combinations of "resolution" and "format"
-    that would result in data that cannot accurately be written.
+    Each run of the test is furthermore expected to exit early with a ValueError for
+    combinations of "resolution" and "format" that would result in data that cannot
+    accurately be written.
     """
-    # Check whether this test will be numerically possible
+    # check whether this test will be numerically possible
     tmpdata = _scale_data_to_unit(data.copy(), [unit] * n_chans)
-    tmpdata = tmpdata * np.atleast_2d((1 / resolution)).T
+    tmpdata = tmpdata * np.atleast_2d(1 / resolution).T
     _, dtype = _chk_fmt(format)
     data_will_fit = _check_data_in_range(tmpdata, dtype)
 
@@ -532,7 +530,7 @@ def test_format_resolution_unit(tmpdir, format, resolution, unit):
     )
 
     if not data_will_fit:
-        # End this test early
+        # end this test early
         match = f"can not be represented in '{format}' given"
         with pytest.raises(ValueError, match=match):
             write_brainvision(**kwargs)
@@ -542,14 +540,14 @@ def test_format_resolution_unit(tmpdir, format, resolution, unit):
     vhdr_fname = tmpdir / fname + ".vhdr"
     raw_written = mne.io.read_raw_brainvision(vhdr_fname=vhdr_fname, preload=True)
 
-    # Check that the correct units were written in the BV file
+    # check that the correct units were written in the BV file
     orig_units = [u for key, u in raw_written._orig_units.items()]
     assert len(set(orig_units)) == 1
     if unit is not None:
         assert orig_units[0] == unit.replace("u", "µ")
 
-    # Check round trip of data: in binary_int16 format, the tolerance
-    # is given by the lowest resolution
+    # check round trip of data: in binary_int16 format, the tolerance is given by the
+    # lowest resolution
     if format == "binary_int16":
         absolute_tolerance = np.atleast_2d(resolution).min()
     else:
@@ -608,7 +606,7 @@ def test_write_multiple_units(tmpdir, unit):
     absolute_tolerance = 0
     assert_allclose(data, raw_written.get_data(), atol=absolute_tolerance)
 
-    # Check that the correct units were written in the BV file
+    # check that the correct units were written in the BV file
     orig_units = [u for key, u in raw_written._orig_units.items()]
     assert len(set(orig_units)) == 1
     assert orig_units[0] == unit.replace("u", "µ")
@@ -626,7 +624,7 @@ def test_write_multiple_units(tmpdir, unit):
 
     raw_written = mne.io.read_raw_brainvision(vhdr_fname=vhdr_fname, preload=True)
 
-    # Check that the correct units were written in the BV file
+    # check that the correct units were written in the BV file
     orig_units = [u for key, u in raw_written._orig_units.items()]
     assert len(set(orig_units)) == 2
     assert all(
@@ -663,7 +661,7 @@ def test_write_unsupported_units(tmpdir):
     absolute_tolerance = 0
     assert_allclose(data, raw_written.get_data(), atol=absolute_tolerance)
 
-    # Check that the correct units were written in the BV file
+    # check that the correct units were written in the BV file
     orig_units = [u for key, u in raw_written._orig_units.items()]
     assert len(set(orig_units)) == 2
     assert all([orig_units[idx] == unit for idx in range(n_chans - 1)])
@@ -768,12 +766,12 @@ def test_event_writing(tmpdir):
     # should be one more, because event[3] is written twice (once per channel)
     assert len(raw.annotations) == len(events) + 1
 
-    # note: mne orders events by onset, use sorted
+    # note: MNE orders events by onset, use sorted
     onsets = np.array([ev["onset"] / raw.info["sfreq"] for ev in events])
     onsets = sorted(onsets) + [1.0]  # add duplicate event (due to channels)
     np.testing.assert_array_equal(raw.annotations.onset, onsets)
 
-    # mne does not (yet; at 1.0.3) read ch_names for annotations from vmrk
+    # MNE does not (yet; at 1.0.3) read ch_names for annotations from vmrk
     np.testing.assert_array_equal(
         [i for i in raw.annotations.ch_names], [() for i in range(len(events) + 1)]
     )
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..3d4d4d8
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[tool.ruff.lint]
+select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
+ignore = ["A002", "D203", "D213"]

From fc6d88da29a31a1cd6306f75b2655081382ad665 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 12:43:56 +0100
Subject: [PATCH 03/10] Remove old config entries

---
 Makefile             | 22 +++++-----------------
 requirements-dev.txt |  6 +-----
 setup.cfg            | 12 ------------
 3 files changed, 6 insertions(+), 34 deletions(-)

diff --git a/Makefile b/Makefile
index a146fd6..9d0d36f 100755
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: all inplace test flake pydocstyle check-manifest isort black pep build-doc dist-build
+.PHONY: all inplace test check-manifest pep build-doc dist-build
 
 all: inplace pep test build-doc dist-build
 
@@ -12,27 +12,15 @@ test:
 	@echo "Running pytest: test modules"
 	@pytest --cov=./pybv --cov-report=xml --verbose
 
-flake:
-	@echo "Running flake8"
-	@flake8 --docstring-convention numpy --count pybv
-
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle
-
 check-manifest:
 	@echo "Running check-manifest"
 	@check-manifest
 
-isort:
-	@echo "Running check-manifest"
-	@isort .
-
-black:
-	@echo "Running black"
-	@black .
+ruff:
+	@echo "Running ruff"
+	@ruff .
 
-pep: flake pydocstyle check-manifest isort black
+pep: ruff check-manifest
 
 build-doc:
 	@echo "Building documentation"
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 023382d..14bebf7 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -4,12 +4,8 @@ check-manifest
 pytest
 pytest-cov
 pytest-sugar
-flake8>=3.9.2
-flake8-docstrings
-pycodestyle
+ruff
 sphinx
 sphinx-copybutton
 numpydoc
-isort
-black
 pre-commit
diff --git a/setup.cfg b/setup.cfg
index 03ad286..3bbbd3f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -54,15 +54,3 @@ export =
 
 [bdist_wheel]
 universal = true
-
-[flake8]
-docstring-convention = numpy
-# Recommend matching the black line length (default 88),
-# rather than using the flake8 default of 79:
-max-line-length = 88
-extend-ignore =
-  # See https://github.com/PyCQA/pycodestyle/issues/373
-  E203
-
-[isort]
-profile=black

From 7197d3f35686c7e7aaff1daf822d1bc61855df27 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 14:04:53 +0100
Subject: [PATCH 04/10] Forgot f in f-string

---
 pybv/io.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pybv/io.py b/pybv/io.py
index b745c4e..6e6ac50 100644
--- a/pybv/io.py
+++ b/pybv/io.py
@@ -394,7 +394,8 @@ def _chk_events(events, ch_names, n_times):
             raise ValueError(f"When array, events must be 2D, but got {events.ndim}")
         if events.shape[1] not in (2, 3):
             raise ValueError(
-                "When array, events must have 2 or 3 columns, but got {events.shape[1]}"
+                "When array, events must have 2 or 3 columns, but got "
+                f"{events.shape[1]}"
             )
         if not all([np.issubdtype(i, np.integer) for i in events.flat]):
             raise ValueError(

From 576e68b087f8eb89e8b88b8eb06b9c1132a758cf Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 14:05:30 +0100
Subject: [PATCH 05/10] Add missing colon

---
 pybv/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pybv/io.py b/pybv/io.py
index 6e6ac50..6bd5cd1 100644
--- a/pybv/io.py
+++ b/pybv/io.py
@@ -394,7 +394,7 @@ def _chk_events(events, ch_names, n_times):
             raise ValueError(f"When array, events must be 2D, but got {events.ndim}")
         if events.shape[1] not in (2, 3):
             raise ValueError(
-                "When array, events must have 2 or 3 columns, but got "
+                "When array, events must have 2 or 3 columns, but got: "
                 f"{events.shape[1]}"
             )
         if not all([np.issubdtype(i, np.integer) for i in events.flat]):

From 1c22aecc3b5e9b7ab380583974cace519a9438aa Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 14:06:13 +0100
Subject: [PATCH 06/10] Add missing space

---
 pybv/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pybv/io.py b/pybv/io.py
index 6bd5cd1..a4fe7c4 100644
--- a/pybv/io.py
+++ b/pybv/io.py
@@ -511,7 +511,7 @@ def _chk_events(events, ch_names, n_times):
             if not isinstance(event["description"], (int, str)):
                 raise ValueError(
                     f"events: when `type` is {event['type']}, `description` must be str"
-                    "or int"
+                    " or int"
                 )
             event["description"] = str(event["description"])
 

From 37b3bf24173b1fb70d19fe40bb16910181df8158 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 14:14:14 +0100
Subject: [PATCH 07/10] Ignore docs directory

---
 docs/conf.py   | 2 +-
 pyproject.toml | 3 +++
 setup.py       | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 8319c1e..d83387b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -45,7 +45,7 @@
 
 # General information about the project.
 project = "pybv"
-copyright = "2018-{}, pybv developers".format(date.today().year)
+copyright = f"2018-{date.today().year}, pybv developers"
 author = "pybv developers"
 version = pybv.__version__
 release = version
diff --git a/pyproject.toml b/pyproject.toml
index 3d4d4d8..54c3ef2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,6 @@
+[tool.ruff]
+exclude = ["docs"]
+
 [tool.ruff.lint]
 select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
 ignore = ["A002", "D203", "D213"]
diff --git a/setup.py b/setup.py
index ec5a1af..0803ccc 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
 
 # get the version
 version = None
-with open(os.path.join("pybv", "__init__.py"), "r") as fid:
+with open(os.path.join("pybv", "__init__.py")) as fid:
     for line in (line.strip() for line in fid):
         if line.startswith("__version__"):
             version_str = line.split("=")[1].strip()

From 912a44687595fb129c1d98426f9d08c849714a0c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 14:17:40 +0100
Subject: [PATCH 08/10] Clean up Makefile

---
 .github/CONTRIBUTING.md            |  2 +-
 .github/workflows/python_tests.yml |  2 +-
 Makefile                           | 10 ++--------
 3 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 1a9d57d..40624ab 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -39,7 +39,7 @@ you can run tests by making use of the `Makefile` and
 From the project root, call:
 
 - `make test` to run tests and coverage
-- `make pep` to run style checks
+- `pre-commit run` to run style checks (Ruff and some additional hooks)
 
 ## Building the documentation
 
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
index 87f9b0f..400b777 100644
--- a/.github/workflows/python_tests.yml
+++ b/.github/workflows/python_tests.yml
@@ -60,7 +60,7 @@ jobs:
     - name: Check formatting
       if: ${{ matrix.platform == 'ubuntu-22.04' && matrix.python-version == '3.11' }}
       run: |
-        make pep
+        make check-manifest
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
     - name: Test with pytest
diff --git a/Makefile b/Makefile
index 9d0d36f..d1e13a0 100755
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
-.PHONY: all inplace test check-manifest pep build-doc dist-build
+.PHONY: all inplace test check-manifest build-doc dist-build
 
-all: inplace pep test build-doc dist-build
+all: inplace check-manifest test build-doc dist-build
 
 inplace:
 	@echo "Installing pybv"
@@ -16,12 +16,6 @@ check-manifest:
 	@echo "Running check-manifest"
 	@check-manifest
 
-ruff:
-	@echo "Running ruff"
-	@ruff .
-
-pep: ruff check-manifest
-
 build-doc:
 	@echo "Building documentation"
 	make -C docs/ clean

From d19515f8a72c36686ff927391088c5afa390e348 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 17:23:44 +0100
Subject: [PATCH 09/10] Do not exclude docs

---
 docs/conf.py                       | 2 +-
 docs/sphinxext/gh_substitutions.py | 6 +++++-
 pyproject.toml                     | 3 ---
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index d83387b..d3db897 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -45,7 +45,7 @@
 
 # General information about the project.
 project = "pybv"
-copyright = f"2018-{date.today().year}, pybv developers"
+copyright = f"2018-{date.today().year}, pybv developers"  # noqa:A001
 author = "pybv developers"
 version = pybv.__version__
 release = version
diff --git a/docs/sphinxext/gh_substitutions.py b/docs/sphinxext/gh_substitutions.py
index bc60766..02b0054 100644
--- a/docs/sphinxext/gh_substitutions.py
+++ b/docs/sphinxext/gh_substitutions.py
@@ -10,8 +10,12 @@
 from docutils.parsers.rst.roles import set_classes
 
 
-def gh_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+def gh_role(name, rawtext, text, lineno, inliner, options=None, content=None):
     """Link to a GitHub issue."""
+    if content is None:
+        content = []
+    if options is None:
+        options = {}
     try:
         # issue/PR mode (issues/PR-num will redirect to pull/PR-num)
         int(text)
diff --git a/pyproject.toml b/pyproject.toml
index 54c3ef2..3d4d4d8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,3 @@
-[tool.ruff]
-exclude = ["docs"]
-
 [tool.ruff.lint]
 select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
 ignore = ["A002", "D203", "D213"]

From 4b84b78c6095085cd0165cfb28998171c5faa589 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Sun, 11 Feb 2024 17:26:42 +0100
Subject: [PATCH 10/10] Do not globally exclude A002

---
 pybv/io.py                   | 4 ++--
 pybv/tests/test_bv_writer.py | 2 +-
 pyproject.toml               | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pybv/io.py b/pybv/io.py
index a4fe7c4..46a5f41 100644
--- a/pybv/io.py
+++ b/pybv/io.py
@@ -688,7 +688,7 @@ def _write_vhdr_file(
     ch_names,
     ref_ch_names,
     orientation,
-    format,
+    format,  # noqa: A002
     resolution,
     units,
 ):
@@ -765,7 +765,7 @@ def _check_data_in_range(data, dtype):
     return True
 
 
-def _write_bveeg_file(eeg_fname, data, orientation, format, resolution, units):
+def _write_bveeg_file(eeg_fname, data, orientation, format, resolution, units):  # noqa: A002
     """Write BrainVision data file."""
     # check the orientation and format
     _chk_multiplexed(orientation)
diff --git a/pybv/tests/test_bv_writer.py b/pybv/tests/test_bv_writer.py
index 055b6cd..3470fba 100644
--- a/pybv/tests/test_bv_writer.py
+++ b/pybv/tests/test_bv_writer.py
@@ -501,7 +501,7 @@ def test_write_read_cycle(tmpdir, meas_date, ref_ch_names):
 @pytest.mark.parametrize("format", SUPPORTED_FORMATS.keys())
 @pytest.mark.parametrize("resolution", resolutions)
 @pytest.mark.parametrize("unit", SUPPORTED_VOLTAGE_SCALINGS)
-def test_format_resolution_unit(tmpdir, format, resolution, unit):
+def test_format_resolution_unit(tmpdir, format, resolution, unit):  # noqa: A002
     """Test different combinations of formats, resolutions, and units.
 
     This test would raise warnings for several cases of "unit" ("Encountered unsupported
diff --git a/pyproject.toml b/pyproject.toml
index 3d4d4d8..e4b728b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,3 @@
 [tool.ruff.lint]
 select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
-ignore = ["A002", "D203", "D213"]
+ignore = ["D203", "D213"]